{ "type" : "object", "properties" : { "pdbx_entity_nonpoly" : { "type" : "object", "properties" : { "comp_id" : { "type" : "string", "description" : "This data item is a pointer to _chem_comp.id in the CHEM_COMP category.", "rcsb_description" : [ { "text" : "This data item is a pointer to _chem_comp.id in the CHEM_COMP category.", "context" : "dictionary" } ] }, "entity_id" : { "type" : "string", "description" : "This data item is a pointer to _entity.id in the ENTITY category.", "rcsb_description" : [ { "text" : "This data item is a pointer to _entity.id in the ENTITY category.", "context" : "dictionary" } ] }, "name" : { "type" : "string", "description" : "A name for the non-polymer entity", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "A name for the non-polymer entity", "context" : "dictionary" }, { "text" : "Name (Entity Nonpoly)", "context" : "brief" } ] }, "rcsb_prd_id" : { "type" : "string", "description" : "For non-polymer BIRD molecules the BIRD identifier for the entity.", "rcsb_description" : [ { "text" : "For non-polymer BIRD molecules the BIRD identifier for the entity.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "entity_id" ] }, "rcsb_latest_revision" : { "type" : "object", "properties" : { "major_revision" : { "type" : "integer", "description" : "The major version number of the latest revision.", "rcsb_description" : [ { "text" : "The major version number of the latest revision.", "context" : "dictionary" } ] }, "minor_revision" : { "type" : "integer", "description" : "The minor version number of the latest revision.", "rcsb_description" : [ { "text" : "The minor version number of the latest revision.", "context" : "dictionary" } ] }, "revision_date" : { "type" : "string", "format" : "date-time", "examples" : [ "2020-02-11", "2018-10-23" ], "description" : "The release date of the latest revision item.", "rcsb_description" : [ { "text" : "The release date of the latest revision item.", "context" : "dictionary" } ] } }, "additionalProperties" : false }, "rcsb_nonpolymer_entity" : { "type" : "object", "properties" : { "details" : { "type" : "string", "description" : "A description of special aspects of the entity.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "A description of special aspects of the entity.", "context" : "dictionary" }, { "text" : "Details (Nonpolymer Entity)", "context" : "brief" } ] }, "formula_weight" : { "type" : "number", "description" : "Formula mass (KDa) of the entity.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "KDa", "rcsb_description" : [ { "text" : "Formula mass (KDa) of the entity.", "context" : "dictionary" }, { "text" : "Formula Weight (Nonpolymer Entity)", "context" : "brief" } ], "rcsb_current_maximum_value" : 12.016, "rcsb_current_minimum_value" : 0.002 }, "pdbx_description" : { "type" : "string", "description" : "A description of the nonpolymer entity.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "A description of the nonpolymer entity.", "context" : "dictionary" }, { "text" : "Description (Nonpolymer Entity)", "context" : "brief" } ] }, "pdbx_number_of_molecules" : { "type" : "integer", "description" : "The number of molecules of the nonpolymer entity in the entry.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of molecules of the nonpolymer entity in the entry.", "context" : "dictionary" }, { "text" : "Number Of Molecules (Nonpolymer Entity)", "context" : "brief" } ], "rcsb_current_maximum_value" : 5345.0, "rcsb_current_minimum_value" : 1.0 } }, "additionalProperties" : false }, "rcsb_nonpolymer_entity_annotation" : { "type" : "array", "items" : { "type" : "object", "properties" : { "annotation_id" : { "type" : "string", "description" : "An identifier for the annotation.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "An identifier for the annotation.", "context" : "dictionary" }, { "text" : "Identifier", "context" : "brief" } ] }, "assignment_version" : { "type" : "string", "examples" : [ "V4_0_2" ], "description" : "Identifies the version of the annotation assignment.", "rcsb_description" : [ { "text" : "Identifies the version of the annotation assignment.", "context" : "dictionary" }, { "text" : "Annotation Version", "context" : "brief" } ] }, "comp_id" : { "type" : "string", "examples" : [ "GTP", "STN" ], "description" : "Non-polymer(ligand) chemical component identifier for the entity.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Non-polymer(ligand) chemical component identifier for the entity.", "context" : "dictionary" }, { "text" : "Component Identifier", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Nonpolymer Molecular Features", "priority_order" : 10 } ] }, "description" : { "type" : "string", "description" : "A description for the annotation.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "A description for the annotation.", "context" : "dictionary" }, { "text" : "Annotation Description", "context" : "brief" } ] }, "name" : { "type" : "string", "description" : "A name for the annotation.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "A name for the annotation.", "context" : "dictionary" }, { "text" : "Name", "context" : "brief" } ] }, "provenance_source" : { "type" : "string", "examples" : [ "PDB" ], "description" : "Code identifying the individual, organization or program that\n assigned the annotation.", "rcsb_description" : [ { "text" : "Code identifying the individual, organization or program that\n assigned the annotation.", "context" : "dictionary" }, { "text" : "Annotation Source", "context" : "brief" } ] }, "type" : { "type" : "string", "enum" : [ "SUBJECT_OF_INVESTIGATION" ], "examples" : [ "SUBJECT_OF_INVESTIGATION" ], "description" : "A type or category of the annotation.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "SUBJECT_OF_INVESTIGATION", "detail" : "Investigated Molecule", "name" : "Investigated Molecule" } ], "rcsb_description" : [ { "text" : "A type or category of the annotation.", "context" : "dictionary" }, { "text" : "Annotation Type", "context" : "brief" } ] }, "annotation_lineage" : { "type" : "array", "items" : { "type" : "object", "properties" : { "depth" : { "type" : "integer", "description" : "Members of the annotation lineage as parent lineage depth (1-N)", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Members of the annotation lineage as parent lineage depth (1-N)", "context" : "dictionary" }, { "text" : "Lineage Depth", "context" : "brief" } ] }, "id" : { "type" : "string", "description" : "Members of the annotation lineage as parent class identifiers.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Members of the annotation lineage as parent class identifiers.", "context" : "dictionary" }, { "text" : "Lineage Identifier", "context" : "brief" } ] }, "name" : { "type" : "string", "description" : "Members of the annotation lineage as parent class names.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Members of the annotation lineage as parent class names.", "context" : "dictionary" }, { "text" : "Lineage Name", "context" : "brief" } ] } }, "additionalProperties" : false }, "uniqueItems" : false, "rcsb_nested_indexing" : true } }, "additionalProperties" : false, "required" : [ "type" ] }, "minItems" : 1, "uniqueItems" : true, "rcsb_nested_indexing" : true, "rcsb_nested_indexing_context" : [ { "category_name" : "annotation_type", "category_path" : "rcsb_nonpolymer_entity_annotation.type", "context_attributes" : [ { "context_value" : "SUBJECT_OF_INVESTIGATION", "attributes" : [ { "examples" : [ "BEZ", "PQM" ], "path" : "rcsb_nonpolymer_entity_annotation.comp_id" } ] } ] } ] }, "rcsb_nonpolymer_entity_container_identifiers" : { "type" : "object", "properties" : { "asym_ids" : { "type" : "array", "items" : { "type" : "string", "examples" : [ "A", "B" ], "description" : "Instance identifiers corresponding to copies of the entity in this container.", "rcsb_description" : [ { "text" : "Instance identifiers corresponding to copies of the entity in this container.", "context" : "dictionary" } ] }, "uniqueItems" : false }, "auth_asym_ids" : { "type" : "array", "items" : { "type" : "string", "examples" : [ "A", "B" ], "description" : "Author instance identifiers corresponding to copies of the entity in this container.", "rcsb_description" : [ { "text" : "Author instance identifiers corresponding to copies of the entity in this container.", "context" : "dictionary" } ] }, "uniqueItems" : false }, "chem_ref_def_id" : { "type" : "string", "examples" : [ "PRD_000010" ], "description" : "The chemical reference definition identifier for the entity in this container.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The chemical reference definition identifier for the entity in this container.", "context" : "dictionary" }, { "text" : "Chem Ref Def Id (Nonpolymer Entity Container Identifiers)", "context" : "brief" } ] }, "entity_id" : { "type" : "string", "examples" : [ "1", "2" ], "description" : "Entity identifier for the container.", "rcsb_description" : [ { "text" : "Entity identifier for the container.", "context" : "dictionary" } ] }, "entry_id" : { "type" : "string", "examples" : [ "4HHB", "1KIP" ], "description" : "Entry identifier for the container.", "rcsb_description" : [ { "text" : "Entry identifier for the container.", "context" : "dictionary" } ] }, "nonpolymer_comp_id" : { "type" : "string", "examples" : [ "GTP", "STN" ], "description" : "Non-polymer(ligand) chemical component identifier for the entity in this container.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Non-polymer(ligand) chemical component identifier for the entity in this container.", "context" : "dictionary" }, { "text" : "Component Identifier", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Nonpolymer Molecular Features", "priority_order" : 5 } ] }, "prd_id" : { "type" : "string", "examples" : [ "PRD_000010" ], "description" : "The BIRD identifier for the entity in this container.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The BIRD identifier for the entity in this container.", "context" : "dictionary" }, { "text" : "Ligand BIRD ID", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Nonpolymer Molecular Features", "priority_order" : 30 } ] }, "rcsb_id" : { "type" : "string", "examples" : [ "6EL3_1" ], "description" : "A unique identifier for each object in this entity container formed by\n an underscore separated concatenation of entry and entity identifiers.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "A unique identifier for each object in this entity container formed by\n an underscore separated concatenation of entry and entity identifiers.", "context" : "dictionary" }, { "text" : "Id (Nonpolymer Entity Container Identifiers)", "context" : "brief" } ] }, "reference_chemical_identifiers_provenance_source" : { "type" : "array", "items" : { "type" : "string", "enum" : [ "PDB", "RCSB" ], "examples" : [ "PDB" ], "description" : "Source of the reference database assignment", "rcsb_description" : [ { "text" : "Source of the reference database assignment", "context" : "dictionary" } ] }, "uniqueItems" : false }, "reference_chemical_identifiers_resource_accession" : { "type" : "array", "items" : { "type" : "string", "examples" : [ "5957", "CHEMBL14249" ], "description" : "Reference resource accession code", "rcsb_description" : [ { "text" : "Reference resource accession code", "context" : "dictionary" } ] }, "uniqueItems" : false }, "reference_chemical_identifiers_resource_name" : { "type" : "array", "items" : { "type" : "string", "enum" : [ "ChEBI", "ChEMBL", "DrugBank", "PubChem" ], "examples" : [ "PubChem", "ChEBI" ], "description" : "Reference resource name", "rcsb_description" : [ { "text" : "Reference resource name", "context" : "dictionary" } ] }, "uniqueItems" : false } }, "additionalProperties" : false, "required" : [ "entity_id", "entry_id" ] }, "rcsb_nonpolymer_entity_feature" : { "type" : "array", "items" : { "type" : "object", "properties" : { "assignment_version" : { "type" : "string", "examples" : [ "V4_0_2" ], "description" : "Identifies the version of the feature assignment.", "rcsb_description" : [ { "text" : "Identifies the version of the feature assignment.", "context" : "dictionary" }, { "text" : "Feature Version", "context" : "brief" } ] }, "comp_id" : { "type" : "string", "examples" : [ "GTP", "STN" ], "description" : "Non-polymer(ligand) chemical component identifier for the entity.", "rcsb_description" : [ { "text" : "Non-polymer(ligand) chemical component identifier for the entity.", "context" : "dictionary" } ] }, "description" : { "type" : "string", "description" : "A description for the feature.", "rcsb_description" : [ { "text" : "A description for the feature.", "context" : "dictionary" }, { "text" : "Feature Description", "context" : "brief" } ] }, "feature_id" : { "type" : "string", "description" : "An identifier for the feature.", "rcsb_description" : [ { "text" : "An identifier for the feature.", "context" : "dictionary" } ] }, "name" : { "type" : "string", "description" : "A name for the feature.", "rcsb_description" : [ { "text" : "A name for the feature.", "context" : "dictionary" }, { "text" : "Name", "context" : "brief" } ] }, "provenance_source" : { "type" : "string", "examples" : [ "PDB" ], "description" : "Code identifying the individual, organization or program that\n assigned the feature.", "rcsb_description" : [ { "text" : "Code identifying the individual, organization or program that\n assigned the feature.", "context" : "dictionary" }, { "text" : "Feature Source", "context" : "brief" } ] }, "type" : { "type" : "string", "enum" : [ "SUBJECT_OF_INVESTIGATION" ], "examples" : [ "SUBJECT_OF_INVESTIGATION" ], "description" : "A type or category of the feature.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "SUBJECT_OF_INVESTIGATION", "detail" : "Investigated Molecule", "name" : "Investigated Molecule" } ], "rcsb_description" : [ { "text" : "A type or category of the feature.", "context" : "dictionary" }, { "text" : "Feature Type", "context" : "brief" } ] }, "value" : { "type" : "number", "description" : "The feature value.", "rcsb_description" : [ { "text" : "The feature value.", "context" : "dictionary" } ] }, "additional_properties" : { "type" : "array", "items" : { "type" : "object", "properties" : { "name" : { "type" : "string", "description" : "The additional property name.", "rcsb_description" : [ { "text" : "The additional property name.", "context" : "dictionary" } ] }, "values" : { "type" : "array", "items" : { "anyOf" : [ { "type" : "string" }, { "type" : "integer" }, { "type" : "number" } ], "examples" : [ "2.54", "300" ], "description" : "The value(s) of the additional property.", "rcsb_description" : [ { "text" : "The value(s) of the additional property.", "context" : "dictionary" } ] }, "uniqueItems" : false } }, "additionalProperties" : false }, "uniqueItems" : false } }, "additionalProperties" : false, "required" : [ "type" ] }, "minItems" : 1, "uniqueItems" : true }, "rcsb_nonpolymer_entity_feature_summary" : { "type" : "array", "items" : { "type" : "object", "properties" : { "comp_id" : { "type" : "string", "examples" : [ "GTP", "STN" ], "description" : "Non-polymer(ligand) chemical component identifier for the entity.", "rcsb_description" : [ { "text" : "Non-polymer(ligand) chemical component identifier for the entity.", "context" : "dictionary" } ] }, "count" : { "type" : "integer", "description" : "The feature count.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The feature count.", "context" : "dictionary" }, { "text" : "Count (Nonpolymer Entity Feature Summary)", "context" : "brief" } ], "rcsb_current_maximum_value" : 1.0, "rcsb_current_minimum_value" : 1.0 }, "maximum_length" : { "type" : "integer", "description" : "The maximum feature length.", "rcsb_description" : [ { "text" : "The maximum feature length.", "context" : "dictionary" } ] }, "maximum_value" : { "type" : "number", "examples" : [ 1.012, 0.813 ], "description" : "The maximum feature value.", "rcsb_description" : [ { "text" : "The maximum feature value.", "context" : "dictionary" } ] }, "minimum_length" : { "type" : "integer", "description" : "The minimum feature length.", "rcsb_description" : [ { "text" : "The minimum feature length.", "context" : "dictionary" } ] }, "minimum_value" : { "type" : "number", "examples" : [ 0.012, 0.00132 ], "description" : "The minimum feature value.", "rcsb_description" : [ { "text" : "The minimum feature value.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "enum" : [ "SUBJECT_OF_INVESTIGATION" ], "examples" : [ "SUBJECT_OF_INVESTIGATION" ], "description" : "Type or category of the feature.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "SUBJECT_OF_INVESTIGATION", "detail" : "Subject molecule of investigation" } ], "rcsb_description" : [ { "text" : "Type or category of the feature.", "context" : "dictionary" }, { "text" : "Type (Nonpolymer Entity Feature Summary)", "context" : "brief" } ] } }, "additionalProperties" : false }, "minItems" : 1, "uniqueItems" : true, "rcsb_nested_indexing" : true, "rcsb_nested_indexing_context" : [ { "category_name" : "feature_summary", "category_path" : "rcsb_nonpolymer_entity_feature_summary.type" } ] }, "rcsb_nonpolymer_entity_keywords" : { "type" : "object", "properties" : { "text" : { "type" : "string", "description" : "Keywords describing this non-polymer entity.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Keywords describing this non-polymer entity.", "context" : "dictionary" }, { "text" : "Text (Nonpolymer Entity Keywords)", "context" : "brief" } ] } }, "additionalProperties" : false }, "rcsb_nonpolymer_entity_name_com" : { "type" : "array", "items" : { "type" : "object", "properties" : { "name" : { "type" : "string", "description" : "A common name for the nonpolymer entity.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "A common name for the nonpolymer entity.", "context" : "dictionary" }, { "text" : "Name (Nonpolymer Entity Name Com)", "context" : "brief" } ] } }, "additionalProperties" : false, "required" : [ "name" ] }, "minItems" : 1, "uniqueItems" : true }, "rcsb_id" : { "type" : "string", "examples" : [ "6EL3_1", "ATP", "PRD_000010", "1KIP-1", "1KIP", "1KIP.A", "2HYV_2" ], "description" : "A unique identifier for each object in this entity container formed by\n an underscore separated concatenation of entry and entity identifiers.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "A unique identifier for each object in this entity container formed by\n an underscore separated concatenation of entry and entity identifiers.", "context" : "dictionary" }, { "text" : "A unique identifier for the chemical definition in this container.", "context" : "dictionary" }, { "text" : "A unique identifier for each object in this assembly container formed by\n a dash separated concatenation of entry and assembly identifiers.", "context" : "dictionary" }, { "text" : "The RCSB entry identifier.", "context" : "dictionary" }, { "text" : "A unique identifier for each object in this entity instance container formed by\n an 'dot' (.) separated concatenation of entry and entity instance identifiers.", "context" : "dictionary" }, { "text" : "A unique identifier for each object in this entry container.", "context" : "dictionary" }, { "text" : "Id", "context" : "brief" } ] }, "chem_comp" : { "type" : "object", "properties" : { "formula" : { "type" : "string", "examples" : [ "C18 H19 N7 O8 S" ], "description" : "The formula for the chemical component. Formulae are written\n according to the following rules:\n\n (1) Only recognized element symbols may be used.\n\n (2) Each element symbol is followed by a 'count' number. A count\n of '1' may be omitted.\n\n (3) A space or parenthesis must separate each cluster of\n (element symbol + count), but in general parentheses are\n not used.\n\n (4) The order of elements depends on whether carbon is\n present or not. If carbon is present, the order should be:\n C, then H, then the other elements in alphabetical order\n of their symbol. If carbon is not present, the elements\n are listed purely in alphabetic order of their symbol. This\n is the 'Hill' system used by Chemical Abstracts.", "rcsb_description" : [ { "text" : "The formula for the chemical component. Formulae are written\n according to the following rules:\n\n (1) Only recognized element symbols may be used.\n\n (2) Each element symbol is followed by a 'count' number. A count\n of '1' may be omitted.\n\n (3) A space or parenthesis must separate each cluster of\n (element symbol + count), but in general parentheses are\n not used.\n\n (4) The order of elements depends on whether carbon is\n present or not. If carbon is present, the order should be:\n C, then H, then the other elements in alphabetical order\n of their symbol. If carbon is not present, the elements\n are listed purely in alphabetic order of their symbol. This\n is the 'Hill' system used by Chemical Abstracts.", "context" : "dictionary" }, { "text" : "Chemical Formula", "context" : "brief" } ] }, "formula_weight" : { "type" : "number", "examples" : [ 120.12, 450.1 ], "description" : "Formula mass of the chemical component.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "daltons", "rcsb_description" : [ { "text" : "Formula mass of the chemical component.", "context" : "dictionary" }, { "text" : "Chemical Component Molecular Weight", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Chemical Components", "priority_order" : 70 } ], "rcsb_current_maximum_value" : 12016.0, "rcsb_current_minimum_value" : 2.014 }, "id" : { "type" : "string", "examples" : [ "ALA", "VAL", "DG", "C" ], "description" : "The value of _chem_comp.id must uniquely identify each item in\n the CHEM_COMP list.\n\n For protein polymer entities, this is the three-letter code for\n the amino acid.\n\n For nucleic acid polymer entities, this is the one-letter code\n for the base.", "rcsb_description" : [ { "text" : "The value of _chem_comp.id must uniquely identify each item in\n the CHEM_COMP list.\n\n For protein polymer entities, this is the three-letter code for\n the amino acid.\n\n For nucleic acid polymer entities, this is the one-letter code\n for the base.", "context" : "dictionary" } ] }, "mon_nstd_parent_comp_id" : { "type" : "array", "items" : { "type" : "string", "description" : "The identifier for the parent component of the nonstandard\n component. May be be a comma separated list if this component\n is derived from multiple components.\n\n Items in this indirectly point to _chem_comp.id in\n the CHEM_COMP category.", "rcsb_description" : [ { "text" : "The identifier for the parent component of the nonstandard\n component. May be be a comma separated list if this component\n is derived from multiple components.\n\n Items in this indirectly point to _chem_comp.id in\n the CHEM_COMP category.", "context" : "dictionary" } ] }, "uniqueItems" : false }, "name" : { "type" : "string", "examples" : [ "alanine", "valine", "adenine", "cytosine" ], "description" : "The full name of the component.", "rcsb_search_context" : [ "exact-match", "full-text", "suggest" ], "rcsb_full_text_priority" : 20, "rcsb_description" : [ { "text" : "The full name of the component.", "context" : "dictionary" }, { "text" : "Chemical Name", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Chemical Components", "priority_order" : 10 } ] }, "one_letter_code" : { "type" : "string", "examples" : [ "A", "B", "R", "N", "D", "C", "Q", "E", "Z", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "U", "O", "X" ], "description" : "For standard polymer components, the one-letter code for\n the component. For non-standard polymer components, the\n one-letter code for parent component if this exists;\n otherwise, the one-letter code should be given as 'X'.\n\n Components that derived from multiple parents components\n are described by a sequence of one-letter-codes.", "rcsb_description" : [ { "text" : "For standard polymer components, the one-letter code for\n the component. For non-standard polymer components, the\n one-letter code for parent component if this exists;\n otherwise, the one-letter code should be given as 'X'.\n\n Components that derived from multiple parents components\n are described by a sequence of one-letter-codes.", "context" : "dictionary" } ] }, "pdbx_ambiguous_flag" : { "type" : "string", "description" : "A preliminary classification used by PDB to indicate\n that the chemistry of this component while described\n as clearly as possible is still ambiguous. Software\n tools may not be able to process this component\n definition.", "rcsb_description" : [ { "text" : "A preliminary classification used by PDB to indicate\n that the chemistry of this component while described\n as clearly as possible is still ambiguous. Software\n tools may not be able to process this component\n definition.", "context" : "dictionary" } ] }, "pdbx_formal_charge" : { "type" : "integer", "description" : "The net integer charge assigned to this component. This is the\n formal charge assignment normally found in chemical diagrams.", "rcsb_description" : [ { "text" : "The net integer charge assigned to this component. This is the\n formal charge assignment normally found in chemical diagrams.", "context" : "dictionary" } ] }, "pdbx_initial_date" : { "type" : "string", "format" : "date", "description" : "Date component was added to database.", "rcsb_description" : [ { "text" : "Date component was added to database.", "context" : "dictionary" } ] }, "pdbx_modified_date" : { "type" : "string", "format" : "date", "description" : "Date component was last modified.", "rcsb_description" : [ { "text" : "Date component was last modified.", "context" : "dictionary" } ] }, "pdbx_processing_site" : { "type" : "string", "enum" : [ "EBI", "PDBC", "PDBE", "PDBJ", "RCSB" ], "description" : "This data item identifies the deposition site that processed\n this chemical component defintion.", "rcsb_description" : [ { "text" : "This data item identifies the deposition site that processed\n this chemical component defintion.", "context" : "dictionary" } ] }, "pdbx_release_status" : { "type" : "string", "enum" : [ "DEL", "HOLD", "HPUB", "OBS", "REF_ONLY", "REL" ], "description" : "This data item holds the current release status for the component.", "rcsb_enum_annotated" : [ { "value" : "DEL", "detail" : "Component definition has been deleted" }, { "value" : "HOLD", "detail" : "On hold until yyyy-mm-dd" }, { "value" : "HPUB", "detail" : "On hold until publication" }, { "value" : "OBS", "detail" : "Component defintion has been obsoleted and replaced by another entry" }, { "value" : "REF_ONLY", "detail" : "Component definition is provided for reference only and will not be used in released entries." }, { "value" : "REL", "detail" : "Released" } ], "rcsb_description" : [ { "text" : "This data item holds the current release status for the component.", "context" : "dictionary" } ] }, "pdbx_replaced_by" : { "type" : "string", "examples" : [ "q11", "tvx" ], "description" : "Identifies the _chem_comp.id of the component that\n has replaced this component.", "rcsb_description" : [ { "text" : "Identifies the _chem_comp.id of the component that\n has replaced this component.", "context" : "dictionary" } ] }, "pdbx_replaces" : { "type" : "string", "examples" : [ "q11", "tvx,atv" ], "description" : "Identifies the _chem_comp.id's of the components\n which have been replaced by this component.\n Multiple id codes should be separated by commas.", "rcsb_description" : [ { "text" : "Identifies the _chem_comp.id's of the components\n which have been replaced by this component.\n Multiple id codes should be separated by commas.", "context" : "dictionary" } ] }, "pdbx_subcomponent_list" : { "type" : "string", "examples" : [ "TSM DPH HIS CHF EMR" ], "description" : "The list of subcomponents contained in this component.", "rcsb_description" : [ { "text" : "The list of subcomponents contained in this component.", "context" : "dictionary" } ] }, "three_letter_code" : { "type" : "string", "examples" : [ "ALA", "ARG", "ASN", "ASP", "ASX", "CYS", "GLN", "GLU", "GLY", "GLX", "HIS", "ILE", "LEU", "LYS", "MET", "PHE", "PRO", "SER", "THR", "TRP", "TYR", "VAL", "1MA", "5MC", "OMC", "1MG", "2MG", "M2G", "7MG", "0MG", "H2U", "5MU", "PSU", "ACE", "FOR", "HOH", "UNK" ], "description" : "For standard polymer components, the common three-letter code for\n the component. Non-standard polymer components and non-polymer\n components are also assigned three-letter-codes.\n\n For ambiguous polymer components three-letter code should\n be given as 'UNK'. Ambiguous ions are assigned the code 'UNX'.\n Ambiguous non-polymer components are assigned the code 'UNL'.", "rcsb_description" : [ { "text" : "For standard polymer components, the common three-letter code for\n the component. Non-standard polymer components and non-polymer\n components are also assigned three-letter-codes.\n\n For ambiguous polymer components three-letter code should\n be given as 'UNK'. Ambiguous ions are assigned the code 'UNX'.\n Ambiguous non-polymer components are assigned the code 'UNL'.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "enum" : [ "D-beta-peptide, C-gamma linking", "D-gamma-peptide, C-delta linking", "D-peptide COOH carboxy terminus", "D-peptide NH3 amino terminus", "D-peptide linking", "D-saccharide", "D-saccharide, alpha linking", "D-saccharide, beta linking", "DNA OH 3 prime terminus", "DNA OH 5 prime terminus", "DNA linking", "L-DNA linking", "L-RNA linking", "L-beta-peptide, C-gamma linking", "L-gamma-peptide, C-delta linking", "L-peptide COOH carboxy terminus", "L-peptide NH3 amino terminus", "L-peptide linking", "L-saccharide", "L-saccharide, alpha linking", "L-saccharide, beta linking", "RNA OH 3 prime terminus", "RNA OH 5 prime terminus", "RNA linking", "non-polymer", "other", "peptide linking", "peptide-like", "saccharide" ], "description" : "For standard polymer components, the type of the monomer.\n Note that monomers that will form polymers are of three types:\n linking monomers, monomers with some type of N-terminal (or 5')\n cap and monomers with some type of C-terminal (or 3') cap.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "D-beta-peptide, C-gamma linking", "detail" : "Iso-peptide linking D-beta peptide" }, { "value" : "D-gamma-peptide, C-delta linking", "detail" : "Iso-peptide linking D-gamma peptide" }, { "value" : "D-peptide COOH carboxy terminus" }, { "value" : "D-peptide NH3 amino terminus" }, { "value" : "D-peptide linking" }, { "value" : "D-saccharide" }, { "value" : "D-saccharide, alpha linking" }, { "value" : "D-saccharide, beta linking" }, { "value" : "DNA OH 3 prime terminus" }, { "value" : "DNA OH 5 prime terminus" }, { "value" : "DNA linking" }, { "value" : "L-DNA linking" }, { "value" : "L-RNA linking" }, { "value" : "L-beta-peptide, C-gamma linking", "detail" : "Iso-peptide linking L-beta peptide" }, { "value" : "L-gamma-peptide, C-delta linking", "detail" : "Iso-peptide linking L-gamma peptide" }, { "value" : "L-peptide COOH carboxy terminus" }, { "value" : "L-peptide NH3 amino terminus" }, { "value" : "L-peptide linking" }, { "value" : "L-saccharide" }, { "value" : "L-saccharide, alpha linking" }, { "value" : "L-saccharide, beta linking" }, { "value" : "RNA OH 3 prime terminus" }, { "value" : "RNA OH 5 prime terminus" }, { "value" : "RNA linking" }, { "value" : "non-polymer" }, { "value" : "other" }, { "value" : "peptide linking" }, { "value" : "peptide-like" }, { "value" : "saccharide" } ], "rcsb_description" : [ { "text" : "For standard polymer components, the type of the monomer.\n Note that monomers that will form polymers are of three types:\n linking monomers, monomers with some type of N-terminal (or 5')\n cap and monomers with some type of C-terminal (or 3') cap.", "context" : "dictionary" }, { "text" : "Chemical Component Type", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Chemical Components", "priority_order" : 25 } ] } }, "additionalProperties" : false, "required" : [ "id" ] }, "pdbx_chem_comp_audit" : { "type" : "array", "items" : { "type" : "object", "properties" : { "action_type" : { "type" : "string", "enum" : [ "Create component", "Initial release", "Modify PCM", "Modify aromatic_flag", "Modify atom id", "Modify backbone", "Modify charge", "Modify component atom id", "Modify component comp_id", "Modify coordinates", "Modify descriptor", "Modify formal charge", "Modify formula", "Modify identifier", "Modify internal type", "Modify leaving atom flag", "Modify linking type", "Modify metal description", "Modify model coordinates code", "Modify name", "Modify one letter code", "Modify parent residue", "Modify processing site", "Modify subcomponent list", "Modify synonyms", "Modify value order", "Obsolete component", "Other modification" ], "description" : "The action associated with this audit record.", "rcsb_description" : [ { "text" : "The action associated with this audit record.", "context" : "dictionary" } ] }, "comp_id" : { "type" : "string", "description" : "This data item is a pointer to _chem_comp.id in the CHEM_COMP\n category.", "rcsb_description" : [ { "text" : "This data item is a pointer to _chem_comp.id in the CHEM_COMP\n category.", "context" : "dictionary" } ] }, "date" : { "type" : "string", "format" : "date", "description" : "The date associated with this audit record.", "rcsb_description" : [ { "text" : "The date associated with this audit record.", "context" : "dictionary" } ] }, "details" : { "type" : "string", "examples" : [ "Added C14 as a leaving atom." ], "description" : "Additional details decribing this change.", "rcsb_description" : [ { "text" : "Additional details decribing this change.", "context" : "dictionary" } ] }, "ordinal" : { "type" : "integer", "description" : "This data item is an ordinal index for the\n PDBX_CHEM_COMP_AUDIT category.", "rcsb_description" : [ { "text" : "This data item is an ordinal index for the\n PDBX_CHEM_COMP_AUDIT category.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "ordinal" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_chem_comp_descriptor" : { "type" : "array", "items" : { "type" : "object", "properties" : { "comp_id" : { "type" : "string", "description" : "This data item is a pointer to _chem_comp.id in the CHEM_COMP\n category.", "rcsb_description" : [ { "text" : "This data item is a pointer to _chem_comp.id in the CHEM_COMP\n category.", "context" : "dictionary" } ] }, "descriptor" : { "type" : "string", "description" : "This data item contains the descriptor value for this\n component.", "rcsb_description" : [ { "text" : "This data item contains the descriptor value for this\n component.", "context" : "dictionary" } ] }, "program" : { "type" : "string", "examples" : [ "OPENEYE", "CACTVS", "DAYLIGHT", "OTHER" ], "description" : "This data item contains the name of the program\n or library used to compute the descriptor.", "rcsb_description" : [ { "text" : "This data item contains the name of the program\n or library used to compute the descriptor.", "context" : "dictionary" } ] }, "program_version" : { "type" : "string", "description" : "This data item contains the version of the program\n or library used to compute the descriptor.", "rcsb_description" : [ { "text" : "This data item contains the version of the program\n or library used to compute the descriptor.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "enum" : [ "InChI", "InChIKey", "InChI_CHARGE", "InChI_FIXEDH", "InChI_ISOTOPE", "InChI_MAIN", "InChI_MAIN_CONNECT", "InChI_MAIN_FORMULA", "InChI_MAIN_HATOM", "InChI_RECONNECT", "InChI_STEREO", "SMILES", "SMILES_CANNONICAL", "SMILES_CANONICAL" ], "description" : "This data item contains the descriptor type.", "rcsb_enum_annotated" : [ { "value" : "InChI", "detail" : "InChI descriptor" }, { "value" : "InChIKey", "detail" : "InChI descriptor- hash key form" }, { "value" : "InChI_CHARGE", "detail" : "InChI descriptor- charge layer" }, { "value" : "InChI_FIXEDH", "detail" : "InChI descriptor- fixed hydrogren layer" }, { "value" : "InChI_ISOTOPE", "detail" : "InChI descriptor- isotopic layer" }, { "value" : "InChI_MAIN", "detail" : "InChI descriptor- main layer" }, { "value" : "InChI_MAIN_CONNECT", "detail" : "InChI descriptor- main layer - atom connection sub-layer" }, { "value" : "InChI_MAIN_FORMULA", "detail" : "InChI descriptor- main layer - chemical formula sub-layer" }, { "value" : "InChI_MAIN_HATOM", "detail" : "InChI descriptor- main layer - hydrogen atom sub-layer" }, { "value" : "InChI_RECONNECT", "detail" : "InChI descriptor- reconnected layer" }, { "value" : "InChI_STEREO", "detail" : "InChI descriptor- stereochemical layer" }, { "value" : "SMILES", "detail" : "SMILES descriptor" }, { "value" : "SMILES_CANNONICAL", "detail" : "deprecated" }, { "value" : "SMILES_CANONICAL", "detail" : "Canonical SMILES descriptor" } ], "rcsb_description" : [ { "text" : "This data item contains the descriptor type.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "comp_id", "program", "program_version", "type" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_chem_comp_feature" : { "type" : "array", "items" : { "type" : "object", "properties" : { "comp_id" : { "type" : "string", "examples" : [ "ABC", "ATP" ], "description" : "The component identifier for this feature.", "rcsb_description" : [ { "text" : "The component identifier for this feature.", "context" : "dictionary" } ] }, "source" : { "type" : "string", "examples" : [ "PDB", "CHEBI", "DRUGBANK", "PUBCHEM" ], "description" : "The information source for the component feature.", "rcsb_description" : [ { "text" : "The information source for the component feature.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "enum" : [ "CARBOHYDRATE ANOMER", "CARBOHYDRATE ISOMER", "CARBOHYDRATE PRIMARY CARBONYL GROUP", "CARBOHYDRATE RING" ], "examples" : [ "CARBOHYDRATE ANOMER", "CARBOHYDRATE ISOMER", "CARBOHYDRATE RING" ], "description" : "The component feature type.", "rcsb_description" : [ { "text" : "The component feature type.", "context" : "dictionary" } ] }, "value" : { "type" : "string", "description" : "The component feature value.", "rcsb_description" : [ { "text" : "The component feature value.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "comp_id", "source", "type", "value" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_chem_comp_identifier" : { "type" : "array", "items" : { "type" : "object", "properties" : { "comp_id" : { "type" : "string", "description" : "This data item is a pointer to _chem_comp.id in the CHEM_COMP\n category.", "rcsb_description" : [ { "text" : "This data item is a pointer to _chem_comp.id in the CHEM_COMP\n category.", "context" : "dictionary" } ] }, "identifier" : { "type" : "string", "description" : "This data item contains the identifier value for this\n component.", "rcsb_description" : [ { "text" : "This data item contains the identifier value for this\n component.", "context" : "dictionary" } ] }, "program" : { "type" : "string", "examples" : [ "OPENEYE", "DAYLIGHT", "ACD", "AUTONOM", "PUBCHEM_CID", "PUBCHEM_SID", "OTHER", "NONE" ], "description" : "This data item contains the name of the program\n or library used to compute the identifier.", "rcsb_description" : [ { "text" : "This data item contains the name of the program\n or library used to compute the identifier.", "context" : "dictionary" } ] }, "program_version" : { "type" : "string", "description" : "This data item contains the version of the program\n or library used to compute the identifier.", "rcsb_description" : [ { "text" : "This data item contains the version of the program\n or library used to compute the identifier.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "enum" : [ "CAS REGISTRY NUMBER", "COMMON NAME", "CONDENSED IUPAC CARB SYMBOL", "CONDENSED IUPAC CARBOHYDRATE SYMBOL", "IUPAC CARB SYMBOL", "IUPAC CARBOHYDRATE SYMBOL", "MDL Identifier", "PUBCHEM Identifier", "SNFG CARB SYMBOL", "SNFG CARBOHYDRATE SYMBOL", "SYNONYM", "SYSTEMATIC NAME" ], "description" : "This data item contains the identifier type.", "rcsb_enum_annotated" : [ { "value" : "CAS REGISTRY NUMBER", "detail" : "Chemical Abstracts Registry Number" }, { "value" : "COMMON NAME", "detail" : "Common chemical name" }, { "value" : "CONDENSED IUPAC CARB SYMBOL", "detail" : "Condensed IUPAC carbohydrate symbol" }, { "value" : "CONDENSED IUPAC CARBOHYDRATE SYMBOL", "detail" : "Condensed IUPAC carbohydrate symbol" }, { "value" : "IUPAC CARB SYMBOL", "detail" : "IUPAC carbohydrate symbol" }, { "value" : "IUPAC CARBOHYDRATE SYMBOL", "detail" : "IUPAC carbohydrate symbol" }, { "value" : "MDL Identifier", "detail" : "Molecular Design Limited Identifier" }, { "value" : "PUBCHEM Identifier", "detail" : "PubChem accession number" }, { "value" : "SNFG CARB SYMBOL", "detail" : "3D-SNFG carbohydrate symbol" }, { "value" : "SNFG CARBOHYDRATE SYMBOL", "detail" : "3D-SNFG carbohydrate symbol" }, { "value" : "SYNONYM", "detail" : "Synonym chemical name" }, { "value" : "SYSTEMATIC NAME", "detail" : "Systematic chemical name" } ], "rcsb_description" : [ { "text" : "This data item contains the identifier type.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "comp_id", "program", "program_version", "type" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_family_prd_audit" : { "type" : "array", "items" : { "type" : "object", "properties" : { "action_type" : { "type" : "string", "enum" : [ "Add PRD", "Create family", "Initial release", "Modify annotation", "Modify citation", "Modify family classification", "Modify family name", "Modify feature", "Modify molecule details", "Modify related structures", "Modify sequence", "Modify synonyms", "Obsolete family", "Obsolete familyt", "Other modification", "Remove PRD" ], "description" : "The action associated with this audit record.", "rcsb_description" : [ { "text" : "The action associated with this audit record.", "context" : "dictionary" } ] }, "annotator" : { "type" : "string", "examples" : [ "JO", "SJ", "KB" ], "description" : "The initials of the annotator creating of modifying the family.", "rcsb_description" : [ { "text" : "The initials of the annotator creating of modifying the family.", "context" : "dictionary" } ] }, "date" : { "type" : "string", "format" : "date", "description" : "The date associated with this audit record.", "rcsb_description" : [ { "text" : "The date associated with this audit record.", "context" : "dictionary" } ] }, "details" : { "type" : "string", "examples" : [ "Revise molecule sequence." ], "description" : "Additional details decribing this change.", "rcsb_description" : [ { "text" : "Additional details decribing this change.", "context" : "dictionary" } ] }, "family_prd_id" : { "type" : "string", "description" : "This data item is a pointer to _pdbx_reference_molecule_family.family_prd_id in the\n\t pdbx_reference_molecule category.", "rcsb_description" : [ { "text" : "This data item is a pointer to _pdbx_reference_molecule_family.family_prd_id in the\n\t pdbx_reference_molecule category.", "context" : "dictionary" } ] }, "processing_site" : { "type" : "string", "examples" : [ "RCSB", "PDBE", "PDBJ", "BMRB", "PDBC" ], "description" : "An identifier for the wwPDB site creating or modifying the family.", "rcsb_description" : [ { "text" : "An identifier for the wwPDB site creating or modifying the family.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "action_type", "date", "family_prd_id" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_prd_audit" : { "type" : "array", "items" : { "type" : "object", "properties" : { "action_type" : { "type" : "string", "enum" : [ "Create molecule", "Initial release", "Modify audit", "Modify class", "Modify linkage", "Modify molecule name", "Modify representation", "Modify sequence", "Modify taxonomy organism", "Modify type", "Obsolete molecule", "Other modification" ], "description" : "The action associated with this audit record.", "rcsb_description" : [ { "text" : "The action associated with this audit record.", "context" : "dictionary" } ] }, "annotator" : { "type" : "string", "examples" : [ "JO", "SJ", "KB" ], "description" : "The initials of the annotator creating of modifying the molecule.", "rcsb_description" : [ { "text" : "The initials of the annotator creating of modifying the molecule.", "context" : "dictionary" } ] }, "date" : { "type" : "string", "format" : "date", "description" : "The date associated with this audit record.", "rcsb_description" : [ { "text" : "The date associated with this audit record.", "context" : "dictionary" } ] }, "details" : { "type" : "string", "examples" : [ "Revise molecule sequence." ], "description" : "Additional details decribing this change.", "rcsb_description" : [ { "text" : "Additional details decribing this change.", "context" : "dictionary" } ] }, "prd_id" : { "type" : "string", "description" : "This data item is a pointer to _pdbx_reference_molecule.prd_id in the\n\t pdbx_reference_molecule category.", "rcsb_description" : [ { "text" : "This data item is a pointer to _pdbx_reference_molecule.prd_id in the\n\t pdbx_reference_molecule category.", "context" : "dictionary" } ] }, "processing_site" : { "type" : "string", "enum" : [ "BMRB", "PDBC", "PDBE", "PDBJ", "RCSB" ], "examples" : [ "RCSB", "PDBE", "PDBJ", "BMRB", "PDBC" ], "description" : "An identifier for the wwPDB site creating or modifying the molecule.", "rcsb_description" : [ { "text" : "An identifier for the wwPDB site creating or modifying the molecule.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "action_type", "date", "prd_id" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_reference_entity_list" : { "type" : "array", "items" : { "type" : "object", "properties" : { "component_id" : { "type" : "integer", "description" : "The component number of this entity within the molecule.", "rcsb_description" : [ { "text" : "The component number of this entity within the molecule.", "context" : "dictionary" } ] }, "details" : { "type" : "string", "description" : "Additional details about this entity.", "rcsb_description" : [ { "text" : "Additional details about this entity.", "context" : "dictionary" } ] }, "prd_id" : { "type" : "string", "description" : "The value of _pdbx_reference_entity_list.prd_id is a reference\n _pdbx_reference_molecule.prd_id in the PDBX_REFERENCE_MOLECULE category.", "rcsb_description" : [ { "text" : "The value of _pdbx_reference_entity_list.prd_id is a reference\n _pdbx_reference_molecule.prd_id in the PDBX_REFERENCE_MOLECULE category.", "context" : "dictionary" } ] }, "ref_entity_id" : { "type" : "string", "description" : "The value of _pdbx_reference_entity_list.ref_entity_id is a unique identifier\n the a constituent entity within this reference molecule.", "rcsb_description" : [ { "text" : "The value of _pdbx_reference_entity_list.ref_entity_id is a unique identifier\n the a constituent entity within this reference molecule.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "enum" : [ "branched", "non-polymer", "polymer", "polymer-like" ], "examples" : [ "polymer", "non-polymer", "branched" ], "description" : "Defines the polymer characteristic of the entity.", "rcsb_description" : [ { "text" : "Defines the polymer characteristic of the entity.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "component_id", "prd_id", "ref_entity_id" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_reference_entity_poly" : { "type" : "array", "items" : { "type" : "object", "properties" : { "db_code" : { "type" : "string", "description" : "The database code for this source information", "rcsb_description" : [ { "text" : "The database code for this source information", "context" : "dictionary" } ] }, "db_name" : { "type" : "string", "description" : "The database name for this source information", "rcsb_description" : [ { "text" : "The database name for this source information", "context" : "dictionary" } ] }, "prd_id" : { "type" : "string", "description" : "The value of _pdbx_reference_entity_poly.prd_id is a reference\n\t _pdbx_reference_entity_list.prd_id in the PDBX_REFERENCE_ENTITY_LIST category.", "rcsb_description" : [ { "text" : "The value of _pdbx_reference_entity_poly.prd_id is a reference\n\t _pdbx_reference_entity_list.prd_id in the PDBX_REFERENCE_ENTITY_LIST category.", "context" : "dictionary" } ] }, "ref_entity_id" : { "type" : "string", "description" : "The value of _pdbx_reference_entity_poly.ref_entity_id is a reference\n to _pdbx_reference_entity_list.ref_entity_id in PDBX_REFERENCE_ENTITY_LIST category.", "rcsb_description" : [ { "text" : "The value of _pdbx_reference_entity_poly.ref_entity_id is a reference\n to _pdbx_reference_entity_list.ref_entity_id in PDBX_REFERENCE_ENTITY_LIST category.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "enum" : [ "nucleic-acid-like", "oligosaccharide", "peptide-like", "polysaccharide-like" ], "examples" : [ "peptide-like" ], "description" : "The type of the polymer.", "rcsb_enum_annotated" : [ { "value" : "nucleic-acid-like", "detail" : "Where the majority of residue linkages are nucleotide sugar phosphate bonds" }, { "value" : "oligosaccharide", "detail" : "Where the majority of residue linkages are sugar to sugar bonds" }, { "value" : "peptide-like", "detail" : "Where the majority of residue linkages are peptide bonds" }, { "value" : "polysaccharide-like", "detail" : "Where the majority of residue linkages are sugar to sugar bonds" } ], "rcsb_description" : [ { "text" : "The type of the polymer.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "prd_id", "ref_entity_id" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_reference_entity_poly_link" : { "type" : "array", "items" : { "type" : "object", "properties" : { "atom_id_1" : { "type" : "string", "description" : "The atom identifier/name in the first of the two components making\n the linkage.", "rcsb_description" : [ { "text" : "The atom identifier/name in the first of the two components making\n the linkage.", "context" : "dictionary" } ] }, "atom_id_2" : { "type" : "string", "description" : "The atom identifier/name in the second of the two components making\n the linkage.", "rcsb_description" : [ { "text" : "The atom identifier/name in the second of the two components making\n the linkage.", "context" : "dictionary" } ] }, "comp_id_1" : { "type" : "string", "description" : "The component identifier in the first of the two components making the\n linkage.\n\n This data item is a pointer to _pdbx_reference_entity_poly_seq.mon_id\n in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.", "rcsb_description" : [ { "text" : "The component identifier in the first of the two components making the\n linkage.\n\n This data item is a pointer to _pdbx_reference_entity_poly_seq.mon_id\n in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.", "context" : "dictionary" } ] }, "comp_id_2" : { "type" : "string", "description" : "The component identifier in the second of the two components making the\n linkage.\n\n This data item is a pointer to _pdbx_reference_entity_poly_seq.mon_id\n in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.", "rcsb_description" : [ { "text" : "The component identifier in the second of the two components making the\n linkage.\n\n This data item is a pointer to _pdbx_reference_entity_poly_seq.mon_id\n in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.", "context" : "dictionary" } ] }, "component_id" : { "type" : "integer", "description" : "The entity component identifier entity containing the linkage.", "rcsb_description" : [ { "text" : "The entity component identifier entity containing the linkage.", "context" : "dictionary" } ] }, "entity_seq_num_1" : { "type" : "integer", "description" : "For a polymer entity, the sequence number in the first of\n the two components making the linkage.\n\n This data item is a pointer to _pdbx_reference_entity_poly_seq.num\n in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.", "rcsb_description" : [ { "text" : "For a polymer entity, the sequence number in the first of\n the two components making the linkage.\n\n This data item is a pointer to _pdbx_reference_entity_poly_seq.num\n in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.", "context" : "dictionary" } ] }, "entity_seq_num_2" : { "type" : "integer", "description" : "For a polymer entity, the sequence number in the second of\n the two components making the linkage.\n\n This data item is a pointer to _pdbx_reference_entity_poly_seq.num\n in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.", "rcsb_description" : [ { "text" : "For a polymer entity, the sequence number in the second of\n the two components making the linkage.\n\n This data item is a pointer to _pdbx_reference_entity_poly_seq.num\n in the PDBX_REFERENCE_ENTITY_POLY_SEQ category.", "context" : "dictionary" } ] }, "link_id" : { "type" : "integer", "description" : "The value of _pdbx_reference_entity_poly_link.link_id uniquely identifies\n a linkage within a polymer entity.", "rcsb_description" : [ { "text" : "The value of _pdbx_reference_entity_poly_link.link_id uniquely identifies\n a linkage within a polymer entity.", "context" : "dictionary" } ] }, "prd_id" : { "type" : "string", "description" : "The value of _pdbx_reference_entity_poly_link.prd_id is a reference\n _pdbx_reference_entity_list.prd_id in the PDBX_REFERENCE_ENTITY_POLY category.", "rcsb_description" : [ { "text" : "The value of _pdbx_reference_entity_poly_link.prd_id is a reference\n _pdbx_reference_entity_list.prd_id in the PDBX_REFERENCE_ENTITY_POLY category.", "context" : "dictionary" } ] }, "ref_entity_id" : { "type" : "string", "description" : "The reference entity id of the polymer entity containing the linkage.\n\n This data item is a pointer to _pdbx_reference_entity_poly.ref_entity_id\n in the PDBX_REFERENCE_ENTITY_POLY category.", "rcsb_description" : [ { "text" : "The reference entity id of the polymer entity containing the linkage.\n\n This data item is a pointer to _pdbx_reference_entity_poly.ref_entity_id\n in the PDBX_REFERENCE_ENTITY_POLY category.", "context" : "dictionary" } ] }, "value_order" : { "type" : "string", "enum" : [ "arom", "delo", "doub", "pi", "poly", "quad", "sing", "trip" ], "description" : "The bond order target for the non-standard linkage.", "rcsb_enum_annotated" : [ { "value" : "arom", "detail" : "aromatic bond" }, { "value" : "delo", "detail" : "delocalised double bond" }, { "value" : "doub", "detail" : "double bond" }, { "value" : "pi", "detail" : "pi bond" }, { "value" : "poly", "detail" : "polymeric bond" }, { "value" : "quad", "detail" : "quadruple bond" }, { "value" : "sing", "detail" : "single bond" }, { "value" : "trip", "detail" : "triple bond" } ], "rcsb_description" : [ { "text" : "The bond order target for the non-standard linkage.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "component_id", "link_id", "prd_id", "ref_entity_id" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_reference_entity_poly_seq" : { "type" : "array", "items" : { "type" : "object", "properties" : { "hetero" : { "type" : "string", "enum" : [ "N", "Y" ], "examples" : [ "N" ], "description" : "A flag to indicate that sequence heterogeneity at this monomer position.", "rcsb_enum_annotated" : [ { "value" : "N", "detail" : "sequence is not heterogeneous at this monomer" }, { "value" : "Y", "detail" : "sequence is heterogeneous at this monomer" } ], "rcsb_description" : [ { "text" : "A flag to indicate that sequence heterogeneity at this monomer position.", "context" : "dictionary" } ] }, "mon_id" : { "type" : "string", "description" : "This data item is the chemical component identifier of monomer.", "rcsb_description" : [ { "text" : "This data item is the chemical component identifier of monomer.", "context" : "dictionary" } ] }, "num" : { "type" : "integer", "description" : "The value of _pdbx_reference_entity_poly_seq.num must uniquely and sequentially\n identify a record in the PDBX_REFERENCE_ENTITY_POLY_SEQ list.\n\n This value is conforms to author numbering conventions and does not map directly\n to the numbering conventions used for _entity_poly_seq.num.", "rcsb_description" : [ { "text" : "The value of _pdbx_reference_entity_poly_seq.num must uniquely and sequentially\n identify a record in the PDBX_REFERENCE_ENTITY_POLY_SEQ list.\n\n This value is conforms to author numbering conventions and does not map directly\n to the numbering conventions used for _entity_poly_seq.num.", "context" : "dictionary" } ] }, "observed" : { "type" : "string", "enum" : [ "N", "Y" ], "examples" : [ "Y" ], "description" : "A flag to indicate that this monomer is observed in the instance example.", "rcsb_enum_annotated" : [ { "value" : "N", "detail" : "not observed" }, { "value" : "Y", "detail" : "observed" } ], "rcsb_description" : [ { "text" : "A flag to indicate that this monomer is observed in the instance example.", "context" : "dictionary" } ] }, "parent_mon_id" : { "type" : "string", "description" : "This data item is the chemical component identifier for the parent component corresponding to this monomer.", "rcsb_description" : [ { "text" : "This data item is the chemical component identifier for the parent component corresponding to this monomer.", "context" : "dictionary" } ] }, "prd_id" : { "type" : "string", "description" : "The value of _pdbx_reference_entity_poly_seq.prd_id is a reference\n\t _pdbx_reference_entity_poly.prd_id in the PDBX_REFERENCE_ENTITY_POLY category.", "rcsb_description" : [ { "text" : "The value of _pdbx_reference_entity_poly_seq.prd_id is a reference\n\t _pdbx_reference_entity_poly.prd_id in the PDBX_REFERENCE_ENTITY_POLY category.", "context" : "dictionary" } ] }, "ref_entity_id" : { "type" : "string", "description" : "The value of _pdbx_reference_entity_poly_seq.ref_entity_id is a reference\n to _pdbx_reference_entity_poly.ref_entity_id in PDBX_REFERENCE_ENTITY_POLY category.", "rcsb_description" : [ { "text" : "The value of _pdbx_reference_entity_poly_seq.ref_entity_id is a reference\n to _pdbx_reference_entity_poly.ref_entity_id in PDBX_REFERENCE_ENTITY_POLY category.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "hetero", "mon_id", "num", "prd_id", "ref_entity_id" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_reference_entity_sequence" : { "type" : "array", "items" : { "type" : "object", "properties" : { "NRP_flag" : { "type" : "string", "enum" : [ "N", "Y" ], "examples" : [ "Y" ], "description" : "A flag to indicate a non-ribosomal entity.", "rcsb_enum_annotated" : [ { "value" : "N", "detail" : "ribosomal" }, { "value" : "Y", "detail" : "non-ribosomal" } ], "rcsb_description" : [ { "text" : "A flag to indicate a non-ribosomal entity.", "context" : "dictionary" } ] }, "one_letter_codes" : { "type" : "string", "description" : "The one-letter-code sequence for this entity. Non-standard monomers are represented as 'X'.", "rcsb_description" : [ { "text" : "The one-letter-code sequence for this entity. Non-standard monomers are represented as 'X'.", "context" : "dictionary" } ] }, "prd_id" : { "type" : "string", "description" : "The value of _pdbx_reference_entity_sequence.prd_id is a reference\n\t _pdbx_reference_entity_list.prd_id in the PDBX_REFERENCE_ENTITY_LIST category.", "rcsb_description" : [ { "text" : "The value of _pdbx_reference_entity_sequence.prd_id is a reference\n\t _pdbx_reference_entity_list.prd_id in the PDBX_REFERENCE_ENTITY_LIST category.", "context" : "dictionary" } ] }, "ref_entity_id" : { "type" : "string", "description" : "The value of _pdbx_reference_entity_sequence.ref_entity_id is a reference\n to _pdbx_reference_entity_list.ref_entity_id in PDBX_REFERENCE_ENTITY_LIST category.", "rcsb_description" : [ { "text" : "The value of _pdbx_reference_entity_sequence.ref_entity_id is a reference\n to _pdbx_reference_entity_list.ref_entity_id in PDBX_REFERENCE_ENTITY_LIST category.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "enum" : [ "peptide-like", "saccharide" ], "examples" : [ "peptide-like", "saccharide" ], "description" : "The monomer type for the sequence.", "rcsb_description" : [ { "text" : "The monomer type for the sequence.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "prd_id", "ref_entity_id" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_reference_entity_src_nat" : { "type" : "array", "items" : { "type" : "object", "properties" : { "atcc" : { "type" : "string", "description" : "The Americal Tissue Culture Collection code for organism from which the entity was isolated.", "rcsb_description" : [ { "text" : "The Americal Tissue Culture Collection code for organism from which the entity was isolated.", "context" : "dictionary" } ] }, "db_code" : { "type" : "string", "description" : "The database code for this source information", "rcsb_description" : [ { "text" : "The database code for this source information", "context" : "dictionary" } ] }, "db_name" : { "type" : "string", "description" : "The database name for this source information", "rcsb_description" : [ { "text" : "The database name for this source information", "context" : "dictionary" } ] }, "ordinal" : { "type" : "integer", "description" : "The value of _pdbx_reference_entity_src_nat.ordinal distinguishes\n\t source details for this entity.", "rcsb_description" : [ { "text" : "The value of _pdbx_reference_entity_src_nat.ordinal distinguishes\n\t source details for this entity.", "context" : "dictionary" } ] }, "organism_scientific" : { "type" : "string", "examples" : [ "Mus musculus" ], "description" : "The scientific name of the organism from which the entity was isolated.", "rcsb_description" : [ { "text" : "The scientific name of the organism from which the entity was isolated.", "context" : "dictionary" } ] }, "prd_id" : { "type" : "string", "description" : "The value of _pdbx_reference_entity_src_nat.prd_id is a reference\n\t _pdbx_reference_entity_list.prd_id in the PDBX_REFERENCE_ENTITY_LIST category.", "rcsb_description" : [ { "text" : "The value of _pdbx_reference_entity_src_nat.prd_id is a reference\n\t _pdbx_reference_entity_list.prd_id in the PDBX_REFERENCE_ENTITY_LIST category.", "context" : "dictionary" } ] }, "ref_entity_id" : { "type" : "string", "description" : "The value of _pdbx_reference_entity_src_nat.ref_entity_id is a reference\n to _pdbx_reference_entity_list.ref_entity_id in PDBX_REFERENCE_ENTITY_LIST category.", "rcsb_description" : [ { "text" : "The value of _pdbx_reference_entity_src_nat.ref_entity_id is a reference\n to _pdbx_reference_entity_list.ref_entity_id in PDBX_REFERENCE_ENTITY_LIST category.", "context" : "dictionary" } ] }, "source" : { "type" : "string", "description" : "The data source for this information.", "rcsb_description" : [ { "text" : "The data source for this information.", "context" : "dictionary" } ] }, "source_id" : { "type" : "string", "description" : "A identifier within the data source for this information.", "rcsb_description" : [ { "text" : "A identifier within the data source for this information.", "context" : "dictionary" } ] }, "taxid" : { "type" : "string", "description" : "The NCBI TaxId of the organism from which the entity was isolated.", "rcsb_description" : [ { "text" : "The NCBI TaxId of the organism from which the entity was isolated.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "ordinal", "prd_id", "ref_entity_id" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_reference_molecule" : { "type" : "object", "properties" : { "chem_comp_id" : { "type" : "string", "examples" : [ "0Z3", "CD9" ], "description" : "For entities represented as single molecules, the identifier\n corresponding to the chemical definition for the molecule.", "rcsb_description" : [ { "text" : "For entities represented as single molecules, the identifier\n corresponding to the chemical definition for the molecule.", "context" : "dictionary" } ] }, "class" : { "type" : "string", "enum" : [ "Antagonist", "Anthelmintic", "Antibiotic", "Antibiotic, Anthelmintic", "Antibiotic, Antimicrobial", "Antibiotic, Antineoplastic", "Anticancer", "Anticoagulant", "Anticoagulant, Antithrombotic", "Antifungal", "Antigen", "Antiinflammatory", "Antimicrobial", "Antimicrobial, Antiparasitic, Antibiotic", "Antimicrobial, Antiretroviral", "Antimicrobial, Antitumor", "Antineoplastic", "Antiparasitic", "Antiretroviral", "Antithrombotic", "Antitumor", "Antiviral", "CASPASE inhibitor", "Chaperone binding", "Drug delivery", "Enzyme inhibitor", "Glycan component", "Growth factor", "Immunosuppressant", "Inducer", "Inhibitor", "Lantibiotic", "Metabolism", "Metal transport", "Nutrient", "Oxidation-reduction", "Protein binding", "Receptor", "Substrate analog", "Synthetic opioid", "Thrombin inhibitor", "Thrombin inhibitor, Trypsin inhibitor", "Toxin", "Transition state mimetic", "Transport activator", "Trypsin inhibitor", "Unknown", "Water retention" ], "description" : "Broadly defines the function of the entity.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Broadly defines the function of the entity.", "context" : "dictionary" }, { "text" : "BIRD Class", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Biologically Interesting Molecules (BIRD)", "priority_order" : 20 } ] }, "class_evidence_code" : { "type" : "string", "description" : "Evidence for the assignment of _pdbx_reference_molecule.class", "rcsb_description" : [ { "text" : "Evidence for the assignment of _pdbx_reference_molecule.class", "context" : "dictionary" } ] }, "compound_details" : { "type" : "string", "description" : "Special details about this molecule.", "rcsb_description" : [ { "text" : "Special details about this molecule.", "context" : "dictionary" } ] }, "description" : { "type" : "string", "description" : "Description of this molecule.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Description of this molecule.", "context" : "dictionary" }, { "text" : "Description (Reference Molecule)", "context" : "brief" } ] }, "formula" : { "type" : "string", "examples" : [ "C18 H19 N7 O8 S" ], "description" : "The formula for the reference entity. Formulae are written\n according to the rules:\n\n 1. Only recognised element symbols may be used.\n\n 2. Each element symbol is followed by a 'count' number. A count\n of '1' may be omitted.\n\n 3. A space or parenthesis must separate each element symbol and\n its count, but in general parentheses are not used.\n\n 4. The order of elements depends on whether or not carbon is\n present. If carbon is present, the order should be: C, then\n H, then the other elements in alphabetical order of their\n symbol. If carbon is not present, the elements are listed\n purely in alphabetic order of their symbol. This is the\n 'Hill' system used by Chemical Abstracts.", "rcsb_description" : [ { "text" : "The formula for the reference entity. Formulae are written\n according to the rules:\n\n 1. Only recognised element symbols may be used.\n\n 2. Each element symbol is followed by a 'count' number. A count\n of '1' may be omitted.\n\n 3. A space or parenthesis must separate each element symbol and\n its count, but in general parentheses are not used.\n\n 4. The order of elements depends on whether or not carbon is\n present. If carbon is present, the order should be: C, then\n H, then the other elements in alphabetical order of their\n symbol. If carbon is not present, the elements are listed\n purely in alphabetic order of their symbol. This is the\n 'Hill' system used by Chemical Abstracts.", "context" : "dictionary" } ] }, "formula_weight" : { "type" : "number", "description" : "Formula mass in daltons of the entity.", "rcsb_description" : [ { "text" : "Formula mass in daltons of the entity.", "context" : "dictionary" } ] }, "name" : { "type" : "string", "examples" : [ "thiostrepton" ], "description" : "A name of the entity.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "A name of the entity.", "context" : "dictionary" }, { "text" : "BIRD Name", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Biologically Interesting Molecules (BIRD)", "priority_order" : 10 } ] }, "prd_id" : { "type" : "string", "examples" : [ "PRD_000001", "PRD_0000010" ], "description" : "The value of _pdbx_reference_molecule.prd_id is the unique identifier\n for the reference molecule in this family.\n\n By convention this ID uniquely identifies the reference molecule in\n in the PDB reference dictionary.\n\n The ID has the template form PRD_dddddd (e.g. PRD_000001)", "rcsb_search_context" : [ "exact-match", "suggest" ], "rcsb_full_text_priority" : 20, "rcsb_description" : [ { "text" : "The value of _pdbx_reference_molecule.prd_id is the unique identifier\n for the reference molecule in this family.\n\n By convention this ID uniquely identifies the reference molecule in\n in the PDB reference dictionary.\n\n The ID has the template form PRD_dddddd (e.g. PRD_000001)", "context" : "dictionary" }, { "text" : "BIRD ID(s)", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Biologically Interesting Molecules (BIRD)", "priority_order" : 5 } ] }, "release_status" : { "type" : "string", "enum" : [ "HOLD", "OBS", "REL", "WAIT" ], "description" : "Defines the current PDB release status for this molecule definition.", "rcsb_description" : [ { "text" : "Defines the current PDB release status for this molecule definition.", "context" : "dictionary" } ] }, "replaced_by" : { "type" : "string", "description" : "Assigns the identifier of the reference molecule that has replaced this molecule.", "rcsb_description" : [ { "text" : "Assigns the identifier of the reference molecule that has replaced this molecule.", "context" : "dictionary" } ] }, "replaces" : { "type" : "string", "description" : "Assigns the identifier for the reference molecule which have been replaced\n by this reference molecule.\n Multiple molecule identifier codes should be separated by commas.", "rcsb_description" : [ { "text" : "Assigns the identifier for the reference molecule which have been replaced\n by this reference molecule.\n Multiple molecule identifier codes should be separated by commas.", "context" : "dictionary" } ] }, "represent_as" : { "type" : "string", "enum" : [ "branched", "polymer", "single molecule" ], "description" : "Defines how this entity is represented in PDB data files.", "rcsb_description" : [ { "text" : "Defines how this entity is represented in PDB data files.", "context" : "dictionary" } ] }, "representative_PDB_id_code" : { "type" : "string", "description" : "The PDB accession code for the entry containing a representative example of this molecule.", "rcsb_description" : [ { "text" : "The PDB accession code for the entry containing a representative example of this molecule.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "enum" : [ "Amino acid", "Aminoglycoside", "Ansamycin", "Anthracycline", "Anthraquinone", "Chalkophore", "Chalkophore, Polypeptide", "Chromophore", "Cyclic depsipeptide", "Cyclic lipopeptide", "Cyclic peptide", "Glycopeptide", "Heterocyclic", "Imino sugar", "Keto acid", "Lipoglycopeptide", "Lipopeptide", "Macrolide", "Non-polymer", "Nucleoside", "Oligopeptide", "Oligosaccharide", "Peptaibol", "Peptide-like", "Polycyclic", "Polypeptide", "Polysaccharide", "Quinolone", "Siderophore", "Thiolactone", "Thiopeptide", "Unknown" ], "examples" : [ "Peptide-like", "Macrolide" ], "description" : "Defines the structural classification of the entity.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Defines the structural classification of the entity.", "context" : "dictionary" }, { "text" : "BIRD Type", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Biologically Interesting Molecules (BIRD)", "priority_order" : 15 } ] }, "type_evidence_code" : { "type" : "string", "description" : "Evidence for the assignment of _pdbx_reference_molecule.type", "rcsb_description" : [ { "text" : "Evidence for the assignment of _pdbx_reference_molecule.type", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "prd_id" ] }, "pdbx_reference_molecule_annotation" : { "type" : "array", "items" : { "type" : "object", "properties" : { "family_prd_id" : { "type" : "string", "description" : "The value of _pdbx_reference_molecule_annotation.family_prd_id is a reference to\n _pdbx_reference_molecule_list.family_prd_id in category PDBX_REFERENCE_MOLECULE_FAMILY_LIST.", "rcsb_description" : [ { "text" : "The value of _pdbx_reference_molecule_annotation.family_prd_id is a reference to\n _pdbx_reference_molecule_list.family_prd_id in category PDBX_REFERENCE_MOLECULE_FAMILY_LIST.", "context" : "dictionary" } ] }, "ordinal" : { "type" : "integer", "description" : "This data item distinguishes anotations for this entity.", "rcsb_description" : [ { "text" : "This data item distinguishes anotations for this entity.", "context" : "dictionary" } ] }, "prd_id" : { "type" : "string", "description" : "This data item is a pointer to _pdbx_reference_molecule.prd_id in the\n PDB_REFERENCE_MOLECULE category.", "rcsb_description" : [ { "text" : "This data item is a pointer to _pdbx_reference_molecule.prd_id in the\n PDB_REFERENCE_MOLECULE category.", "context" : "dictionary" } ] }, "source" : { "type" : "string", "examples" : [ "depositor provided", "from UniProt Entry P200311" ], "description" : "The source of the annoation for this entity.", "rcsb_description" : [ { "text" : "The source of the annoation for this entity.", "context" : "dictionary" } ] }, "text" : { "type" : "string", "examples" : [ "antigen binding", "glucose transporter activity" ], "description" : "Text describing the annotation for this entity.", "rcsb_description" : [ { "text" : "Text describing the annotation for this entity.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "examples" : [ "Function", "Use", "Pharmacology", "Mechanism_of_Action", "Biological_Activity", "Inhibitor_Class", "Therapeutic_Category", "Research_Use", "Other_annotation" ], "description" : "Type of annotation for this entity.", "rcsb_description" : [ { "text" : "Type of annotation for this entity.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "family_prd_id", "ordinal" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_reference_molecule_details" : { "type" : "array", "items" : { "type" : "object", "properties" : { "family_prd_id" : { "type" : "string", "description" : "The value of _pdbx_reference_molecule_details.family_prd_id is a reference to\n _pdbx_reference_molecule_list.family_prd_id' in category PDBX_REFERENCE_MOLECULE_FAMILY.", "rcsb_description" : [ { "text" : "The value of _pdbx_reference_molecule_details.family_prd_id is a reference to\n _pdbx_reference_molecule_list.family_prd_id' in category PDBX_REFERENCE_MOLECULE_FAMILY.", "context" : "dictionary" } ] }, "ordinal" : { "type" : "integer", "description" : "The value of _pdbx_reference_molecule_details.ordinal is an ordinal that\n distinguishes each descriptive text for this entity.", "rcsb_description" : [ { "text" : "The value of _pdbx_reference_molecule_details.ordinal is an ordinal that\n distinguishes each descriptive text for this entity.", "context" : "dictionary" } ] }, "source" : { "type" : "string", "description" : "A data source of this information (e.g. PubMed, Merck Index)", "rcsb_description" : [ { "text" : "A data source of this information (e.g. PubMed, Merck Index)", "context" : "dictionary" } ] }, "source_id" : { "type" : "string", "description" : "A identifier within the data source for this information.", "rcsb_description" : [ { "text" : "A identifier within the data source for this information.", "context" : "dictionary" } ] }, "text" : { "type" : "string", "description" : "The text of the description of special aspects of the entity.", "rcsb_description" : [ { "text" : "The text of the description of special aspects of the entity.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "family_prd_id", "ordinal" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_reference_molecule_family" : { "type" : "object", "properties" : { "family_prd_id" : { "type" : "string", "description" : "The value of _pdbx_reference_entity.family_prd_id must uniquely identify a record in the\n PDBX_REFERENCE_MOLECULE_FAMILY list.\n\n By convention this ID uniquely identifies the reference family in\n in the PDB reference dictionary.\n\n The ID has the template form FAM_dddddd (e.g. FAM_000001)", "rcsb_description" : [ { "text" : "The value of _pdbx_reference_entity.family_prd_id must uniquely identify a record in the\n PDBX_REFERENCE_MOLECULE_FAMILY list.\n\n By convention this ID uniquely identifies the reference family in\n in the PDB reference dictionary.\n\n The ID has the template form FAM_dddddd (e.g. FAM_000001)", "context" : "dictionary" } ] }, "name" : { "type" : "string", "examples" : [ "actinomycin", "adriamycin" ], "description" : "The entity family name.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The entity family name.", "context" : "dictionary" }, { "text" : "Name (Reference Molecule Family)", "context" : "brief" } ] }, "release_status" : { "type" : "string", "enum" : [ "HOLD", "OBS", "REL", "WAIT" ], "description" : "Assigns the current PDB release status for this family.", "rcsb_description" : [ { "text" : "Assigns the current PDB release status for this family.", "context" : "dictionary" } ] }, "replaced_by" : { "type" : "string", "description" : "Assigns the identifier of the family that has replaced this component.", "rcsb_description" : [ { "text" : "Assigns the identifier of the family that has replaced this component.", "context" : "dictionary" } ] }, "replaces" : { "type" : "string", "description" : "Assigns the identifier for the family which have been replaced by this family.\n Multiple family identifier codes should be separated by commas.", "rcsb_description" : [ { "text" : "Assigns the identifier for the family which have been replaced by this family.\n Multiple family identifier codes should be separated by commas.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "family_prd_id" ] }, "pdbx_reference_molecule_features" : { "type" : "array", "items" : { "type" : "object", "properties" : { "family_prd_id" : { "type" : "string", "description" : "The value of _pdbx_reference_molecule_features.family_prd_id is a reference to\n _pdbx_reference_molecule_list.family_prd_id in category PDBX_REFERENCE_MOLECULE_FAMILY_LIST.", "rcsb_description" : [ { "text" : "The value of _pdbx_reference_molecule_features.family_prd_id is a reference to\n _pdbx_reference_molecule_list.family_prd_id in category PDBX_REFERENCE_MOLECULE_FAMILY_LIST.", "context" : "dictionary" } ] }, "ordinal" : { "type" : "integer", "description" : "The value of _pdbx_reference_molecule_features.ordinal distinguishes\n\t each feature for this entity.", "rcsb_description" : [ { "text" : "The value of _pdbx_reference_molecule_features.ordinal distinguishes\n\t each feature for this entity.", "context" : "dictionary" } ] }, "prd_id" : { "type" : "string", "description" : "The value of _pdbx_reference_molecule_features.prd_id is a reference\n\t _pdbx_reference_molecule.prd_id in the PDBX_REFERENCE_MOLECULE category.", "rcsb_description" : [ { "text" : "The value of _pdbx_reference_molecule_features.prd_id is a reference\n\t _pdbx_reference_molecule.prd_id in the PDBX_REFERENCE_MOLECULE category.", "context" : "dictionary" } ] }, "source" : { "type" : "string", "examples" : [ "PDB", "CHEBI", "DRUGBANK", "PUBCHEM" ], "description" : "The information source for the component feature.", "rcsb_description" : [ { "text" : "The information source for the component feature.", "context" : "dictionary" } ] }, "source_ordinal" : { "type" : "integer", "description" : "The value of _pdbx_reference_molecule_features.source_ordinal provides\n\t the priority order of features from a particular source or database.", "rcsb_description" : [ { "text" : "The value of _pdbx_reference_molecule_features.source_ordinal provides\n\t the priority order of features from a particular source or database.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "examples" : [ "FUNCTION", "ENZYME INHIBITED", "STRUCTURE IMAGE URL" ], "description" : "The entity feature type.", "rcsb_description" : [ { "text" : "The entity feature type.", "context" : "dictionary" } ] }, "value" : { "type" : "string", "description" : "The entity feature value.", "rcsb_description" : [ { "text" : "The entity feature value.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "family_prd_id", "ordinal", "prd_id" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_reference_molecule_list" : { "type" : "array", "items" : { "type" : "object", "properties" : { "family_prd_id" : { "type" : "string", "description" : "The value of _pdbx_reference_molecule_list.family_prd_id is a reference to\n _pdbx_reference_molecule_family.family_prd_id' in category PDBX_REFERENCE_MOLECULE_FAMILY.", "rcsb_description" : [ { "text" : "The value of _pdbx_reference_molecule_list.family_prd_id is a reference to\n _pdbx_reference_molecule_family.family_prd_id' in category PDBX_REFERENCE_MOLECULE_FAMILY.", "context" : "dictionary" } ] }, "prd_id" : { "type" : "string", "description" : "The value of _pdbx_reference_molecule_list.prd_id is the unique identifier\n for the reference molecule in this family.\n\n By convention this ID uniquely identifies the reference molecule in\n in the PDB reference dictionary.\n\n The ID has the template form PRD_dddddd (e.g. PRD_000001)", "rcsb_description" : [ { "text" : "The value of _pdbx_reference_molecule_list.prd_id is the unique identifier\n for the reference molecule in this family.\n\n By convention this ID uniquely identifies the reference molecule in\n in the PDB reference dictionary.\n\n The ID has the template form PRD_dddddd (e.g. PRD_000001)", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "family_prd_id", "prd_id" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_reference_molecule_related_structures" : { "type" : "array", "items" : { "type" : "object", "properties" : { "citation_id" : { "type" : "string", "description" : "A link to related reference information in the citation category.", "rcsb_description" : [ { "text" : "A link to related reference information in the citation category.", "context" : "dictionary" } ] }, "db_accession" : { "type" : "string", "examples" : [ "143108" ], "description" : "The database accession code for the related structure reference.", "rcsb_description" : [ { "text" : "The database accession code for the related structure reference.", "context" : "dictionary" } ] }, "db_code" : { "type" : "string", "examples" : [ "QEFHUE" ], "description" : "The database identifier code for the related structure reference.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The database identifier code for the related structure reference.", "context" : "dictionary" }, { "text" : "Db Code (Reference Molecule Related Structures)", "context" : "brief" } ] }, "db_name" : { "type" : "string", "examples" : [ "CCDC" ], "description" : "The database name for the related structure reference.", "rcsb_description" : [ { "text" : "The database name for the related structure reference.", "context" : "dictionary" } ] }, "family_prd_id" : { "type" : "string", "description" : "The value of _pdbx_reference_molecule_related_structures.family_prd_id is a reference to\n _pdbx_reference_molecule_list.family_prd_id in category PDBX_REFERENCE_MOLECULE_FAMILY_LIST.", "rcsb_description" : [ { "text" : "The value of _pdbx_reference_molecule_related_structures.family_prd_id is a reference to\n _pdbx_reference_molecule_list.family_prd_id in category PDBX_REFERENCE_MOLECULE_FAMILY_LIST.", "context" : "dictionary" } ] }, "formula" : { "type" : "string", "examples" : [ "C18 H19 N7 O8 S" ], "description" : "The formula for the reference entity. Formulae are written\n according to the rules:\n\n 1. Only recognised element symbols may be used.\n\n 2. Each element symbol is followed by a 'count' number. A count\n of '1' may be omitted.\n\n 3. A space or parenthesis must separate each element symbol and\n its count, but in general parentheses are not used.\n\n 4. The order of elements depends on whether or not carbon is\n present. If carbon is present, the order should be: C, then\n H, then the other elements in alphabetical order of their\n symbol. If carbon is not present, the elements are listed\n purely in alphabetic order of their symbol. This is the\n 'Hill' system used by Chemical Abstracts.", "rcsb_description" : [ { "text" : "The formula for the reference entity. Formulae are written\n according to the rules:\n\n 1. Only recognised element symbols may be used.\n\n 2. Each element symbol is followed by a 'count' number. A count\n of '1' may be omitted.\n\n 3. A space or parenthesis must separate each element symbol and\n its count, but in general parentheses are not used.\n\n 4. The order of elements depends on whether or not carbon is\n present. If carbon is present, the order should be: C, then\n H, then the other elements in alphabetical order of their\n symbol. If carbon is not present, the elements are listed\n purely in alphabetic order of their symbol. This is the\n 'Hill' system used by Chemical Abstracts.", "context" : "dictionary" } ] }, "name" : { "type" : "string", "examples" : [ "actinomycn" ], "description" : "The chemical name for the structure entry in the related database", "rcsb_description" : [ { "text" : "The chemical name for the structure entry in the related database", "context" : "dictionary" } ] }, "ordinal" : { "type" : "integer", "description" : "The value of _pdbx_reference_molecule_related_structures.ordinal distinguishes\n related structural data for each entity.", "rcsb_description" : [ { "text" : "The value of _pdbx_reference_molecule_related_structures.ordinal distinguishes\n related structural data for each entity.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "family_prd_id", "ordinal" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_reference_molecule_synonyms" : { "type" : "array", "items" : { "type" : "object", "properties" : { "family_prd_id" : { "type" : "string", "description" : "The value of _pdbx_reference_molecule_synonyms.family_prd_id is a reference to\n _pdbx_reference_molecule_list.family_prd_id in category PDBX_REFERENCE_MOLECULE_FAMILY_LIST.", "rcsb_description" : [ { "text" : "The value of _pdbx_reference_molecule_synonyms.family_prd_id is a reference to\n _pdbx_reference_molecule_list.family_prd_id in category PDBX_REFERENCE_MOLECULE_FAMILY_LIST.", "context" : "dictionary" } ] }, "name" : { "type" : "string", "examples" : [ "thiostrepton" ], "description" : "A synonym name for the entity.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "A synonym name for the entity.", "context" : "dictionary" }, { "text" : "Name (Reference Molecule Synonyms)", "context" : "brief" } ] }, "ordinal" : { "type" : "integer", "description" : "The value of _pdbx_reference_molecule_synonyms.ordinal is an ordinal\n\t to distinguish synonyms for this entity.", "rcsb_description" : [ { "text" : "The value of _pdbx_reference_molecule_synonyms.ordinal is an ordinal\n\t to distinguish synonyms for this entity.", "context" : "dictionary" } ] }, "prd_id" : { "type" : "string", "description" : "The value of _pdbx_reference_molecule_synonyms.prd_id is a reference\n\t _pdbx_reference_molecule.prd_id in the PDBX_REFERENCE_MOLECULE category.", "rcsb_description" : [ { "text" : "The value of _pdbx_reference_molecule_synonyms.prd_id is a reference\n\t _pdbx_reference_molecule.prd_id in the PDBX_REFERENCE_MOLECULE category.", "context" : "dictionary" } ] }, "source" : { "type" : "string", "examples" : [ "CAS" ], "description" : "The source of this synonym name for the entity.", "rcsb_description" : [ { "text" : "The source of this synonym name for the entity.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "family_prd_id", "ordinal", "prd_id" ] }, "minItems" : 1, "uniqueItems" : true }, "rcsb_bird_citation" : { "type" : "array", "items" : { "type" : "object", "properties" : { "id" : { "type" : "string", "examples" : [ "1", "2" ], "description" : "The value of _rcsb_bird_citation.id must uniquely identify a record in the\n rcsb_bird_citation list.", "rcsb_description" : [ { "text" : "The value of _rcsb_bird_citation.id must uniquely identify a record in the\n rcsb_bird_citation list.", "context" : "dictionary" } ] }, "journal_abbrev" : { "type" : "string", "examples" : [ "J.Mol.Biol.", "J. Mol. Biol." ], "description" : "Abbreviated name of the cited journal as given in the\n Chemical Abstracts Service Source Index.", "rcsb_description" : [ { "text" : "Abbreviated name of the cited journal as given in the\n Chemical Abstracts Service Source Index.", "context" : "dictionary" }, { "text" : "The PDB (i.e., the Chemical Abstracts) abbreviation for a journal. If you do not know the abbreviation, then give the complete name of the journal and we will try and find it for you. If it is a book or other monographic work, state the full title.", "context" : "deposition" } ] }, "journal_volume" : { "type" : "string", "examples" : [ "174" ], "description" : "Volume number of the journal cited; relevant for journal\n articles.", "rcsb_description" : [ { "text" : "Volume number of the journal cited; relevant for journal\n articles.", "context" : "dictionary" }, { "text" : "The volume number of the journal in which the article appeared. Example: 317", "context" : "deposition" } ] }, "page_first" : { "type" : "string", "description" : "The first page of the rcsb_bird_citation; relevant for journal\n articles, books and book chapters.", "rcsb_description" : [ { "text" : "The first page of the rcsb_bird_citation; relevant for journal\n articles, books and book chapters.", "context" : "dictionary" }, { "text" : "The starting page number of this article.", "context" : "deposition" } ] }, "page_last" : { "type" : "string", "description" : "The last page of the rcsb_bird_citation; relevant for journal\n articles, books and book chapters.", "rcsb_description" : [ { "text" : "The last page of the rcsb_bird_citation; relevant for journal\n articles, books and book chapters.", "context" : "dictionary" }, { "text" : "The last page number of this article.", "context" : "deposition" } ] }, "pdbx_database_id_DOI" : { "type" : "string", "examples" : [ "10.2345/S1384107697000225" ], "description" : "Document Object Identifier used by doi.org to uniquely\n specify bibliographic entry.", "rcsb_description" : [ { "text" : "Document Object Identifier used by doi.org to uniquely\n specify bibliographic entry.", "context" : "dictionary" }, { "text" : "The document Object Identifier used by doi.org to uniquely specify bibliographic entry", "context" : "deposition" } ] }, "pdbx_database_id_PubMed" : { "type" : "integer", "description" : "Ascession number used by PubMed to categorize a specific\n bibliographic entry.", "rcsb_description" : [ { "text" : "Ascession number used by PubMed to categorize a specific\n bibliographic entry.", "context" : "dictionary" }, { "text" : "The accession number used by PubMed to categorize a specific bibliographic entry", "context" : "deposition" } ] }, "rcsb_authors" : { "type" : "array", "items" : { "type" : "string", "examples" : [ "Bleary, Percival R." ], "description" : "Names of the authors of the citation; relevant for journal\n articles, books and book chapters. Names are separated by vertical bars.\n\n The family name(s), followed by a comma and including any\n dynastic components, precedes the first name(s) or initial(s).", "rcsb_description" : [ { "text" : "Names of the authors of the citation; relevant for journal\n articles, books and book chapters. Names are separated by vertical bars.\n\n The family name(s), followed by a comma and including any\n dynastic components, precedes the first name(s) or initial(s).", "context" : "dictionary" } ] }, "uniqueItems" : false }, "title" : { "type" : "string", "examples" : [ "Structure of diferric duck ovotransferrin\n at 2.35 Angstroms resolution." ], "description" : "The title of the rcsb_bird_citation; relevant for journal articles, books\n and book chapters.", "rcsb_description" : [ { "text" : "The title of the rcsb_bird_citation; relevant for journal articles, books\n and book chapters.", "context" : "dictionary" }, { "text" : "Title of the article or chapter or part of a book. This should be marked NULL if the author(s) listed wrote the entire book (or other work) and no sub-section of the book is being cited. Example: The Structure of Crystalline Profilin-Beta-Actin", "context" : "deposition" } ] }, "year" : { "type" : "integer", "description" : "The year of the rcsb_bird_citation; relevant for journal articles, books\n and book chapters.", "rcsb_description" : [ { "text" : "The year of the rcsb_bird_citation; relevant for journal articles, books\n and book chapters.", "context" : "dictionary" }, { "text" : "The year of publication of the article. Example: 2002", "context" : "deposition" } ] } }, "additionalProperties" : false, "required" : [ "id" ] }, "minItems" : 1, "uniqueItems" : true }, "rcsb_chem_comp_annotation" : { "type" : "array", "items" : { "type" : "object", "properties" : { "annotation_id" : { "type" : "string", "description" : "An identifier for the annotation.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "An identifier for the annotation.", "context" : "dictionary" }, { "text" : "Identifier", "context" : "brief" } ] }, "assignment_version" : { "type" : "string", "examples" : [ "V4_0_2" ], "description" : "Identifies the version of the annotation assignment.", "rcsb_description" : [ { "text" : "Identifies the version of the annotation assignment.", "context" : "dictionary" }, { "text" : "Annotation Version", "context" : "brief" } ] }, "description" : { "type" : "string", "description" : "A description for the annotation.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "A description for the annotation.", "context" : "dictionary" }, { "text" : "Annotation Description", "context" : "brief" } ] }, "name" : { "type" : "string", "description" : "A name for the annotation.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "A name for the annotation.", "context" : "dictionary" }, { "text" : "Name", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Chemical Components", "priority_order" : 100 } ] }, "provenance_source" : { "type" : "string", "examples" : [ "RESID", "UniProt", "PDB" ], "description" : "Code identifying the individual, organization or program that\n assigned the annotation.", "rcsb_description" : [ { "text" : "Code identifying the individual, organization or program that\n assigned the annotation.", "context" : "dictionary" }, { "text" : "Annotation Source", "context" : "brief" } ] }, "type" : { "type" : "string", "enum" : [ "ATC", "Carbohydrate Anomer", "Carbohydrate Isomer", "Carbohydrate Primary Carbonyl Group", "Carbohydrate Ring", "Generating Enzyme", "Modification Type", "PSI-MOD" ], "examples" : [ "PSI-MOD" ], "description" : "A type or category of the annotation.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "ATC", "detail" : "Anatomical Therapeutic Chemical Classification System (ATC) from the World Health Organization (WHO)", "name" : "ATC (WHO)" }, { "value" : "Carbohydrate Anomer", "detail" : "Carbohydrate Anomeric Form", "name" : "Carbohydrate Anomer" }, { "value" : "Carbohydrate Isomer", "detail" : "Carbohydrate Isomeric Form", "name" : "Carbohydrate Isomer" }, { "value" : "Carbohydrate Primary Carbonyl Group", "detail" : "Carbohydrate Primary Carbonyl Group", "name" : "Carbohydrate Primary Carbonyl Group" }, { "value" : "Carbohydrate Ring", "detail" : "Carbohydrate Ring Type", "name" : "Carbohydrate Ring" }, { "value" : "Generating Enzyme", "detail" : "Enzyme generating residue modification (RESID)", "name" : "RESID Generating Enzyme" }, { "value" : "Modification Type", "detail" : "Modified residue classification (RESID)", "name" : "RESID Modification" }, { "value" : "PSI-MOD", "detail" : "Protein Modification Ontology", "name" : "PSI-MOD" } ], "rcsb_description" : [ { "text" : "A type or category of the annotation.", "context" : "dictionary" }, { "text" : "Annotation Type", "context" : "brief" } ] }, "annotation_lineage" : { "type" : "array", "items" : { "type" : "object", "properties" : { "depth" : { "type" : "integer", "description" : "Members of the annotation lineage as parent lineage depth (1-N)", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Members of the annotation lineage as parent lineage depth (1-N)", "context" : "dictionary" }, { "text" : "Lineage Depth", "context" : "brief" } ], "rcsb_current_maximum_value" : 18.0, "rcsb_current_minimum_value" : 1.0 }, "id" : { "type" : "string", "description" : "Members of the annotation lineage as parent class identifiers.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Members of the annotation lineage as parent class identifiers.", "context" : "dictionary" }, { "text" : "Lineage Identifier", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Chemical Components", "priority_order" : 110 } ] }, "name" : { "type" : "string", "description" : "Members of the annotation lineage as parent class names.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Members of the annotation lineage as parent class names.", "context" : "dictionary" }, { "text" : "Lineage Name", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Chemical Components", "priority_order" : 105 } ] } }, "additionalProperties" : false }, "uniqueItems" : false } }, "additionalProperties" : false }, "minItems" : 1, "uniqueItems" : true, "rcsb_nested_indexing" : true, "rcsb_nested_indexing_context" : [ { "category_name" : "annotation_type", "category_path" : "rcsb_chem_comp_annotation.type", "context_attributes" : [ { "context_value" : "ATC", "attributes" : [ { "examples" : [ "G02CB02", "C03CC01" ], "path" : "rcsb_chem_comp_annotation.annotation_lineage.id" }, { "examples" : [ "lisuride", "etacrynic acid" ], "path" : "rcsb_chem_comp_annotation.annotation_lineage.name" } ] }, { "context_value" : "PSI-MOD", "attributes" : [ { "examples" : [ "MOD:00599", "MOD:01680" ], "path" : "rcsb_chem_comp_annotation.annotation_lineage.id" }, { "examples" : [ "monomethylated residue", "alpha-amino monomethylated residue" ], "path" : "rcsb_chem_comp_annotation.annotation_lineage.name" } ] }, { "context_value" : "Generating Enzyme", "attributes" : [ { "examples" : [ "protein N-terminal methyltransferase (EC 2.1.1.-)", "autocatalytic" ], "path" : "rcsb_chem_comp_annotation.name" } ] }, { "context_value" : "Modification Type", "attributes" : [ { "examples" : [ "Thyroxine", "N4-methylasparagine" ], "path" : "rcsb_chem_comp_annotation.name" } ] }, { "context_value" : "Carbohydrate Anomer", "attributes" : [ { "examples" : [ "alpha", "beta" ], "path" : "rcsb_chem_comp_annotation.name" } ] }, { "context_value" : "Carbohydrate Isomer", "attributes" : [ { "examples" : [ "D", "L" ], "path" : "rcsb_chem_comp_annotation.name" } ] }, { "context_value" : "Carbohydrate Ring", "attributes" : [ { "examples" : [ "pyranose", "furanose" ], "path" : "rcsb_chem_comp_annotation.name" } ] }, { "context_value" : "Carbohydrate Primary Carbonyl Group", "attributes" : [ { "examples" : [ "aldose", "ketose" ], "path" : "rcsb_chem_comp_annotation.name" } ] } ] } ] }, "rcsb_chem_comp_container_identifiers" : { "type" : "object", "properties" : { "atc_codes" : { "type" : "array", "items" : { "type" : "string", "examples" : [ "G03FA02", "S02AA11", "S03AA03", "J01XB02", "A07AA05", "S01AA18" ], "description" : "The Anatomical Therapeutic Chemical (ATC) Classification System identifiers corresponding\n to the chemical component.", "rcsb_description" : [ { "text" : "The Anatomical Therapeutic Chemical (ATC) Classification System identifiers corresponding\n to the chemical component.", "context" : "dictionary" } ] }, "uniqueItems" : false }, "comp_id" : { "type" : "string", "examples" : [ "ATP", "STI" ], "description" : "The chemical component identifier.", "rcsb_search_context" : [ "exact-match", "suggest" ], "rcsb_full_text_priority" : 20, "rcsb_description" : [ { "text" : "The chemical component identifier.", "context" : "dictionary" }, { "text" : "Chemical ID(s)", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Chemical Components", "priority_order" : 5 } ] }, "drugbank_id" : { "type" : "string", "examples" : [ "DB00781", "DB15263" ], "description" : "The DrugBank identifier corresponding to the chemical component.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The DrugBank identifier corresponding to the chemical component.", "context" : "dictionary" }, { "text" : "DrugBank ID(s)", "context" : "brief" } ] }, "prd_id" : { "type" : "string", "examples" : [ "PRD_000010" ], "description" : "The BIRD definition identifier.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The BIRD definition identifier.", "context" : "dictionary" }, { "text" : "BIRD ID(s)", "context" : "brief" } ] }, "rcsb_id" : { "type" : "string", "examples" : [ "ATP", "PRD_000010" ], "description" : "A unique identifier for the chemical definition in this container.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "A unique identifier for the chemical definition in this container.", "context" : "dictionary" }, { "text" : "Id (Chem Comp Container Identifiers)", "context" : "brief" } ] }, "subcomponent_ids" : { "type" : "array", "items" : { "type" : "string", "description" : "The list of subcomponents contained in this component.", "rcsb_description" : [ { "text" : "The list of subcomponents contained in this component.", "context" : "dictionary" } ] }, "uniqueItems" : false } }, "additionalProperties" : false, "required" : [ "comp_id" ] }, "rcsb_chem_comp_descriptor" : { "type" : "object", "properties" : { "InChI" : { "type" : "string", "examples" : [ "InChI=1S/C3H6FO6P/c4-1-2(3(5)6)10-11(7,8)9/h2H,1H2,(H,5,6)(H2,7,8,9)/t2-/m0/s1" ], "description" : "Standard IUPAC International Chemical Identifier (InChI) descriptor for the chemical component.\n\n InChI, the IUPAC International Chemical Identifier,\n by Stephen R Heller, Alan McNaught, Igor Pletnev, Stephen Stein and Dmitrii Tchekhovskoi,\n Journal of Cheminformatics, 2015, 7:23;", "rcsb_description" : [ { "text" : "Standard IUPAC International Chemical Identifier (InChI) descriptor for the chemical component.\n\n InChI, the IUPAC International Chemical Identifier,\n by Stephen R Heller, Alan McNaught, Igor Pletnev, Stephen Stein and Dmitrii Tchekhovskoi,\n Journal of Cheminformatics, 2015, 7:23;", "context" : "dictionary" } ] }, "InChIKey" : { "type" : "string", "examples" : [ "BNOCDEBUFVJMQI-REOHCLBHSA-N" ], "description" : "Standard IUPAC International Chemical Identifier (InChI) descriptor key\n for the chemical component\n\n InChI, the IUPAC International Chemical Identifier,\n by Stephen R Heller, Alan McNaught, Igor Pletnev, Stephen Stein and Dmitrii Tchekhovskoi,\n Journal of Cheminformatics, 2015, 7:23", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Standard IUPAC International Chemical Identifier (InChI) descriptor key\n for the chemical component\n\n InChI, the IUPAC International Chemical Identifier,\n by Stephen R Heller, Alan McNaught, Igor Pletnev, Stephen Stein and Dmitrii Tchekhovskoi,\n Journal of Cheminformatics, 2015, 7:23", "context" : "dictionary" }, { "text" : "InChiKey", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Chemical Components", "priority_order" : 65 } ] }, "SMILES" : { "type" : "string", "examples" : [ "OC(=O)[CH](CF)O[P](O)(O)=O" ], "description" : "Simplified molecular-input line-entry system (SMILES) descriptor for the chemical component.\n\n Weininger D (February 1988). \"SMILES, a chemical language and information system. 1.\n Introduction to methodology and encoding rules\". Journal of Chemical Information and Modeling. 28 (1): 31-6.\n\n Weininger D, Weininger A, Weininger JL (May 1989).\n \"SMILES. 2. Algorithm for generation of unique SMILES notation\",\n Journal of Chemical Information and Modeling. 29 (2): 97-101.", "rcsb_description" : [ { "text" : "Simplified molecular-input line-entry system (SMILES) descriptor for the chemical component.\n\n Weininger D (February 1988). \"SMILES, a chemical language and information system. 1.\n Introduction to methodology and encoding rules\". Journal of Chemical Information and Modeling. 28 (1): 31-6.\n\n Weininger D, Weininger A, Weininger JL (May 1989).\n \"SMILES. 2. Algorithm for generation of unique SMILES notation\",\n Journal of Chemical Information and Modeling. 29 (2): 97-101.", "context" : "dictionary" } ] }, "SMILES_stereo" : { "type" : "string", "examples" : [ "OC(=O)[C@H](CF)O[P](O)(O)=O" ], "description" : "Simplified molecular-input line-entry system (SMILES) descriptor for the chemical\n component including stereochemical features.\n\n Weininger D (February 1988). \"SMILES, a chemical language and information system. 1.\n Introduction to methodology and encoding rules\".\n Journal of Chemical Information and Modeling. 28 (1): 31-6.\n\n Weininger D, Weininger A, Weininger JL (May 1989).\n \"SMILES. 2. Algorithm for generation of unique SMILES notation\".\n Journal of Chemical Information and Modeling. 29 (2): 97-101.", "rcsb_description" : [ { "text" : "Simplified molecular-input line-entry system (SMILES) descriptor for the chemical\n component including stereochemical features.\n\n Weininger D (February 1988). \"SMILES, a chemical language and information system. 1.\n Introduction to methodology and encoding rules\".\n Journal of Chemical Information and Modeling. 28 (1): 31-6.\n\n Weininger D, Weininger A, Weininger JL (May 1989).\n \"SMILES. 2. Algorithm for generation of unique SMILES notation\".\n Journal of Chemical Information and Modeling. 29 (2): 97-101.", "context" : "dictionary" } ] }, "comp_id" : { "type" : "string", "description" : "The chemical component identifier.", "rcsb_description" : [ { "text" : "The chemical component identifier.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "comp_id" ] }, "rcsb_chem_comp_info" : { "type" : "object", "properties" : { "atom_count" : { "type" : "integer", "description" : "Chemical component total atom count", "rcsb_description" : [ { "text" : "Chemical component total atom count", "context" : "dictionary" } ] }, "atom_count_chiral" : { "type" : "integer", "description" : "Chemical component chiral atom count", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Chemical component chiral atom count", "context" : "dictionary" }, { "text" : "Chemical Component Chiral Atom Count", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Chemical Components", "priority_order" : 80 } ], "rcsb_current_maximum_value" : 64.0, "rcsb_current_minimum_value" : 0.0 }, "atom_count_heavy" : { "type" : "integer", "description" : "Chemical component heavy atom count", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Chemical component heavy atom count", "context" : "dictionary" }, { "text" : "Chemical Component Nonhydrogen Atom Count", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Chemical Components", "priority_order" : 75 } ], "rcsb_current_maximum_value" : 240.0, "rcsb_current_minimum_value" : 0.0 }, "bond_count" : { "type" : "integer", "description" : "Chemical component total bond count", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Chemical component total bond count", "context" : "dictionary" }, { "text" : "Chemical Component Bond Count", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Chemical Components", "priority_order" : 85 } ], "rcsb_current_maximum_value" : 446.0, "rcsb_current_minimum_value" : 0.0 }, "bond_count_aromatic" : { "type" : "integer", "description" : "Chemical component aromatic bond count", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Chemical component aromatic bond count", "context" : "dictionary" }, { "text" : "Chemical Component Aromatic Bond Count", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Chemical Components", "priority_order" : 90 } ], "rcsb_current_maximum_value" : 116.0, "rcsb_current_minimum_value" : 0.0 }, "comp_id" : { "type" : "string", "description" : "The chemical component identifier.", "rcsb_description" : [ { "text" : "The chemical component identifier.", "context" : "dictionary" } ] }, "initial_deposition_date" : { "type" : "string", "format" : "date", "examples" : [ "2016-09-11" ], "description" : "The date the chemical definition was first deposited in the PDB repository.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The date the chemical definition was first deposited in the PDB repository.", "context" : "dictionary" }, { "text" : "Chemical Component Deposition Date", "context" : "brief" } ], "rcsb_current_maximum_value" : 1.7822592E12, "rcsb_current_minimum_value" : 9.313056E11 }, "initial_release_date" : { "type" : "string", "format" : "date", "examples" : [ "2016-09-11" ], "description" : "The initial date the chemical definition was released in the PDB repository.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The initial date the chemical definition was released in the PDB repository.", "context" : "dictionary" }, { "text" : "Chemical Component Release Date", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Chemical Components", "priority_order" : 20 } ], "rcsb_current_maximum_value" : 1.7840736E12, "rcsb_current_minimum_value" : 1.052352E11 }, "release_status" : { "type" : "string", "enum" : [ "DEL", "HOLD", "HPUB", "OBS", "REF_ONLY", "REL" ], "examples" : [ "REL" ], "description" : "The release status of the chemical definition.", "rcsb_enum_annotated" : [ { "value" : "DEL", "detail" : "Component definition has been deleted" }, { "value" : "HOLD", "detail" : "On hold until yyyy-mm-dd" }, { "value" : "HPUB", "detail" : "On hold until publication" }, { "value" : "OBS", "detail" : "Component defintion has been obsoleted and replaced by another definition" }, { "value" : "REF_ONLY", "detail" : "Component definition is provided for reference only and will not be used in released entries." }, { "value" : "REL", "detail" : "Released" } ], "rcsb_description" : [ { "text" : "The release status of the chemical definition.", "context" : "dictionary" } ] }, "revision_date" : { "type" : "string", "format" : "date", "examples" : [ "2016-10-12" ], "description" : "The date of last revision of the chemical definition.", "rcsb_description" : [ { "text" : "The date of last revision of the chemical definition.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "comp_id" ] }, "rcsb_chem_comp_related" : { "type" : "array", "items" : { "type" : "object", "properties" : { "comp_id" : { "type" : "string", "description" : "The value of _rcsb_chem_comp_related.comp_id is a reference to\n a chemical component definition.", "rcsb_description" : [ { "text" : "The value of _rcsb_chem_comp_related.comp_id is a reference to\n a chemical component definition.", "context" : "dictionary" } ] }, "ordinal" : { "type" : "integer", "description" : "The value of _rcsb_chem_comp_related.ordinal distinguishes\n related examples for each chemical component.", "rcsb_description" : [ { "text" : "The value of _rcsb_chem_comp_related.ordinal distinguishes\n related examples for each chemical component.", "context" : "dictionary" } ] }, "related_mapping_method" : { "type" : "string", "enum" : [ "assigned by DrugBank resource", "assigned by PDB", "assigned by PubChem resource", "matching ChEMBL ID in Pharos", "matching InChIKey in DrugBank", "matching InChIKey in PubChem", "matching InChIKey-prefix in DrugBank", "matching by RESID resource" ], "examples" : [ "assigned by DrugBank resource" ], "description" : "The method used to establish the resource correspondence.", "rcsb_enum_annotated" : [ { "value" : "assigned by DrugBank resource", "detail" : "Correspondence assigned by the DrugBank resource" }, { "value" : "assigned by PDB", "detail" : "Correspondence assigned by PDB" }, { "value" : "assigned by PubChem resource", "detail" : "Correspondence assigned by the PubChem resource" }, { "value" : "matching ChEMBL ID in Pharos", "detail" : "Correspondence established by matching ChEMBL ID in Pharos" }, { "value" : "matching InChIKey in DrugBank", "detail" : "Correspondence established by matching InChIKey in DrugBank" }, { "value" : "matching InChIKey in PubChem", "detail" : "Correspondence established by matching InChIKey in PubChem" }, { "value" : "matching InChIKey-prefix in DrugBank", "detail" : "Correspondence established by matching InChIKey prefix in DrugBank" }, { "value" : "matching by RESID resource", "detail" : "Correspondence assigned by the RESID resource" } ], "rcsb_description" : [ { "text" : "The method used to establish the resource correspondence.", "context" : "dictionary" } ] }, "resource_accession_code" : { "type" : "string", "examples" : [ "124832" ], "description" : "The resource identifier code for the related chemical reference.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The resource identifier code for the related chemical reference.", "context" : "dictionary" }, { "text" : "Identifier Codes", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Chemical Components", "priority_order" : 95 } ] }, "resource_name" : { "type" : "string", "enum" : [ "CAS", "CCDC/CSD", "COD", "ChEBI", "ChEMBL", "DrugBank", "Pharos", "PubChem", "RESID" ], "examples" : [ "CCDC/CSD" ], "description" : "The resource name for the related chemical reference.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "CAS", "detail" : "Chemical Abstracts Service (CAS) Registry Number", "name" : "CAS Registry Number" }, { "value" : "CCDC/CSD", "detail" : "Cambridge Crystallographic Data Center", "name" : "CCDC/CSD" }, { "value" : "COD", "detail" : "Crystallography Open Database", "name" : "COD" }, { "value" : "ChEBI", "detail" : "Chemical Entities of Biological Interest (ChEBI)", "name" : "ChEBI" }, { "value" : "ChEMBL", "detail" : "ChEMBL, manually curated database of bioactive molecules with drug-like properties", "name" : "ChEMBL" }, { "value" : "DrugBank", "detail" : "DrugBank, database containing information on drugs and drug targets", "name" : "DrugBank" }, { "value" : "Pharos", "detail" : "User interface to the Knowledge Management Center (KMC) for the Illuminating the Druggable Genome (IDG)", "name" : "Pharos" }, { "value" : "PubChem", "detail" : "NCBI PubChem Resource", "name" : "PubChem" }, { "value" : "RESID", "detail" : "RESID Database of Protein Modifications", "name" : "RESID" } ], "rcsb_description" : [ { "text" : "The resource name for the related chemical reference.", "context" : "dictionary" }, { "text" : "Resource Name", "context" : "brief" } ] } }, "additionalProperties" : false, "required" : [ "comp_id", "ordinal" ] }, "minItems" : 1, "uniqueItems" : true, "rcsb_nested_indexing" : true, "rcsb_nested_indexing_context" : [ { "category_name" : "related_resource", "category_path" : "rcsb_chem_comp_related.resource_name", "context_attributes" : [ { "context_value" : "DrugBank", "attributes" : [ { "examples" : [ "DB06830", "DB07255" ], "path" : "rcsb_chem_comp_related.resource_accession_code" } ] }, { "context_value" : "CCDC/CSD", "attributes" : [ { "examples" : [ "QAXDEZ", "XEGJEA" ], "path" : "rcsb_chem_comp_related.resource_accession_code" } ] }, { "context_value" : "COD", "attributes" : [ { "examples" : [ 2236573, 7229993 ], "path" : "rcsb_chem_comp_related.resource_accession_code" } ] }, { "context_value" : "RESID", "attributes" : [ { "examples" : [ "AA0078", "AA0034" ], "path" : "rcsb_chem_comp_related.resource_accession_code" } ] }, { "context_value" : "PubChem", "attributes" : [ { "examples" : [ 3082729, 5289380 ], "path" : "rcsb_chem_comp_related.resource_accession_code" } ] }, { "context_value" : "ChEBI", "attributes" : [ { "examples" : [ "CHEBI:151557", "CHEBI:6198" ], "path" : "rcsb_chem_comp_related.resource_accession_code" } ] }, { "context_value" : "ChEMBL", "attributes" : [ { "examples" : [ "CHEMBL1165239", "CHEMBL3330255" ], "path" : "rcsb_chem_comp_related.resource_accession_code" } ] }, { "context_value" : "CAS", "attributes" : [ { "examples" : [ "2133-34-8", "30565-25-4" ], "path" : "rcsb_chem_comp_related.resource_accession_code" } ] }, { "context_value" : "Pharos", "attributes" : [ { "examples" : [ "CHEMBL1165239", "CHEMBL3330255" ], "path" : "rcsb_chem_comp_related.resource_accession_code" } ] } ] } ] }, "rcsb_chem_comp_synonyms" : { "type" : "array", "items" : { "type" : "object", "properties" : { "comp_id" : { "type" : "string", "description" : "The chemical component to which this synonym applies.", "rcsb_description" : [ { "text" : "The chemical component to which this synonym applies.", "context" : "dictionary" } ] }, "name" : { "type" : "string", "examples" : [ "Ursonic acid", "Talotrexin", "4-oxodecanedioic acid" ], "description" : "The synonym of this particular chemical component.", "rcsb_search_context" : [ "full-text", "suggest" ], "rcsb_full_text_priority" : 20, "rcsb_description" : [ { "text" : "The synonym of this particular chemical component.", "context" : "dictionary" }, { "text" : "Chemical Synonyms", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Chemical Components", "priority_order" : 15 } ] }, "ordinal" : { "type" : "integer", "description" : "This data item is an ordinal index for the\n RCSB_CHEM_COMP_SYNONYMS category.", "rcsb_description" : [ { "text" : "This data item is an ordinal index for the\n RCSB_CHEM_COMP_SYNONYMS category.", "context" : "dictionary" } ] }, "provenance_source" : { "type" : "string", "enum" : [ "ACDLabs", "Author", "ChEBI", "ChEMBL", "DrugBank", "GMML", "Lexichem", "OpenEye OEToolkits", "OpenEye/Lexichem", "PDB Reference Data", "PDB Reference Data (Preferred)", "PDB-CARE", "PubChem", "RESID" ], "description" : "The provenance of this synonym.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The provenance of this synonym.", "context" : "dictionary" }, { "text" : "Chemical Synonym Provenance Source", "context" : "brief" } ] }, "type" : { "type" : "string", "enum" : [ "Brand Name", "Common Name", "Condensed IUPAC Carbohydrate Symbol", "IUPAC Carbohydrate Symbol", "Preferred Common Name", "Preferred Name", "Preferred Synonym", "SNFG Carbohydrate Symbol", "Synonym", "Systematic Name" ], "description" : "This data item contains the synonym type.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "Brand Name", "detail" : "Product chemical name" }, { "value" : "Common Name", "detail" : "Common chemical name" }, { "value" : "Condensed IUPAC Carbohydrate Symbol", "detail" : "Condensed IUPAC carbohydrate symbol" }, { "value" : "IUPAC Carbohydrate Symbol", "detail" : "IUPAC carbohydrate symbol" }, { "value" : "Preferred Common Name", "detail" : "Preferred common chemical name" }, { "value" : "Preferred Name", "detail" : "Preferred chemical name" }, { "value" : "Preferred Synonym", "detail" : "Preferred synonym chemical name" }, { "value" : "SNFG Carbohydrate Symbol", "detail" : "3D-SNFG carbohydrate symbol" }, { "value" : "Synonym", "detail" : "Synonym chemical name" }, { "value" : "Systematic Name", "detail" : "Systematic chemical name" } ], "rcsb_description" : [ { "text" : "This data item contains the synonym type.", "context" : "dictionary" }, { "text" : "Chemical Synonym Type", "context" : "brief" } ] } }, "additionalProperties" : false, "required" : [ "comp_id", "ordinal" ] }, "minItems" : 1, "uniqueItems" : true }, "rcsb_chem_comp_target" : { "type" : "array", "items" : { "type" : "object", "properties" : { "comp_id" : { "type" : "string", "description" : "The value of _rcsb_chem_comp_target.comp_id is a reference to\n a chemical component definition.", "rcsb_description" : [ { "text" : "The value of _rcsb_chem_comp_target.comp_id is a reference to\n a chemical component definition.", "context" : "dictionary" } ] }, "interaction_type" : { "type" : "string", "description" : "The type of target interaction.", "rcsb_description" : [ { "text" : "The type of target interaction.", "context" : "dictionary" } ] }, "name" : { "type" : "string", "description" : "The chemical component target name.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The chemical component target name.", "context" : "dictionary" }, { "text" : "Drug Target Name", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Chemical Components", "priority_order" : 30 } ] }, "ordinal" : { "type" : "integer", "description" : "The value of _rcsb_chem_comp_target.ordinal distinguishes\n related examples for each chemical component.", "rcsb_description" : [ { "text" : "The value of _rcsb_chem_comp_target.ordinal distinguishes\n related examples for each chemical component.", "context" : "dictionary" } ] }, "provenance_source" : { "type" : "string", "enum" : [ "DrugBank", "PDB Primary Data" ], "description" : "A code indicating the provenance of the target interaction assignment", "rcsb_description" : [ { "text" : "A code indicating the provenance of the target interaction assignment", "context" : "dictionary" } ] }, "reference_database_accession_code" : { "type" : "string", "examples" : [ "Q9HD40" ], "description" : "The reference identifier code for the target interaction reference.", "rcsb_description" : [ { "text" : "The reference identifier code for the target interaction reference.", "context" : "dictionary" } ] }, "reference_database_name" : { "type" : "string", "enum" : [ "UniProt" ], "examples" : [ "UniProt" ], "description" : "The reference database name for the target interaction.", "rcsb_description" : [ { "text" : "The reference database name for the target interaction.", "context" : "dictionary" } ] }, "target_actions" : { "type" : "array", "items" : { "type" : "string", "description" : "The mechanism of action of the chemical component - target interaction.", "rcsb_description" : [ { "text" : "The mechanism of action of the chemical component - target interaction.", "context" : "dictionary" } ] }, "uniqueItems" : false } }, "additionalProperties" : false, "required" : [ "comp_id", "ordinal" ] }, "minItems" : 1, "uniqueItems" : true }, "rcsb_schema_container_identifiers" : { "type" : "array", "items" : { "type" : "object", "properties" : { "collection_name" : { "type" : "string", "description" : "Collection name associated with the data in the container.", "rcsb_description" : [ { "text" : "Collection name associated with the data in the container.", "context" : "dictionary" } ] }, "collection_schema_version" : { "type" : "string", "description" : "Version string for the schema and collection.", "rcsb_description" : [ { "text" : "Version string for the schema and collection.", "context" : "dictionary" } ] }, "schema_name" : { "type" : "string", "description" : "Schema name associated with the data in the container.", "rcsb_description" : [ { "text" : "Schema name associated with the data in the container.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "collection_name", "schema_name" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_struct_assembly" : { "type" : "object", "properties" : { "details" : { "type" : "string", "examples" : [ "The icosahedral virus particle." ], "description" : "A description of special aspects of the macromolecular assembly.\n\n In the PDB, 'representative helical assembly', 'complete point assembly',\n\t 'complete icosahedral assembly', 'software_defined_assembly', 'author_defined_assembly',\n\t and 'author_and_software_defined_assembly' are considered \"biologically relevant assemblies.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "A description of special aspects of the macromolecular assembly.\n\n In the PDB, 'representative helical assembly', 'complete point assembly',\n\t 'complete icosahedral assembly', 'software_defined_assembly', 'author_defined_assembly',\n\t and 'author_and_software_defined_assembly' are considered \"biologically relevant assemblies.", "context" : "dictionary" }, { "text" : "Details (Struct Assembly)", "context" : "brief" } ] }, "id" : { "type" : "string", "description" : "The value of _pdbx_struct_assembly.id must uniquely identify a record in\n the PDBX_STRUCT_ASSEMBLY list.", "rcsb_description" : [ { "text" : "The value of _pdbx_struct_assembly.id must uniquely identify a record in\n the PDBX_STRUCT_ASSEMBLY list.", "context" : "dictionary" } ] }, "method_details" : { "type" : "string", "description" : "Provides details of the method used to determine or\n compute the assembly.", "rcsb_description" : [ { "text" : "Provides details of the method used to determine or\n compute the assembly.", "context" : "dictionary" } ] }, "oligomeric_count" : { "type" : "integer", "description" : "The number of polymer molecules in the assembly.", "rcsb_description" : [ { "text" : "The number of polymer molecules in the assembly.", "context" : "dictionary" } ] }, "oligomeric_details" : { "type" : "string", "examples" : [ "monomer", "octameric", "tetradecameric", "eicosameric", "21-meric", "60-meric", "180-meric", "helical" ], "description" : "Provides the details of the oligomeric state of the assembly.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Provides the details of the oligomeric state of the assembly.", "context" : "dictionary" }, { "text" : "Enter the oligomeric state of your system. You may select unknown if you have no biophysical evidence to support any choice.", "context" : "deposition" }, { "text" : "Oligomeric Details (Struct Assembly)", "context" : "brief" } ] }, "rcsb_candidate_assembly" : { "type" : "string", "enum" : [ "N", "Y" ], "examples" : [ "Y" ], "description" : "Candidate macromolecular assembly.\n\n Excludes the following cases classified in pdbx_struct_asembly.details:\n\n 'crystal asymmetric unit', 'crystal asymmetric unit, crystal frame', 'helical asymmetric unit',\n 'helical asymmetric unit, std helical frame','icosahedral 23 hexamer', 'icosahedral asymmetric unit',\n 'icosahedral asymmetric unit, std point frame','icosahedral pentamer', 'pentasymmetron capsid unit',\n 'point asymmetric unit', 'point asymmetric unit, std point frame','trisymmetron capsid unit',\n and 'deposited_coordinates'.", "rcsb_description" : [ { "text" : "Candidate macromolecular assembly.\n\n Excludes the following cases classified in pdbx_struct_asembly.details:\n\n 'crystal asymmetric unit', 'crystal asymmetric unit, crystal frame', 'helical asymmetric unit',\n 'helical asymmetric unit, std helical frame','icosahedral 23 hexamer', 'icosahedral asymmetric unit',\n 'icosahedral asymmetric unit, std point frame','icosahedral pentamer', 'pentasymmetron capsid unit',\n 'point asymmetric unit', 'point asymmetric unit, std point frame','trisymmetron capsid unit',\n and 'deposited_coordinates'.", "context" : "dictionary" } ] }, "rcsb_details" : { "type" : "string", "enum" : [ "author_and_software_defined_assembly", "author_defined_assembly", "software_defined_assembly" ], "examples" : [ "author_and_software_defined_assembly" ], "description" : "A filtered description of the macromolecular assembly.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "A filtered description of the macromolecular assembly.", "context" : "dictionary" }, { "text" : "Details (Struct Assembly)", "context" : "brief" } ] } }, "additionalProperties" : false, "required" : [ "id" ] }, "pdbx_struct_assembly_auth_evidence" : { "type" : "array", "items" : { "type" : "object", "properties" : { "assembly_id" : { "type" : "string", "description" : "This item references an assembly in pdbx_struct_assembly", "rcsb_description" : [ { "text" : "This item references an assembly in pdbx_struct_assembly", "context" : "dictionary" } ] }, "details" : { "type" : "string", "examples" : [ "Homology to bacteriorhodopsin", "Helical filament was observed by negative staining and Cryo-EM" ], "description" : "Provides any additional information regarding the evidence of this assembly", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Provides any additional information regarding the evidence of this assembly", "context" : "dictionary" }, { "text" : "Assembly Experimental Support Details", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Assembly Features", "priority_order" : 75 } ] }, "experimental_support" : { "type" : "string", "enum" : [ "NMR Distance Restraints", "NMR relaxation study", "SAXS", "assay for oligomerization", "cross-linking", "electron microscopy", "equilibrium centrifugation", "fluorescence resonance energy transfer", "gel filtration", "homology", "immunoprecipitation", "isothermal titration calorimetry", "light scattering", "mass spectrometry", "microscopy", "native gel electrophoresis", "none", "scanning transmission electron microscopy", "surface plasmon resonance" ], "description" : "Provides the experimental method to determine the state of this assembly", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Provides the experimental method to determine the state of this assembly", "context" : "dictionary" }, { "text" : "Assembly Experimental Support", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Assembly Features", "priority_order" : 70 } ] }, "id" : { "type" : "string", "description" : "Identifies a unique record in pdbx_struct_assembly_auth_evidence.", "rcsb_description" : [ { "text" : "Identifies a unique record in pdbx_struct_assembly_auth_evidence.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "assembly_id", "id" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_struct_assembly_gen" : { "type" : "array", "items" : { "type" : "object", "properties" : { "assembly_id" : { "type" : "string", "description" : "This data item is a pointer to _pdbx_struct_assembly.id in the\n PDBX_STRUCT_ASSEMBLY category.", "rcsb_description" : [ { "text" : "This data item is a pointer to _pdbx_struct_assembly.id in the\n PDBX_STRUCT_ASSEMBLY category.", "context" : "dictionary" } ] }, "asym_id_list" : { "type" : "array", "items" : { "type" : "string", "description" : "This data item is a pointer to _struct_asym.id in\n the STRUCT_ASYM category.\n\n This item may be expressed as a comma separated list of identifiers.", "rcsb_description" : [ { "text" : "This data item is a pointer to _struct_asym.id in\n the STRUCT_ASYM category.\n\n This item may be expressed as a comma separated list of identifiers.", "context" : "dictionary" } ] }, "uniqueItems" : false }, "oper_expression" : { "type" : "string", "examples" : [ "(1)", "(1,2,5)", "(1-60)", "(1-60)(61)" ], "description" : "Identifies the operation of collection of operations\n from category PDBX_STRUCT_OPER_LIST.\n\n Operation expressions may have the forms:\n\n (1) the single operation 1\n (1,2,5) the operations 1, 2, 5\n (1-4) the operations 1,2,3 and 4\n (1,2)(3,4) the combinations of operations\n 3 and 4 followed by 1 and 2 (i.e.\n the cartesian product of parenthetical\n groups applied from right to left)", "rcsb_description" : [ { "text" : "Identifies the operation of collection of operations\n from category PDBX_STRUCT_OPER_LIST.\n\n Operation expressions may have the forms:\n\n (1) the single operation 1\n (1,2,5) the operations 1, 2, 5\n (1-4) the operations 1,2,3 and 4\n (1,2)(3,4) the combinations of operations\n 3 and 4 followed by 1 and 2 (i.e.\n the cartesian product of parenthetical\n groups applied from right to left)", "context" : "dictionary" } ] }, "ordinal" : { "type" : "integer", "description" : "This data item is an ordinal index for the\n PDBX_STRUCT_ASSEMBLY category.", "rcsb_description" : [ { "text" : "This data item is an ordinal index for the\n PDBX_STRUCT_ASSEMBLY category.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "ordinal" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_struct_assembly_prop" : { "type" : "array", "items" : { "type" : "object", "properties" : { "assembly_id" : { "type" : "string", "description" : "The identifier for the assembly used in category PDBX_STRUCT_ASSEMBLY.", "rcsb_description" : [ { "text" : "The identifier for the assembly used in category PDBX_STRUCT_ASSEMBLY.", "context" : "dictionary" } ] }, "biol_id" : { "type" : "string", "description" : "The identifier for the assembly used in category PDBX_STRUCT_ASSEMBLY.", "rcsb_description" : [ { "text" : "The identifier for the assembly used in category PDBX_STRUCT_ASSEMBLY.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "enum" : [ "ABSA (A^2)", "MORE", "SSA (A^2)" ], "description" : "The property type for the assembly.\n ABSA (A^2) is the \"Total buried surface area (A^2)\"\n SSA (A^2) is \"Surface area for the complex (A^2)\"\n MORE is \"Internal energy (kcal/mol)\"", "rcsb_description" : [ { "text" : "The property type for the assembly.\n ABSA (A^2) is the \"Total buried surface area (A^2)\"\n SSA (A^2) is \"Surface area for the complex (A^2)\"\n MORE is \"Internal energy (kcal/mol)\"", "context" : "dictionary" } ] }, "value" : { "type" : "string", "description" : "The value of the assembly property.", "rcsb_description" : [ { "text" : "The value of the assembly property.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "biol_id", "type" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_struct_oper_list" : { "type" : "array", "items" : { "type" : "object", "properties" : { "id" : { "type" : "string", "description" : "This identifier code must uniquely identify a\n record in the PDBX_STRUCT_OPER_LIST list.", "rcsb_description" : [ { "text" : "This identifier code must uniquely identify a\n record in the PDBX_STRUCT_OPER_LIST list.", "context" : "dictionary" } ] }, "matrix_1_1" : { "type" : "number", "description" : "The [1][1] element of the 3x3 matrix component of the\n transformation operation.", "rcsb_description" : [ { "text" : "The [1][1] element of the 3x3 matrix component of the\n transformation operation.", "context" : "dictionary" } ] }, "matrix_1_2" : { "type" : "number", "description" : "The [1][2] element of the 3x3 matrix component of the\n transformation operation.", "rcsb_description" : [ { "text" : "The [1][2] element of the 3x3 matrix component of the\n transformation operation.", "context" : "dictionary" } ] }, "matrix_1_3" : { "type" : "number", "description" : "The [1][3] element of the 3x3 matrix component of the\n transformation operation.", "rcsb_description" : [ { "text" : "The [1][3] element of the 3x3 matrix component of the\n transformation operation.", "context" : "dictionary" } ] }, "matrix_2_1" : { "type" : "number", "description" : "The [2][1] element of the 3x3 matrix component of the\n transformation operation.", "rcsb_description" : [ { "text" : "The [2][1] element of the 3x3 matrix component of the\n transformation operation.", "context" : "dictionary" } ] }, "matrix_2_2" : { "type" : "number", "description" : "The [2][2] element of the 3x3 matrix component of the\n transformation operation.", "rcsb_description" : [ { "text" : "The [2][2] element of the 3x3 matrix component of the\n transformation operation.", "context" : "dictionary" } ] }, "matrix_2_3" : { "type" : "number", "description" : "The [2][3] element of the 3x3 matrix component of the\n transformation operation.", "rcsb_description" : [ { "text" : "The [2][3] element of the 3x3 matrix component of the\n transformation operation.", "context" : "dictionary" } ] }, "matrix_3_1" : { "type" : "number", "description" : "The [3][1] element of the 3x3 matrix component of the\n transformation operation.", "rcsb_description" : [ { "text" : "The [3][1] element of the 3x3 matrix component of the\n transformation operation.", "context" : "dictionary" } ] }, "matrix_3_2" : { "type" : "number", "description" : "The [3][2] element of the 3x3 matrix component of the\n transformation operation.", "rcsb_description" : [ { "text" : "The [3][2] element of the 3x3 matrix component of the\n transformation operation.", "context" : "dictionary" } ] }, "matrix_3_3" : { "type" : "number", "description" : "The [3][3] element of the 3x3 matrix component of the\n transformation operation.", "rcsb_description" : [ { "text" : "The [3][3] element of the 3x3 matrix component of the\n transformation operation.", "context" : "dictionary" } ] }, "name" : { "type" : "string", "examples" : [ "1_555", "two-fold rotation" ], "description" : "A descriptive name for the transformation operation.", "rcsb_description" : [ { "text" : "A descriptive name for the transformation operation.", "context" : "dictionary" } ] }, "symmetry_operation" : { "type" : "string", "examples" : [ "x,y,z", "x+1/2,y,-z" ], "description" : "The symmetry operation corresponding to the transformation operation.", "rcsb_description" : [ { "text" : "The symmetry operation corresponding to the transformation operation.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "enum" : [ "2D crystal symmetry operation", "3D crystal symmetry operation", "build 2D crystal asymmetric unit", "build 3D crystal asymmetric unit", "build helical asymmetric unit", "build point asymmetric unit", "crystal symmetry operation", "helical symmetry operation", "identity operation", "point symmetry operation", "transform to 2D crystal frame", "transform to 3D crystal frame", "transform to crystal frame", "transform to helical frame", "transform to point frame" ], "description" : "A code to indicate the type of operator.", "rcsb_description" : [ { "text" : "A code to indicate the type of operator.", "context" : "dictionary" } ] }, "vector_1" : { "type" : "number", "description" : "The [1] element of the three-element vector component of the\n transformation operation.", "rcsb_description" : [ { "text" : "The [1] element of the three-element vector component of the\n transformation operation.", "context" : "dictionary" } ] }, "vector_2" : { "type" : "number", "description" : "The [2] element of the three-element vector component of the\n transformation operation.", "rcsb_description" : [ { "text" : "The [2] element of the three-element vector component of the\n transformation operation.", "context" : "dictionary" } ] }, "vector_3" : { "type" : "number", "description" : "The [3] element of the three-element vector component of the\n transformation operation.", "rcsb_description" : [ { "text" : "The [3] element of the three-element vector component of the\n transformation operation.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "id" ] }, "minItems" : 1, "uniqueItems" : true }, "rcsb_assembly_annotation" : { "type" : "array", "items" : { "type" : "object", "properties" : { "annotation_id" : { "type" : "string", "description" : "An identifier for the annotation.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "An identifier for the annotation.", "context" : "dictionary" }, { "text" : "Annotation Id (Assembly Annotation)", "context" : "brief" } ] }, "assignment_version" : { "type" : "string", "description" : "Identifies the version of the annotation assignment.", "rcsb_description" : [ { "text" : "Identifies the version of the annotation assignment.", "context" : "dictionary" } ] }, "description" : { "type" : "string", "description" : "A description for the annotation.", "rcsb_description" : [ { "text" : "A description for the annotation.", "context" : "dictionary" } ] }, "name" : { "type" : "string", "description" : "A name for the annotation.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "A name for the annotation.", "context" : "dictionary" }, { "text" : "Name (Assembly Annotation)", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Assembly Features", "priority_order" : 105 } ] }, "provenance_source" : { "type" : "string", "examples" : [ "MCSA" ], "description" : "Code identifying the individual, organization or program that assigned the annotation.", "rcsb_description" : [ { "text" : "Code identifying the individual, organization or program that assigned the annotation.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "enum" : [ "MCSA" ], "description" : "A type or category of the annotation.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "MCSA", "detail" : "A set of catalytically active residues according to the M-CSA.", "name" : "Mechanism and Catalytic Site Atlas" } ], "rcsb_description" : [ { "text" : "A type or category of the annotation.", "context" : "dictionary" }, { "text" : "Type (Assembly Annotation)", "context" : "brief" } ] }, "additional_properties" : { "type" : "array", "items" : { "type" : "object", "properties" : { "name" : { "type" : "string", "enum" : [ "MCSA_MOTIF_COMPATIBILITY" ], "description" : "The additional property name.", "rcsb_enum_annotated" : [ { "value" : "MCSA_MOTIF_COMPATIBILITY", "detail" : "Internal enum that captures whether a M-CSA motif supports visualization and/or structure motif searching." } ], "rcsb_description" : [ { "text" : "The additional property name.", "context" : "dictionary" } ] }, "values" : { "type" : "array", "items" : { "anyOf" : [ { "type" : "string" }, { "type" : "integer" }, { "type" : "number" } ], "examples" : [ "SUPPORTED" ], "description" : "The value(s) of the additional property.", "rcsb_description" : [ { "text" : "The value(s) of the additional property.", "context" : "dictionary" } ] }, "uniqueItems" : false } }, "additionalProperties" : false }, "uniqueItems" : false } }, "additionalProperties" : false }, "minItems" : 1, "uniqueItems" : true, "rcsb_nested_indexing" : true, "rcsb_nested_indexing_context" : [ { "category_name" : "annotation_type", "category_path" : "rcsb_assembly_annotation.type", "context_attributes" : [ { "context_value" : "MCSA", "attributes" : [ { "examples" : [ "Glutamate racemase", "Leucyl aminopeptidase" ], "path" : "rcsb_assembly_annotation.name" } ] } ] } ] }, "rcsb_assembly_container_identifiers" : { "type" : "object", "properties" : { "assembly_id" : { "type" : "string", "examples" : [ "1", "5" ], "description" : "Assembly identifier for the container.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Assembly identifier for the container.", "context" : "dictionary" }, { "text" : "Assembly ID(s)", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "ID(s) and Keywords", "priority_order" : 25 } ] }, "entry_id" : { "type" : "string", "description" : "Entry identifier for the container.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Entry identifier for the container.", "context" : "dictionary" }, { "text" : "Entry Id (Assembly Container Identifiers)", "context" : "brief" } ] }, "interface_ids" : { "type" : "array", "items" : { "type" : "string", "examples" : [ "1A00-1.1" ], "description" : "List of binary interface Ids within the assembly (it points to interface id collection).", "rcsb_description" : [ { "text" : "List of binary interface Ids within the assembly (it points to interface id collection).", "context" : "dictionary" } ] }, "minItems" : 1, "uniqueItems" : true }, "rcsb_id" : { "type" : "string", "examples" : [ "1KIP-1" ], "description" : "A unique identifier for each object in this assembly container formed by\n a dash separated concatenation of entry and assembly identifiers.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "A unique identifier for each object in this assembly container formed by\n a dash separated concatenation of entry and assembly identifiers.", "context" : "dictionary" }, { "text" : "Id (Assembly Container Identifiers)", "context" : "brief" } ] } }, "additionalProperties" : false, "required" : [ "assembly_id", "entry_id" ] }, "rcsb_assembly_feature" : { "type" : "array", "items" : { "type" : "object", "properties" : { "assignment_version" : { "type" : "string", "description" : "Identifies the version of the feature assignment.", "rcsb_description" : [ { "text" : "Identifies the version of the feature assignment.", "context" : "dictionary" } ] }, "description" : { "type" : "string", "description" : "A description for the feature.", "rcsb_description" : [ { "text" : "A description for the feature.", "context" : "dictionary" } ] }, "feature_id" : { "type" : "string", "description" : "An identifier for the feature.", "rcsb_description" : [ { "text" : "An identifier for the feature.", "context" : "dictionary" } ] }, "name" : { "type" : "string", "description" : "A name for the feature.", "rcsb_description" : [ { "text" : "A name for the feature.", "context" : "dictionary" } ] }, "provenance_source" : { "type" : "string", "examples" : [ "MCSA" ], "description" : "Code identifying the individual, organization or program that assigned the feature.", "rcsb_description" : [ { "text" : "Code identifying the individual, organization or program that assigned the feature.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "enum" : [ "MCSA" ], "description" : "A type or category of the feature.", "rcsb_enum_annotated" : [ { "value" : "MCSA", "detail" : "A set of catalytically active residues according to the M-CSA.", "name" : "Mechanism and Catalytic Site Atlas" } ], "rcsb_description" : [ { "text" : "A type or category of the feature.", "context" : "dictionary" } ] }, "additional_properties" : { "type" : "array", "items" : { "type" : "object", "properties" : { "name" : { "type" : "string", "enum" : [ "MCSA_MOTIF_COMPATIBILITY" ], "description" : "The additional property name.", "rcsb_enum_annotated" : [ { "value" : "MCSA_MOTIF_COMPATIBILITY", "detail" : "Internal enum that captures whether a M-CSA motif supports visualization and/or structure motif searching." } ], "rcsb_description" : [ { "text" : "The additional property name.", "context" : "dictionary" } ] }, "values" : { "type" : "array", "items" : { "anyOf" : [ { "type" : "string" }, { "type" : "integer" }, { "type" : "number" } ], "examples" : [ "SUPPORTED" ], "description" : "The value(s) of the additional property.", "rcsb_description" : [ { "text" : "The value(s) of the additional property.", "context" : "dictionary" } ] }, "uniqueItems" : false } }, "additionalProperties" : false }, "uniqueItems" : false }, "feature_positions" : { "type" : "array", "items" : { "type" : "object", "properties" : { "asym_id" : { "type" : "string", "examples" : [ "A", "B" ], "description" : "An identifier of polymer chain (label_asym_id) corresponding to the feature assignment.", "rcsb_description" : [ { "text" : "An identifier of polymer chain (label_asym_id) corresponding to the feature assignment.", "context" : "dictionary" } ] }, "beg_seq_id" : { "type" : "integer", "description" : "An identifier for the monomer at which this segment of the feature begins.", "rcsb_description" : [ { "text" : "An identifier for the monomer at which this segment of the feature begins.", "context" : "dictionary" } ] }, "end_seq_id" : { "type" : "integer", "description" : "An identifier for the monomer at which this segment of the feature ends.", "rcsb_description" : [ { "text" : "An identifier for the monomer at which this segment of the feature ends.", "context" : "dictionary" } ] }, "struct_oper_list" : { "type" : "array", "items" : { "type" : "string", "examples" : [ "P", "63" ], "description" : "Identifies the list of operations from the category pdbx_struct_oper_list. One item in array per operator applied. The order follows how operators are applied.", "rcsb_description" : [ { "text" : "Identifies the list of operations from the category pdbx_struct_oper_list. One item in array per operator applied. The order follows how operators are applied.", "context" : "dictionary" } ] }, "uniqueItems" : false, "minLength" : 1, "maxLength" : 2 }, "values" : { "type" : "array", "items" : { "type" : "number", "examples" : [ 1.5, 0.25 ], "description" : "The value(s) of the feature over the monomer segment.", "rcsb_description" : [ { "text" : "The value(s) of the feature over the monomer segment.", "context" : "dictionary" } ] }, "uniqueItems" : false } }, "additionalProperties" : false, "required" : [ "asym_id", "beg_seq_id", "struct_oper_list" ] }, "uniqueItems" : false } }, "additionalProperties" : false }, "minItems" : 1, "uniqueItems" : true }, "rcsb_assembly_info" : { "type" : "object", "properties" : { "assembly_id" : { "type" : "string", "description" : "Entity identifier for the container.", "rcsb_description" : [ { "text" : "Entity identifier for the container.", "context" : "dictionary" } ] }, "atom_count" : { "type" : "integer", "description" : "The assembly non-hydrogen atomic coordinate count.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The assembly non-hydrogen atomic coordinate count.", "context" : "dictionary" }, { "text" : "Number of Non-Hydrogen Atoms per Assembly", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Assembly Features", "priority_order" : 5 } ], "rcsb_current_maximum_value" : 3.995928E7, "rcsb_current_minimum_value" : 0.0 }, "branched_atom_count" : { "type" : "integer", "description" : "The assembly non-hydrogen branched entity atomic coordinate count.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The assembly non-hydrogen branched entity atomic coordinate count.", "context" : "dictionary" }, { "text" : "Branched Atom Count (Assembly Info)", "context" : "brief" } ], "rcsb_current_maximum_value" : 92664.0, "rcsb_current_minimum_value" : 0.0 }, "branched_entity_count" : { "type" : "integer", "description" : "The number of distinct branched entities in the generated assembly.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of distinct branched entities in the generated assembly.", "context" : "dictionary" }, { "text" : "Branched Entity Count (Assembly Info)", "context" : "brief" } ], "rcsb_current_maximum_value" : 22.0, "rcsb_current_minimum_value" : 0.0 }, "branched_entity_instance_count" : { "type" : "integer", "description" : "The number of branched instances in the generated assembly data set.\n This is the total count of branched entity instances generated in the assembly coordinate data.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of branched instances in the generated assembly data set.\n This is the total count of branched entity instances generated in the assembly coordinate data.", "context" : "dictionary" }, { "text" : "Branched Entity Instance Count (Assembly Info)", "context" : "brief" } ], "rcsb_current_maximum_value" : 780.0, "rcsb_current_minimum_value" : 0.0 }, "deuterated_water_count" : { "type" : "integer", "description" : "The assembly deuterated water molecule count.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The assembly deuterated water molecule count.", "context" : "dictionary" }, { "text" : "Number of Deuterated Water Molecules per Assembly", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Assembly Features", "priority_order" : 20 } ], "rcsb_current_maximum_value" : 2228.0, "rcsb_current_minimum_value" : 0.0 }, "entry_id" : { "type" : "string", "examples" : [ "1KIP" ], "description" : "The PDB entry accession code.", "rcsb_description" : [ { "text" : "The PDB entry accession code.", "context" : "dictionary" } ] }, "formula_weight" : { "type" : "number", "examples" : [ 110.0, 235.0 ], "description" : "Formula mass (KDa) of the assembly.", "rcsb_units" : "kilodaltons", "rcsb_description" : [ { "text" : "Formula mass (KDa) of the assembly.", "context" : "dictionary" } ] }, "hydrogen_atom_count" : { "type" : "integer", "description" : "The assembly hydrogen atomic coordinate count.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The assembly hydrogen atomic coordinate count.", "context" : "dictionary" }, { "text" : "Number of Hydrogen Atoms per Assembly", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Assembly Features", "priority_order" : 10 } ], "rcsb_current_maximum_value" : 5812500.0, "rcsb_current_minimum_value" : 0.0 }, "modeled_polymer_monomer_count" : { "type" : "integer", "description" : "The number of modeled polymer monomers in the assembly coordinate data.\n This is the total count of monomers with reported coordinate data for all polymer\n entity instances in the generated assembly coordinate data.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of modeled polymer monomers in the assembly coordinate data.\n This is the total count of monomers with reported coordinate data for all polymer\n entity instances in the generated assembly coordinate data.", "context" : "dictionary" }, { "text" : "Number of Modeled Polymer Residues per Assembly", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Assembly Features", "priority_order" : 30 } ], "rcsb_current_maximum_value" : 5086680.0, "rcsb_current_minimum_value" : 0.0 }, "na_polymer_entity_types" : { "type" : "string", "enum" : [ "DNA (only)", "DNA/RNA (only)", "NA-hybrid (only)", "Other", "RNA (only)" ], "examples" : [ "DNA (only)" ], "description" : "Nucleic acid polymer entity type categories describing the generated assembly.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "DNA (only)", "detail" : "DNA entity/entities only" }, { "value" : "DNA/RNA (only)", "detail" : "Both DNA and RNA polymer entities" }, { "value" : "NA-hybrid (only)", "detail" : "NA-hybrid entity/entities only" }, { "value" : "Other", "detail" : "Another polymer type composition" }, { "value" : "RNA (only)", "detail" : "RNA entity/entities only" } ], "rcsb_description" : [ { "text" : "Nucleic acid polymer entity type categories describing the generated assembly.", "context" : "dictionary" }, { "text" : "Na Polymer Entity Types (Assembly Info)", "context" : "brief" } ] }, "nonpolymer_atom_count" : { "type" : "integer", "description" : "The assembly non-hydrogen non-polymer entity atomic coordinate count.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The assembly non-hydrogen non-polymer entity atomic coordinate count.", "context" : "dictionary" }, { "text" : "Nonpolymer Atom Count (Assembly Info)", "context" : "brief" } ], "rcsb_current_maximum_value" : 206954.0, "rcsb_current_minimum_value" : 0.0 }, "nonpolymer_entity_count" : { "type" : "integer", "description" : "The number of distinct non-polymer entities in the generated assembly exclusive of solvent.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of distinct non-polymer entities in the generated assembly exclusive of solvent.", "context" : "dictionary" }, { "text" : "Nonpolymer Entity Count (Assembly Info)", "context" : "brief" } ], "rcsb_current_maximum_value" : 30.0, "rcsb_current_minimum_value" : 0.0 }, "nonpolymer_entity_instance_count" : { "type" : "integer", "description" : "The number of non-polymer instances in the generated assembly data set exclusive of solvent.\n This is the total count of non-polymer entity instances generated in the assembly coordinate data.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of non-polymer instances in the generated assembly data set exclusive of solvent.\n This is the total count of non-polymer entity instances generated in the assembly coordinate data.", "context" : "dictionary" }, { "text" : "Number of Non-polymer Instances per Assembly", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Assembly Features", "priority_order" : 45 } ], "rcsb_current_maximum_value" : 5280.0, "rcsb_current_minimum_value" : 0.0 }, "num_heterologous_interface_entities" : { "type" : "integer", "description" : "Number of heterologous (both binding sites are different) interface entities", "rcsb_description" : [ { "text" : "Number of heterologous (both binding sites are different) interface entities", "context" : "dictionary" } ] }, "num_heteromeric_interface_entities" : { "type" : "integer", "description" : "Number of heteromeric (both partners are different polymeric entities) interface entities", "rcsb_description" : [ { "text" : "Number of heteromeric (both partners are different polymeric entities) interface entities", "context" : "dictionary" } ] }, "num_homomeric_interface_entities" : { "type" : "integer", "description" : "Number of homomeric (both partners are the same polymeric entity) interface entities", "rcsb_description" : [ { "text" : "Number of homomeric (both partners are the same polymeric entity) interface entities", "context" : "dictionary" } ] }, "num_interface_entities" : { "type" : "integer", "description" : "Number of polymer-polymer interface entities, grouping equivalent interfaces at the entity level (i.e. same entity_ids on either side, with similar but not identical binding sites)", "rcsb_description" : [ { "text" : "Number of polymer-polymer interface entities, grouping equivalent interfaces at the entity level (i.e. same entity_ids on either side, with similar but not identical binding sites)", "context" : "dictionary" } ] }, "num_interfaces" : { "type" : "integer", "description" : "Number of geometrically equivalent (i.e. same asym_ids on either side) polymer-polymer interfaces in the assembly", "rcsb_description" : [ { "text" : "Number of geometrically equivalent (i.e. same asym_ids on either side) polymer-polymer interfaces in the assembly", "context" : "dictionary" } ] }, "num_isologous_interface_entities" : { "type" : "integer", "description" : "Number of isologous (both binding sites are same, i.e. interface is symmetric) interface entities", "rcsb_description" : [ { "text" : "Number of isologous (both binding sites are same, i.e. interface is symmetric) interface entities", "context" : "dictionary" } ] }, "num_na_interface_entities" : { "type" : "integer", "description" : "Number of nucleic acid-nucleic acid interface entities", "rcsb_description" : [ { "text" : "Number of nucleic acid-nucleic acid interface entities", "context" : "dictionary" } ] }, "num_prot_na_interface_entities" : { "type" : "integer", "description" : "Number of protein-nucleic acid interface entities", "rcsb_description" : [ { "text" : "Number of protein-nucleic acid interface entities", "context" : "dictionary" } ] }, "num_protein_interface_entities" : { "type" : "integer", "description" : "Number of protein-protein interface entities", "rcsb_description" : [ { "text" : "Number of protein-protein interface entities", "context" : "dictionary" } ] }, "polymer_atom_count" : { "type" : "integer", "description" : "The assembly non-hydrogen polymer entity atomic coordinate count.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The assembly non-hydrogen polymer entity atomic coordinate count.", "context" : "dictionary" }, { "text" : "Polymer Atom Count (Assembly Info)", "context" : "brief" } ], "rcsb_current_maximum_value" : 3.995928E7, "rcsb_current_minimum_value" : 0.0 }, "polymer_composition" : { "type" : "string", "enum" : [ "DNA", "DNA/RNA", "NA-hybrid", "NA/oligosaccharide", "RNA", "heteromeric protein", "homomeric protein", "oligosaccharide", "other", "other type composition", "other type pair", "protein/NA", "protein/NA/oligosaccharide", "protein/oligosaccharide" ], "examples" : [ "homomeric protein" ], "description" : "Categories describing the polymer entity composition for the generated assembly.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "DNA", "detail" : "DNA entity/entities only" }, { "value" : "DNA/RNA", "detail" : "Both DNA and RNA polymer entities" }, { "value" : "NA-hybrid", "detail" : "DNA/RNA hybrid entity/entities only" }, { "value" : "NA/oligosaccharide", "detail" : "Both NA and oligosaccharide entities" }, { "value" : "RNA", "detail" : "RNA entity/entities only" }, { "value" : "heteromeric protein", "detail" : "multiple protein entities" }, { "value" : "homomeric protein", "detail" : "single protein entity" }, { "value" : "oligosaccharide", "detail" : "One of more oligosaccharide entities" }, { "value" : "other", "detail" : "Neither an individual protein, nucleic acid polymer nor oligosaccharide entity" }, { "value" : "other type composition", "detail" : "Other combinations of 3 or more polymer types" }, { "value" : "other type pair", "detail" : "Other combinations of 2 polymer types" }, { "value" : "protein/NA", "detail" : "Both protein and nucleic acid polymer entities" }, { "value" : "protein/NA/oligosaccharide", "detail" : "Protein, nucleic acid, and oligosaccharide entities" }, { "value" : "protein/oligosaccharide", "detail" : "Both protein and oligosaccharide entities" } ], "rcsb_description" : [ { "text" : "Categories describing the polymer entity composition for the generated assembly.", "context" : "dictionary" }, { "text" : "Polymer Composition (Assembly Info)", "context" : "brief" } ] }, "polymer_entity_count" : { "type" : "integer", "description" : "The number of distinct polymer entities in the generated assembly.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of distinct polymer entities in the generated assembly.", "context" : "dictionary" }, { "text" : "Polymer Entity Count (Assembly Info)", "context" : "brief" } ], "rcsb_current_maximum_value" : 455.0, "rcsb_current_minimum_value" : 0.0 }, "polymer_entity_count_DNA" : { "type" : "integer", "description" : "The number of distinct DNA polymer entities in the generated assembly.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of distinct DNA polymer entities in the generated assembly.", "context" : "dictionary" }, { "text" : "Polymer Entity Count Dna (Assembly Info)", "context" : "brief" } ], "rcsb_current_maximum_value" : 455.0, "rcsb_current_minimum_value" : 0.0 }, "polymer_entity_count_RNA" : { "type" : "integer", "description" : "The number of distinct RNA polymer entities in the generated assembly.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of distinct RNA polymer entities in the generated assembly.", "context" : "dictionary" }, { "text" : "Polymer Entity Count Rna (Assembly Info)", "context" : "brief" } ], "rcsb_current_maximum_value" : 36.0, "rcsb_current_minimum_value" : 0.0 }, "polymer_entity_count_nucleic_acid" : { "type" : "integer", "description" : "The number of distinct nucleic acid polymer entities (DNA or RNA) in the generated assembly.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of distinct nucleic acid polymer entities (DNA or RNA) in the generated assembly.", "context" : "dictionary" }, { "text" : "Polymer Entity Count Nucleic Acid (Assembly Info)", "context" : "brief" } ], "rcsb_current_maximum_value" : 455.0, "rcsb_current_minimum_value" : 0.0 }, "polymer_entity_count_nucleic_acid_hybrid" : { "type" : "integer", "description" : "The number of distinct hybrid nucleic acid polymer entities in the generated assembly.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of distinct hybrid nucleic acid polymer entities in the generated assembly.", "context" : "dictionary" }, { "text" : "Polymer Entity Count Nucleic Acid Hybrid (Assembly Info)", "context" : "brief" } ], "rcsb_current_maximum_value" : 2.0, "rcsb_current_minimum_value" : 0.0 }, "polymer_entity_count_protein" : { "type" : "integer", "description" : "The number of distinct protein polymer entities in the generated assembly.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of distinct protein polymer entities in the generated assembly.", "context" : "dictionary" }, { "text" : "Polymer Entity Count Protein (Assembly Info)", "context" : "brief" } ], "rcsb_current_maximum_value" : 165.0, "rcsb_current_minimum_value" : 0.0 }, "polymer_entity_instance_count" : { "type" : "integer", "description" : "The number of polymer instances in the generated assembly data set.\n This is the total count of polymer entity instances generated in the assembly coordinate data.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of polymer instances in the generated assembly data set.\n This is the total count of polymer entity instances generated in the assembly coordinate data.", "context" : "dictionary" }, { "text" : "Number of Polymer Instances (Chains) per Assembly", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Assembly Features", "priority_order" : 40 } ], "rcsb_current_maximum_value" : 8280.0, "rcsb_current_minimum_value" : 0.0 }, "polymer_entity_instance_count_DNA" : { "type" : "integer", "description" : "The number of DNA polymer instances in the generated assembly data set.\n This is the total count of DNA polymer entity instances generated in the assembly coordinate data.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of DNA polymer instances in the generated assembly data set.\n This is the total count of DNA polymer entity instances generated in the assembly coordinate data.", "context" : "dictionary" }, { "text" : "Number of DNA Instances (Chains) per Assembly", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Assembly Features", "priority_order" : 55 } ], "rcsb_current_maximum_value" : 455.0, "rcsb_current_minimum_value" : 0.0 }, "polymer_entity_instance_count_RNA" : { "type" : "integer", "description" : "The number of RNA polymer instances in the generated assembly data set.\n This is the total count of RNA polymer entity instances generated in the assembly coordinate data.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of RNA polymer instances in the generated assembly data set.\n This is the total count of RNA polymer entity instances generated in the assembly coordinate data.", "context" : "dictionary" }, { "text" : "Number of RNA Instances (Chains) per Assembly", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Assembly Features", "priority_order" : 60 } ], "rcsb_current_maximum_value" : 180.0, "rcsb_current_minimum_value" : 0.0 }, "polymer_entity_instance_count_nucleic_acid" : { "type" : "integer", "description" : "The number of nucleic acid polymer instances in the generated assembly data set.\n This is the total count of nucleic acid polymer entity instances generated in the assembly coordinate data.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of nucleic acid polymer instances in the generated assembly data set.\n This is the total count of nucleic acid polymer entity instances generated in the assembly coordinate data.", "context" : "dictionary" }, { "text" : "Polymer Entity Instance Count Nucleic Acid (Assembly Info)", "context" : "brief" } ], "rcsb_current_maximum_value" : 455.0, "rcsb_current_minimum_value" : 0.0 }, "polymer_entity_instance_count_nucleic_acid_hybrid" : { "type" : "integer", "description" : "The number of hybrid nucleic acide polymer instances in the generated assembly data set.\n This is the total count of hybrid nucleic acid polymer entity instances generated in the assembly coordinate data.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of hybrid nucleic acide polymer instances in the generated assembly data set.\n This is the total count of hybrid nucleic acid polymer entity instances generated in the assembly coordinate data.", "context" : "dictionary" }, { "text" : "Number of NA Hybrid Instances (Chains) per Assembly", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Assembly Features", "priority_order" : 65 } ], "rcsb_current_maximum_value" : 8.0, "rcsb_current_minimum_value" : 0.0 }, "polymer_entity_instance_count_protein" : { "type" : "integer", "description" : "The number of protein polymer instances in the generated assembly data set.\n This is the total count of protein polymer entity instances generated in the assembly coordinate data.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of protein polymer instances in the generated assembly data set.\n This is the total count of protein polymer entity instances generated in the assembly coordinate data.", "context" : "dictionary" }, { "text" : "Number of Protein Instances (Chains) per Assembly", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Assembly Features", "priority_order" : 50 } ], "rcsb_current_maximum_value" : 8280.0, "rcsb_current_minimum_value" : 0.0 }, "polymer_monomer_count" : { "type" : "integer", "description" : "The number of polymer monomers in sample entity instances comprising the assembly data set.\n This is the total count of monomers for all polymer entity instances\n in the generated assembly coordinate data.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of polymer monomers in sample entity instances comprising the assembly data set.\n This is the total count of monomers for all polymer entity instances\n in the generated assembly coordinate data.", "context" : "dictionary" }, { "text" : "Number of Polymer Residues per Assembly", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Assembly Features", "priority_order" : 25 } ], "rcsb_current_maximum_value" : 5340600.0, "rcsb_current_minimum_value" : 0.0 }, "selected_polymer_entity_types" : { "type" : "string", "enum" : [ "Nucleic acid (only)", "Other", "Protein (only)", "Protein/NA" ], "examples" : [ "Protein (only)" ], "description" : "Selected polymer entity type categories describing the generated assembly.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "Nucleic acid (only)", "detail" : "Nucleic acid (DNA, RNA, NA-hybrid entity/entities only" }, { "value" : "Other", "detail" : "Another polymer type composition" }, { "value" : "Protein (only)", "detail" : "protein entity/entities only" }, { "value" : "Protein/NA", "detail" : "Both protein and nucleic acid (DNA or RNA) polymer entities" } ], "rcsb_description" : [ { "text" : "Selected polymer entity type categories describing the generated assembly.", "context" : "dictionary" }, { "text" : "Selected Polymer Entity Types (Assembly Info)", "context" : "brief" } ] }, "solvent_atom_count" : { "type" : "integer", "description" : "The assembly non-hydrogen solvent atomic coordinate count.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The assembly non-hydrogen solvent atomic coordinate count.", "context" : "dictionary" }, { "text" : "Number of Water Molecules per Assembly", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Assembly Features", "priority_order" : 15 } ], "rcsb_current_maximum_value" : 78540.0, "rcsb_current_minimum_value" : 0.0 }, "solvent_entity_count" : { "type" : "integer", "description" : "The number of distinct solvent entities in the generated assembly.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of distinct solvent entities in the generated assembly.", "context" : "dictionary" }, { "text" : "Solvent Entity Count (Assembly Info)", "context" : "brief" } ], "rcsb_current_maximum_value" : 1.0, "rcsb_current_minimum_value" : 0.0 }, "solvent_entity_instance_count" : { "type" : "integer", "description" : "The number of solvent instances in the generated assembly data set.\n This is the total count of solvent entity instances generated in the assembly coordinate data.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of solvent instances in the generated assembly data set.\n This is the total count of solvent entity instances generated in the assembly coordinate data.", "context" : "dictionary" }, { "text" : "Solvent Entity Instance Count (Assembly Info)", "context" : "brief" } ], "rcsb_current_maximum_value" : 901.0, "rcsb_current_minimum_value" : 0.0 }, "total_assembly_buried_surface_area" : { "type" : "number", "description" : "Total buried surface area calculated as the sum of buried surface areas over all interfaces", "rcsb_description" : [ { "text" : "Total buried surface area calculated as the sum of buried surface areas over all interfaces", "context" : "dictionary" } ] }, "total_number_interface_residues" : { "type" : "integer", "description" : "Total number of interfacing residues in the assembly, calculated as the sum of interfacing residues over all interfaces", "rcsb_description" : [ { "text" : "Total number of interfacing residues in the assembly, calculated as the sum of interfacing residues over all interfaces", "context" : "dictionary" } ] }, "unmodeled_polymer_monomer_count" : { "type" : "integer", "description" : "The number of unmodeled polymer monomers in the assembly coordinate data. This is\n the total count of monomers with unreported coordinate data for all polymer\n entity instances in the generated assembly coordinate data.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of unmodeled polymer monomers in the assembly coordinate data. This is\n the total count of monomers with unreported coordinate data for all polymer\n entity instances in the generated assembly coordinate data.", "context" : "dictionary" }, { "text" : "Number of Unmodeled Polymer Residues per Assembly", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Assembly Features", "priority_order" : 35 } ], "rcsb_current_maximum_value" : 515880.0, "rcsb_current_minimum_value" : 0.0 } }, "additionalProperties" : false, "required" : [ "entry_id" ] }, "rcsb_struct_symmetry" : { "type" : "array", "items" : { "type" : "object", "properties" : { "kind" : { "type" : "string", "enum" : [ "Global Symmetry", "Local Symmetry", "Pseudo Symmetry" ], "description" : "The granularity at which the symmetry calculation is performed. In 'Global Symmetry' all polymeric\n subunits in assembly are used. In 'Local Symmetry' only a subset of polymeric subunits is considered.\n In 'Pseudo Symmetry' the threshold for subunits similarity is relaxed.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The granularity at which the symmetry calculation is performed. In 'Global Symmetry' all polymeric\n subunits in assembly are used. In 'Local Symmetry' only a subset of polymeric subunits is considered.\n In 'Pseudo Symmetry' the threshold for subunits similarity is relaxed.", "context" : "dictionary" }, { "text" : "Symmetry Class", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Assembly Features", "priority_order" : 100 } ] }, "oligomeric_state" : { "type" : "string", "examples" : [ "Homo 2-mer", "Homo 2-mer", "Hetero 3-mer" ], "description" : "Oligomeric state refers to a composition of polymeric subunits in quaternary structure.\n Quaternary structure may be composed either exclusively of several copies of identical subunits,\n in which case they are termed homo-oligomers, or alternatively by at least one copy of different\n subunits (hetero-oligomers). Quaternary structure composed of a single subunit is denoted as 'Monomer'.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Oligomeric state refers to a composition of polymeric subunits in quaternary structure.\n Quaternary structure may be composed either exclusively of several copies of identical subunits,\n in which case they are termed homo-oligomers, or alternatively by at least one copy of different\n subunits (hetero-oligomers). Quaternary structure composed of a single subunit is denoted as 'Monomer'.", "context" : "dictionary" }, { "text" : "Oligomeric State", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Assembly Features", "priority_order" : 90 } ] }, "stoichiometry" : { "type" : "array", "items" : { "type" : "string", "description" : "Stoichiometry of a complex represents the quantitative description and composition of its subunits.", "rcsb_description" : [ { "text" : "Stoichiometry of a complex represents the quantitative description and composition of its subunits.", "context" : "dictionary" } ] }, "minItems" : 1, "uniqueItems" : true }, "symbol" : { "type" : "string", "examples" : [ "C1", "D3", "N" ], "description" : "Symmetry symbol refers to point group or helical symmetry of identical polymeric subunits in Schoenflies notation.\n Contains point group symbol (e.g., C2, C5, D2, T, O, I) or H for helical symmetry.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Symmetry symbol refers to point group or helical symmetry of identical polymeric subunits in Schoenflies notation.\n Contains point group symbol (e.g., C2, C5, D2, T, O, I) or H for helical symmetry.", "context" : "dictionary" }, { "text" : "Symmetry Symbol", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Assembly Features", "priority_order" : 85 } ] }, "type" : { "type" : "string", "enum" : [ "Asymmetric", "Cyclic", "Dihedral", "Helical", "Icosahedral", "Octahedral", "Tetrahedral" ], "description" : "Symmetry type refers to point group or helical symmetry of identical polymeric subunits.\n Contains point group types (e.g. Cyclic, Dihedral) or Helical for helical symmetry.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Symmetry type refers to point group or helical symmetry of identical polymeric subunits.\n Contains point group types (e.g. Cyclic, Dihedral) or Helical for helical symmetry.", "context" : "dictionary" }, { "text" : "Symmetry Type", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Assembly Features", "priority_order" : 95 } ] }, "rotation_axes" : { "type" : "array", "items" : { "type" : "object", "properties" : { "end" : { "type" : "array", "items" : { "type" : "number", "description" : "coordinate", "rcsb_description" : [ { "text" : "coordinate", "context" : "dictionary" } ] }, "uniqueItems" : false, "minItems" : 3, "maxItems" : 3, "description" : "Describes x,y,z coordinates of the end point of the symmetry axis." }, "order" : { "type" : "integer", "description" : "The number of times (order of rotation) that a subunit can be repeated by a rotation operation,\n being transformed into a new state indistinguishable from its starting state.", "rcsb_description" : [ { "text" : "The number of times (order of rotation) that a subunit can be repeated by a rotation operation,\n being transformed into a new state indistinguishable from its starting state.", "context" : "dictionary" } ] }, "start" : { "type" : "array", "items" : { "type" : "number", "description" : "coordinate", "rcsb_description" : [ { "text" : "coordinate", "context" : "dictionary" } ] }, "uniqueItems" : false, "minItems" : 3, "maxItems" : 3, "description" : "Describes x,y,z coordinates of the start point of the symmetry axis." } }, "additionalProperties" : false, "description" : "The orientation of the principal rotation (symmetry) axis.", "required" : [ "end", "start" ] }, "uniqueItems" : true, "minItems" : 1, "description" : "Specifies a single or multiple rotation axes through the same point." }, "clusters" : { "type" : "array", "items" : { "type" : "object", "properties" : { "members" : { "type" : "array", "items" : { "type" : "object", "properties" : { "asym_id" : { "type" : "string", "description" : "Internal chain ID used in mmCIF files to uniquely identify structural elements in the asymmetric unit.", "rcsb_description" : [ { "text" : "Internal chain ID used in mmCIF files to uniquely identify structural elements in the asymmetric unit.", "context" : "dictionary" } ] }, "pdbx_struct_oper_list_ids" : { "type" : "array", "items" : { "type" : "string" }, "minItems" : 1, "description" : "Optional list of operator ids (pdbx_struct_oper_list.id) as appears in pdbx_struct_assembly_gen.oper_expression." } }, "additionalProperties" : false, "description" : "Subunits that belong to the cluster, identified by asym_id and optionally by assembly operator id(s).", "required" : [ "asym_id" ] }, "minItems" : 1, "uniqueItems" : true }, "avg_rmsd" : { "type" : "number", "description" : "Average RMSD between members of a given cluster.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "Average RMSD between members of a given cluster.", "context" : "dictionary" }, { "text" : "Average RMSD", "context" : "brief" } ], "rcsb_current_maximum_value" : 80.22285641881933, "rcsb_current_minimum_value" : 0.0 } }, "additionalProperties" : false, "required" : [ "members" ] }, "uniqueItems" : true, "minItems" : 1, "description" : "Clusters describe grouping of identical subunits." } }, "additionalProperties" : false, "required" : [ "clusters", "kind", "oligomeric_state", "stoichiometry", "symbol", "type" ] }, "minItems" : 1, "uniqueItems" : true, "rcsb_nested_indexing" : true }, "rcsb_struct_symmetry_lineage" : { "type" : "array", "items" : { "type" : "object", "properties" : { "depth" : { "type" : "integer", "description" : "Hierarchy depth.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Hierarchy depth.", "context" : "dictionary" }, { "text" : "Depth (Struct Symmetry Lineage)", "context" : "brief" } ], "rcsb_current_maximum_value" : 3.0, "rcsb_current_minimum_value" : 0.0 }, "id" : { "type" : "string", "examples" : [ "Global Symmetry.Cyclic.C2.Homo 2-mer" ], "description" : "Automatically assigned ID to uniquely identify the symmetry term in the Protein Symmetry Browser.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Automatically assigned ID to uniquely identify the symmetry term in the Protein Symmetry Browser.", "context" : "dictionary" }, { "text" : "Protein Symmetry (Browser ID)", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Assembly Features", "priority_order" : 80 } ] }, "name" : { "type" : "string", "examples" : [ "Asymmetric", "Global Symmetry", "C1", "Hetero 3-mer" ], "description" : "A human-readable term describing protein symmetry.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "A human-readable term describing protein symmetry.", "context" : "dictionary" }, { "text" : "Symmetry Name", "context" : "brief" } ] } }, "additionalProperties" : false }, "minItems" : 1, "uniqueItems" : true, "rcsb_nested_indexing" : true }, "rcsb_struct_symmetry_provenance_code" : { "type" : "string", "description" : "The title and version of software package used for symmetry calculations.", "rcsb_description" : [ { "text" : "The title and version of software package used for symmetry calculations.", "context" : "dictionary" } ] }, "rcsb_repository_holdings_current" : { "type" : "object", "properties" : { "repository_content_types" : { "type" : "array", "items" : { "type" : "string", "enum" : [ "2fo-fc Map", "Combined NMR data (NEF)", "Combined NMR data (NMR-STAR)", "FASTA sequence", "Map Coefficients", "NMR chemical shifts", "NMR restraints V1", "NMR restraints V2", "assembly PDB", "assembly mmCIF", "entry PDB", "entry PDB bundle", "entry PDBML", "entry mmCIF", "fo-fc Map", "structure factors", "validation 2fo-fc coefficients", "validation data mmCIF", "validation fo-fc coefficients", "validation report", "validation slider image" ], "examples" : [ "entry mmCIF" ], "description" : "The list of content types associated with this entry.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The list of content types associated with this entry.", "context" : "dictionary" }, { "text" : "Content Types Available in the Repository", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Structure Details", "priority_order" : 75 } ] }, "uniqueItems" : false } }, "additionalProperties" : false }, "rcsb_repository_holdings_current_entry_container_identifiers" : { "type" : "object", "properties" : { "assembly_ids" : { "type" : "array", "items" : { "type" : "string", "examples" : [ "1", "2", "3" ], "description" : "The assembly id codes.", "rcsb_description" : [ { "text" : "The assembly id codes.", "context" : "dictionary" } ] }, "uniqueItems" : false }, "entry_id" : { "type" : "string", "examples" : [ "1KIP" ], "description" : "The PDB entry accession code.", "rcsb_description" : [ { "text" : "The PDB entry accession code.", "context" : "dictionary" } ] }, "rcsb_id" : { "type" : "string", "examples" : [ "1KIP" ], "description" : "The RCSB entry identifier.", "rcsb_description" : [ { "text" : "The RCSB entry identifier.", "context" : "dictionary" } ] }, "update_id" : { "type" : "string", "examples" : [ "2018_23" ], "description" : "Identifier for the current data exchange status record.", "rcsb_description" : [ { "text" : "Identifier for the current data exchange status record.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "entry_id" ] }, "pdbx_struct_special_symmetry" : { "type" : "array", "items" : { "type" : "object", "properties" : { "PDB_model_num" : { "type" : "integer", "description" : "Part of the identifier for the molecular component.\n\nThis data item is a pointer to _atom_site.pdbx_PDB_model_num in the\nATOM_SITE category.", "rcsb_description" : [ { "text" : "Part of the identifier for the molecular component.\n\nThis data item is a pointer to _atom_site.pdbx_PDB_model_num in the\nATOM_SITE category.", "context" : "dictionary" } ] }, "auth_seq_id" : { "type" : "string", "description" : "Part of the identifier for the molecular component.\n\n This data item is a pointer to _atom_site.auth_seq_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "Part of the identifier for the molecular component.\n\n This data item is a pointer to _atom_site.auth_seq_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "id" : { "type" : "integer", "description" : "The value of _pdbx_struct_special_symmetry.id must uniquely identify\n each item in the PDBX_STRUCT_SPECIAL_SYMMETRY list.\n\n This is an integer serial number.", "rcsb_description" : [ { "text" : "The value of _pdbx_struct_special_symmetry.id must uniquely identify\n each item in the PDBX_STRUCT_SPECIAL_SYMMETRY list.\n\n This is an integer serial number.", "context" : "dictionary" } ] }, "label_asym_id" : { "type" : "string", "description" : "Part of the identifier for the molecular component.\n\n This data item is a pointer to _atom_site.label_asym_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "Part of the identifier for the molecular component.\n\n This data item is a pointer to _atom_site.label_asym_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "label_comp_id" : { "type" : "string", "description" : "Part of the identifier for the molecular component.\n\n This data item is a pointer to _atom_site.label_comp_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "Part of the identifier for the molecular component.\n\n This data item is a pointer to _atom_site.label_comp_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "id" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_vrpt_summary_entity_fit_to_map" : { "type" : "array", "items" : { "type" : "object", "properties" : { "PDB_model_num" : { "type" : "integer", "description" : "The unique model number from _atom_site.pdbx_PDB_model_num.", "rcsb_description" : [ { "text" : "The unique model number from _atom_site.pdbx_PDB_model_num.", "context" : "dictionary" } ] }, "Q_score" : { "type" : "number", "description" : "The calculated average Q-score.", "rcsb_description" : [ { "text" : "The calculated average Q-score.", "context" : "dictionary" }, { "text" : "Polymer Instance Average Q-Score", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Polymer Instance (Chain) Features", "priority_order" : 25 } ], "rcsb_search_context" : [ "default-match" ], "rcsb_current_maximum_value" : 0.99, "rcsb_current_minimum_value" : -0.238 }, "average_residue_inclusion" : { "type" : "number", "description" : "The average of the residue inclusions for all residues in this instance", "rcsb_description" : [ { "text" : "The average of the residue inclusions for all residues in this instance", "context" : "dictionary" } ] } }, "additionalProperties" : false }, "minItems" : 1, "uniqueItems" : true }, "pdbx_vrpt_summary_entity_geometry" : { "type" : "array", "items" : { "type" : "object", "properties" : { "PDB_model_num" : { "type" : "integer", "description" : "The unique model number from _atom_site.pdbx_PDB_model_num.", "rcsb_description" : [ { "text" : "The unique model number from _atom_site.pdbx_PDB_model_num.", "context" : "dictionary" } ] }, "angles_RMSZ" : { "type" : "number", "description" : "The overall root mean square of the Z-score for deviations of bond angles in comparison to \n\"standard geometry\" made using the MolProbity dangle program.\nStandard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996).", "rcsb_description" : [ { "text" : "The overall root mean square of the Z-score for deviations of bond angles in comparison to \n\"standard geometry\" made using the MolProbity dangle program.\nStandard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996).", "context" : "dictionary" } ] }, "average_residue_inclusion" : { "type" : "number", "description" : "The average of the residue inclusions for all residues in this instance", "rcsb_description" : [ { "text" : "The average of the residue inclusions for all residues in this instance", "context" : "dictionary" } ] }, "bonds_RMSZ" : { "type" : "number", "description" : "The overall root mean square of the Z-score for deviations of bond lengths in comparison to \n\"standard geometry\" made using the MolProbity dangle program.\nStandard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996).", "rcsb_description" : [ { "text" : "The overall root mean square of the Z-score for deviations of bond lengths in comparison to \n\"standard geometry\" made using the MolProbity dangle program.\nStandard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996).", "context" : "dictionary" } ] }, "num_angles_RMSZ" : { "type" : "integer", "description" : "The number of bond angles compared to \"standard geometry\" made using the MolProbity dangle program.\nStandard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996).", "rcsb_description" : [ { "text" : "The number of bond angles compared to \"standard geometry\" made using the MolProbity dangle program.\nStandard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996).", "context" : "dictionary" } ] }, "num_bonds_RMSZ" : { "type" : "integer", "description" : "The number of bond lengths compared to \"standard geometry\" made using the MolProbity dangle program.\nStandard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996).", "rcsb_description" : [ { "text" : "The number of bond lengths compared to \"standard geometry\" made using the MolProbity dangle program.\nStandard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996).", "context" : "dictionary" } ] } }, "additionalProperties" : false }, "minItems" : 1, "uniqueItems" : true }, "rcsb_nonpolymer_entity_instance_container_identifiers" : { "type" : "object", "properties" : { "asym_id" : { "type" : "string", "description" : "Instance identifier for this container.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Instance identifier for this container.", "context" : "dictionary" }, { "text" : "Asym Id (Nonpolymer Entity Instance Container Identifiers)", "context" : "brief" } ] }, "auth_asym_id" : { "type" : "string", "description" : "Author instance identifier for this container.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Author instance identifier for this container.", "context" : "dictionary" }, { "text" : "Auth Asym Id (Nonpolymer Entity Instance Container Identifiers)", "context" : "brief" } ] }, "auth_seq_id" : { "type" : "string", "description" : "Residue number for non-polymer entity instance.", "rcsb_description" : [ { "text" : "Residue number for non-polymer entity instance.", "context" : "dictionary" } ] }, "comp_id" : { "type" : "string", "description" : "Component identifier for non-polymer entity instance.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Component identifier for non-polymer entity instance.", "context" : "dictionary" }, { "text" : "Comp Id (Nonpolymer Entity Instance Container Identifiers)", "context" : "brief" } ] }, "entity_id" : { "type" : "string", "description" : "Entity identifier for the container.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Entity identifier for the container.", "context" : "dictionary" }, { "text" : "Entity Id (Nonpolymer Entity Instance Container Identifiers)", "context" : "brief" } ] }, "entry_id" : { "type" : "string", "description" : "Entry identifier for the container.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Entry identifier for the container.", "context" : "dictionary" }, { "text" : "Entry Id (Nonpolymer Entity Instance Container Identifiers)", "context" : "brief" } ] }, "rcsb_id" : { "type" : "string", "examples" : [ "1KIP.A" ], "description" : "A unique identifier for each object in this entity instance container formed by\n an 'dot' (.) separated concatenation of entry and entity instance identifiers.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "A unique identifier for each object in this entity instance container formed by\n an 'dot' (.) separated concatenation of entry and entity instance identifiers.", "context" : "dictionary" }, { "text" : "Id (Nonpolymer Entity Instance Container Identifiers)", "context" : "brief" } ] } }, "additionalProperties" : false, "required" : [ "asym_id", "entry_id" ] }, "rcsb_nonpolymer_instance_annotation" : { "type" : "array", "items" : { "type" : "object", "properties" : { "annotation_id" : { "type" : "string", "description" : "An identifier for the annotation.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "An identifier for the annotation.", "context" : "dictionary" }, { "text" : "Identifier", "context" : "brief" } ] }, "assignment_version" : { "type" : "string", "examples" : [ "V4_0_2" ], "description" : "Identifies the version of the annotation assignment.", "rcsb_description" : [ { "text" : "Identifies the version of the annotation assignment.", "context" : "dictionary" }, { "text" : "Annotation Version", "context" : "brief" } ] }, "comp_id" : { "type" : "string", "examples" : [ "ATP" ], "description" : "Non-polymer (ligand) chemical component identifier.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Non-polymer (ligand) chemical component identifier.", "context" : "dictionary" }, { "text" : "Component Identifier", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Nonpolymer Molecular Features", "priority_order" : 15 } ] }, "description" : { "type" : "string", "description" : "A description for the annotation.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "A description for the annotation.", "context" : "dictionary" }, { "text" : "Annotation Description", "context" : "brief" } ] }, "name" : { "type" : "string", "description" : "A name for the annotation.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "A name for the annotation.", "context" : "dictionary" }, { "text" : "Name", "context" : "brief" } ] }, "ordinal" : { "type" : "integer", "description" : "Ordinal identifier for this category", "rcsb_description" : [ { "text" : "Ordinal identifier for this category", "context" : "dictionary" } ] }, "provenance_source" : { "type" : "string", "examples" : [ "PDB" ], "description" : "Code identifying the individual, organization or program that\n assigned the annotation.", "rcsb_description" : [ { "text" : "Code identifying the individual, organization or program that\n assigned the annotation.", "context" : "dictionary" }, { "text" : "Annotation Source", "context" : "brief" } ] }, "type" : { "type" : "string", "enum" : [ "HAS_COVALENT_LINKAGE", "HAS_METAL_COORDINATION_LINKAGE", "HAS_NO_COVALENT_LINKAGE", "IS_RSCC_OUTLIER", "IS_RSRZ_OUTLIER" ], "examples" : [ "HAS_COVALENT_LINKAGE" ], "description" : "A type or category of the annotation.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "HAS_COVALENT_LINKAGE", "detail" : "Ligands with inter-molecular covalent interactions involving non-metal elements such as Carbon, Nitrogen, Oxygen, Phosphorus, and Sulfur", "name" : "Has Covalent Linkage" }, { "value" : "HAS_METAL_COORDINATION_LINKAGE", "detail" : "Ligands involved in metal coordination", "name" : "Has Metal Coordination" }, { "value" : "HAS_NO_COVALENT_LINKAGE", "detail" : "Ligands with no inter-molecular covalent interactions, but may be involved in metal coordination or other non-bonded interactions", "name" : "Has No Covalent Linkage" }, { "value" : "IS_RSCC_OUTLIER", "detail" : "Non-polymer is a real space density correlation value outlier (< 0.65)", "name" : "Real space density correlation value outlier" }, { "value" : "IS_RSRZ_OUTLIER", "detail" : "Non-polymer is a real space R-value Z score outlier (> 2)", "name" : "Real space R-value Z score outlier" } ], "rcsb_description" : [ { "text" : "A type or category of the annotation.", "context" : "dictionary" }, { "text" : "Annotation Type", "context" : "brief" } ] }, "annotation_lineage" : { "type" : "array", "items" : { "type" : "object", "properties" : { "depth" : { "type" : "integer", "description" : "Members of the annotation lineage as parent lineage depth (1-N)", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Members of the annotation lineage as parent lineage depth (1-N)", "context" : "dictionary" }, { "text" : "Lineage Depth", "context" : "brief" } ] }, "id" : { "type" : "string", "description" : "Members of the annotation lineage as parent class identifiers.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Members of the annotation lineage as parent class identifiers.", "context" : "dictionary" }, { "text" : "Lineage Identifier", "context" : "brief" } ] }, "name" : { "type" : "string", "description" : "Members of the annotation lineage as parent class names.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Members of the annotation lineage as parent class names.", "context" : "dictionary" }, { "text" : "Lineage Name", "context" : "brief" } ] } }, "additionalProperties" : false }, "uniqueItems" : false, "rcsb_nested_indexing" : true } }, "additionalProperties" : false, "required" : [ "ordinal", "type" ] }, "minItems" : 1, "uniqueItems" : true, "rcsb_nested_indexing" : true, "rcsb_nested_indexing_context" : [ { "category_name" : "annotation_type", "category_path" : "rcsb_nonpolymer_instance_annotation.type", "context_attributes" : [ { "context_value" : "HAS_COVALENT_LINKAGE", "attributes" : [ { "examples" : [ "BMZ", "ATP" ], "path" : "rcsb_nonpolymer_instance_annotation.comp_id" } ] }, { "context_value" : "HAS_METAL_COORDINATION_LINKAGE", "attributes" : [ { "examples" : [ "SF4", "HEM" ], "path" : "rcsb_nonpolymer_instance_annotation.comp_id" } ] }, { "context_value" : "HAS_NO_COVALENT_LINKAGE", "attributes" : [ { "examples" : [ "J5C", "DID" ], "path" : "rcsb_nonpolymer_instance_annotation.comp_id" } ] } ] } ] }, "rcsb_nonpolymer_instance_feature" : { "type" : "array", "items" : { "type" : "object", "properties" : { "assignment_version" : { "type" : "string", "examples" : [ "V4_0_2" ], "description" : "Identifies the version of the feature assignment.", "rcsb_description" : [ { "text" : "Identifies the version of the feature assignment.", "context" : "dictionary" }, { "text" : "Feature Version", "context" : "brief" } ] }, "comp_id" : { "type" : "string", "description" : "Component identifier for non-polymer entity instance.", "rcsb_description" : [ { "text" : "Component identifier for non-polymer entity instance.", "context" : "dictionary" } ] }, "description" : { "type" : "string", "description" : "A description for the feature.", "rcsb_description" : [ { "text" : "A description for the feature.", "context" : "dictionary" }, { "text" : "Feature Description", "context" : "brief" } ] }, "feature_id" : { "type" : "string", "description" : "An identifier for the feature.", "rcsb_description" : [ { "text" : "An identifier for the feature.", "context" : "dictionary" } ] }, "name" : { "type" : "string", "description" : "A name for the feature.", "rcsb_description" : [ { "text" : "A name for the feature.", "context" : "dictionary" }, { "text" : "Name", "context" : "brief" } ] }, "ordinal" : { "type" : "integer", "description" : "Ordinal identifier for this category", "rcsb_description" : [ { "text" : "Ordinal identifier for this category", "context" : "dictionary" } ] }, "provenance_source" : { "type" : "string", "examples" : [ "PDB" ], "description" : "Code identifying the individual, organization or program that\n assigned the feature.", "rcsb_description" : [ { "text" : "Code identifying the individual, organization or program that\n assigned the feature.", "context" : "dictionary" }, { "text" : "Feature Source", "context" : "brief" } ] }, "type" : { "type" : "string", "enum" : [ "HAS_COVALENT_LINKAGE", "HAS_METAL_COORDINATION_LINKAGE", "MODELED_ATOMS", "MOGUL_ANGLE_OUTLIER", "MOGUL_ANGLE_OUTLIERS", "MOGUL_BOND_OUTLIER", "MOGUL_BOND_OUTLIERS", "MOGUL_RING_OUTLIERS", "MOGUL_TORSION_OUTLIERS", "RSCC_OUTLIER", "RSRZ_OUTLIER", "STEREO_OUTLIER", "STEREO_OUTLIERS" ], "examples" : [ "RSRZ_OUTLIER", "MOGUL_BOND_OUTLIER" ], "description" : "A type or category of the feature.", "rcsb_enum_annotated" : [ { "value" : "HAS_COVALENT_LINKAGE", "detail" : "Has a covalent attachment" }, { "value" : "HAS_METAL_COORDINATION_LINKAGE", "detail" : "Has a metal coordination attachment" }, { "value" : "MODELED_ATOMS", "detail" : "Number of modeled atoms" }, { "value" : "MOGUL_ANGLE_OUTLIER", "detail" : "Mogul bond angle outlier" }, { "value" : "MOGUL_ANGLE_OUTLIERS", "detail" : "Number of angle outliers as reported by MOGUL" }, { "value" : "MOGUL_BOND_OUTLIER", "detail" : "Mogul bond distance outlier" }, { "value" : "MOGUL_BOND_OUTLIERS", "detail" : "Number of bond outliers as reported by MOGUL" }, { "value" : "MOGUL_RING_OUTLIERS", "detail" : "Number of ring outliers as reported by MOGUL" }, { "value" : "MOGUL_TORSION_OUTLIERS", "detail" : "Number of torsion outliers as reported by MOGUL" }, { "value" : "RSCC_OUTLIER", "detail" : "Real space density correlation value < 0.65" }, { "value" : "RSRZ_OUTLIER", "detail" : "Real space R-value Z score > 2" }, { "value" : "STEREO_OUTLIER", "detail" : "Stereochemical/chirality outlier" }, { "value" : "STEREO_OUTLIERS", "detail" : "Number of stereo outliers" } ], "rcsb_description" : [ { "text" : "A type or category of the feature.", "context" : "dictionary" }, { "text" : "Feature Type", "context" : "brief" } ] }, "feature_value" : { "type" : "array", "items" : { "type" : "object", "properties" : { "comp_id" : { "type" : "string", "examples" : [ "ATP,", "STN" ], "description" : "The chemical component identifier for the instance of the feature value.", "rcsb_description" : [ { "text" : "The chemical component identifier for the instance of the feature value.", "context" : "dictionary" } ] }, "details" : { "type" : "string", "examples" : [ "C1,C2", "C1,C2,C3" ], "description" : "Specific details about the feature.", "rcsb_description" : [ { "text" : "Specific details about the feature.", "context" : "dictionary" } ] }, "reference" : { "type" : "number", "examples" : [ 5.0, 0.25 ], "description" : "The reference value of the feature.", "rcsb_description" : [ { "text" : "The reference value of the feature.", "context" : "dictionary" } ] }, "reported" : { "type" : "number", "examples" : [ 5.0, 0.25 ], "description" : "The reported value of the feature.", "rcsb_description" : [ { "text" : "The reported value of the feature.", "context" : "dictionary" } ] }, "uncertainty_estimate" : { "type" : "number", "examples" : [ 1.0, -1.5 ], "description" : "The estimated uncertainty of the reported feature value.", "rcsb_description" : [ { "text" : "The estimated uncertainty of the reported feature value.", "context" : "dictionary" } ] }, "uncertainty_estimate_type" : { "type" : "string", "enum" : [ "Z-Score" ], "examples" : [ "Z-score" ], "description" : "The type of estimated uncertainty for the reported feature value.", "rcsb_enum_annotated" : [ { "value" : "Z-Score", "detail" : "Number of standard deviation units from the reference distribution mean" } ], "rcsb_description" : [ { "text" : "The type of estimated uncertainty for the reported feature value.", "context" : "dictionary" } ] } }, "additionalProperties" : false }, "uniqueItems" : false }, "additional_properties" : { "type" : "array", "items" : { "type" : "object", "properties" : { "name" : { "type" : "string", "examples" : [ "bond_distance", "bond_angle" ], "description" : "The additional property name.", "rcsb_description" : [ { "text" : "The additional property name.", "context" : "dictionary" } ] }, "values" : { "type" : "array", "items" : { "anyOf" : [ { "type" : "string" }, { "type" : "integer" }, { "type" : "number" } ], "examples" : [ "2.54", "300" ], "description" : "The value(s) of the additional property.", "rcsb_description" : [ { "text" : "The value(s) of the additional property.", "context" : "dictionary" } ] }, "uniqueItems" : false } }, "additionalProperties" : false }, "uniqueItems" : false } }, "additionalProperties" : false, "required" : [ "ordinal" ] }, "minItems" : 1, "uniqueItems" : true }, "rcsb_nonpolymer_instance_feature_summary" : { "type" : "array", "items" : { "type" : "object", "properties" : { "comp_id" : { "type" : "string", "description" : "Component identifier for non-polymer entity instance.", "rcsb_description" : [ { "text" : "Component identifier for non-polymer entity instance.", "context" : "dictionary" } ] }, "count" : { "type" : "integer", "description" : "The feature count.", "rcsb_description" : [ { "text" : "The feature count.", "context" : "dictionary" } ] }, "coverage" : { "type" : "number", "examples" : [ 0.5, 0.95 ], "description" : "The fractional feature coverage relative to the full entity sequence.", "rcsb_description" : [ { "text" : "The fractional feature coverage relative to the full entity sequence.", "context" : "dictionary" } ] }, "maximum_length" : { "type" : "integer", "description" : "The maximum feature length.", "rcsb_description" : [ { "text" : "The maximum feature length.", "context" : "dictionary" } ] }, "maximum_value" : { "type" : "number", "examples" : [ 1.012, 0.813 ], "description" : "The maximum feature value.", "rcsb_description" : [ { "text" : "The maximum feature value.", "context" : "dictionary" } ] }, "minimum_length" : { "type" : "integer", "description" : "The minimum feature length.", "rcsb_description" : [ { "text" : "The minimum feature length.", "context" : "dictionary" } ] }, "minimum_value" : { "type" : "number", "examples" : [ 0.012, 0.00132 ], "description" : "The minimum feature value.", "rcsb_description" : [ { "text" : "The minimum feature value.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "enum" : [ "HAS_COVALENT_LINKAGE", "HAS_METAL_COORDINATION_LINKAGE", "MODELED_ATOMS", "MOGUL_ANGLE_OUTLIER", "MOGUL_ANGLE_OUTLIERS", "MOGUL_BOND_OUTLIER", "MOGUL_BOND_OUTLIERS", "MOGUL_RING_OUTLIERS", "MOGUL_TORSION_OUTLIERS", "RSCC_OUTLIER", "RSRZ_OUTLIER", "STEREO_OUTLIER", "STEREO_OUTLIERS" ], "examples" : [ "RSRZ_OUTLIER", "MOGUL_BOND_OUTLIER" ], "description" : "Type or category of the feature.", "rcsb_enum_annotated" : [ { "value" : "HAS_COVALENT_LINKAGE", "detail" : "Has a covalent attachment" }, { "value" : "HAS_METAL_COORDINATION_LINKAGE", "detail" : "Has a metal coordination attachment" }, { "value" : "MODELED_ATOMS", "detail" : "Number of modeled atoms" }, { "value" : "MOGUL_ANGLE_OUTLIER", "detail" : "Mogul bond angle outlier" }, { "value" : "MOGUL_ANGLE_OUTLIERS", "detail" : "Number of angle outliers as reported by MOGUL" }, { "value" : "MOGUL_BOND_OUTLIER", "detail" : "Mogul bond distance outlier" }, { "value" : "MOGUL_BOND_OUTLIERS", "detail" : "Number of bond outliers as reported by MOGUL" }, { "value" : "MOGUL_RING_OUTLIERS", "detail" : "Number of ring outliers as reported by MOGUL" }, { "value" : "MOGUL_TORSION_OUTLIERS", "detail" : "Number of torsion outliers as reported by MOGUL" }, { "value" : "RSCC_OUTLIER", "detail" : "Real space density correlation value < 0.65" }, { "value" : "RSRZ_OUTLIER", "detail" : "Real space R-value Z score > 2" }, { "value" : "STEREO_OUTLIER", "detail" : "Stereochemical/chirality outlier" }, { "value" : "STEREO_OUTLIERS", "detail" : "Number of stereo outliers" } ], "rcsb_description" : [ { "text" : "Type or category of the feature.", "context" : "dictionary" } ] } }, "additionalProperties" : false }, "minItems" : 1, "uniqueItems" : true }, "rcsb_nonpolymer_instance_validation_score" : { "type" : "array", "items" : { "type" : "object", "properties" : { "Q_score" : { "type" : "number", "examples" : [ 0.528, 0.712 ], "description" : "The Q-score for the non-polymer instance.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The Q-score for the non-polymer instance.", "context" : "dictionary" }, { "text" : "Ligand Q-Score", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Nonpolymer Molecular Features", "priority_order" : 20 } ], "rcsb_current_maximum_value" : 0.985, "rcsb_current_minimum_value" : -0.763 }, "RSCC" : { "type" : "number", "examples" : [ 0.9, 0.55 ], "description" : "The real space correlation coefficient (RSCC) for the non-polymer entity instance.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The real space correlation coefficient (RSCC) for the non-polymer entity instance.", "context" : "dictionary" }, { "text" : "Real Space Correlation Coefficient", "context" : "brief" } ], "rcsb_current_maximum_value" : 1.0, "rcsb_current_minimum_value" : -1.0 }, "RSR" : { "type" : "number", "examples" : [ 0.15, 0.35 ], "description" : "The real space R-value (RSR) for the non-polymer entity instance.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The real space R-value (RSR) for the non-polymer entity instance.", "context" : "dictionary" }, { "text" : "Real Space R-value (RSR)", "context" : "brief" } ], "rcsb_current_maximum_value" : 5.267, "rcsb_current_minimum_value" : 0.0 }, "alt_id" : { "type" : "string", "description" : "Alternate conformer identifier for the non-polymer entity instance.", "rcsb_description" : [ { "text" : "Alternate conformer identifier for the non-polymer entity instance.", "context" : "dictionary" } ] }, "average_occupancy" : { "type" : "number", "examples" : [ 1.0, 0.83 ], "description" : "The average heavy atom occupancy for coordinate records for the non-polymer entity instance.", "rcsb_description" : [ { "text" : "The average heavy atom occupancy for coordinate records for the non-polymer entity instance.", "context" : "dictionary" } ] }, "completeness" : { "type" : "number", "examples" : [ 1.0, 0.83 ], "description" : "The reported fraction of atomic coordinate records for the non-polymer entity instance.", "rcsb_description" : [ { "text" : "The reported fraction of atomic coordinate records for the non-polymer entity instance.", "context" : "dictionary" } ] }, "intermolecular_clashes" : { "type" : "integer", "description" : "The number of intermolecular MolProbity clashes cacluated for reported atomic coordinate records.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of intermolecular MolProbity clashes cacluated for reported atomic coordinate records.", "context" : "dictionary" }, { "text" : "Number of Intermolecular Vlashes", "context" : "brief" } ], "rcsb_current_maximum_value" : 168.0, "rcsb_current_minimum_value" : 0.0 }, "is_best_instance" : { "type" : "string", "enum" : [ "N", "Y" ], "examples" : [ "Y", "N" ], "description" : "This molecular instance is ranked as the best quality instance of this nonpolymer entity.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "N", "detail" : "The molecular instance is not ranked as best instance of the molecule" }, { "value" : "Y", "detail" : "The molecular instance is ranked as the best instance of the molecule" } ], "rcsb_description" : [ { "text" : "This molecular instance is ranked as the best quality instance of this nonpolymer entity.", "context" : "dictionary" }, { "text" : "Highest Ranking Ligand Instance in Structure", "context" : "brief" } ] }, "is_subject_of_investigation" : { "type" : "string", "enum" : [ "N", "Y" ], "examples" : [ "Y", "N" ], "description" : "This molecular entity is identified as the subject of the current study.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "N", "detail" : "Molecule instance is not the subject of the current investigation" }, { "value" : "Y", "detail" : "Molecule instance is the subject of the current investigation" } ], "rcsb_description" : [ { "text" : "This molecular entity is identified as the subject of the current study.", "context" : "dictionary" }, { "text" : "Ligand Identified as Subject of Investigation", "context" : "brief" } ] }, "is_subject_of_investigation_provenance" : { "type" : "string", "enum" : [ "Author", "RCSB" ], "examples" : [ "Author", "RCSB" ], "description" : "The provenance for the selection of the molecular entity identified as the subject of the current study.", "rcsb_enum_annotated" : [ { "value" : "Author", "detail" : "The entry author is the source of the selection of the molecular entity of interest" }, { "value" : "RCSB", "detail" : "RCSB is the source of the selection of the molecular entity of interest" } ], "rcsb_description" : [ { "text" : "The provenance for the selection of the molecular entity identified as the subject of the current study.", "context" : "dictionary" } ] }, "mogul_angle_outliers" : { "type" : "integer", "description" : "Number of bond angle outliers obtained from a CCDC Mogul survey of bond angles in the CSD small\n molecule crystal structure database. Outliers are defined as bond angles that have a Z-score\n less than -2 or greater than 2.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Number of bond angle outliers obtained from a CCDC Mogul survey of bond angles in the CSD small\n molecule crystal structure database. Outliers are defined as bond angles that have a Z-score\n less than -2 or greater than 2.", "context" : "dictionary" }, { "text" : "Number of Bond Angle Outliers (|Z|>2)", "context" : "brief" } ], "rcsb_current_maximum_value" : 76.0, "rcsb_current_minimum_value" : 0.0 }, "mogul_angles_RMSZ" : { "type" : "number", "examples" : [ 7.22, 1.16 ], "description" : "The root-mean-square value of the Z-scores of bond angles for the non-polymer instance in degrees\nobtained from a CCDC Mogul survey of bond angles in the CSD small molecule crystal structure database.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "degrees", "rcsb_description" : [ { "text" : "The root-mean-square value of the Z-scores of bond angles for the non-polymer instance in degrees\nobtained from a CCDC Mogul survey of bond angles in the CSD small molecule crystal structure database.", "context" : "dictionary" }, { "text" : "Root-Mean-Aquare Value of the Z-scores for Bond Angles", "context" : "brief" } ], "rcsb_current_maximum_value" : 50.87, "rcsb_current_minimum_value" : 0.0 }, "mogul_bond_outliers" : { "type" : "integer", "description" : "Number of bond distance outliers obtained from a CCDC Mogul survey of bond lengths in the CSD small\n molecule crystal structure database. Outliers are defined as bond distances that have a Z-score\n less than -2 or greater than 2.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Number of bond distance outliers obtained from a CCDC Mogul survey of bond lengths in the CSD small\n molecule crystal structure database. Outliers are defined as bond distances that have a Z-score\n less than -2 or greater than 2.", "context" : "dictionary" }, { "text" : "Number of Bond Distance Outliers (|Z|>2)", "context" : "brief" } ], "rcsb_current_maximum_value" : 75.0, "rcsb_current_minimum_value" : 0.0 }, "mogul_bonds_RMSZ" : { "type" : "number", "examples" : [ 0.69, 1.32 ], "description" : "The root-mean-square value of the Z-scores of bond lengths for the nonpolymer instance in Angstroms\nobtained from a CCDC Mogul survey of bond lengths in the CSD small molecule crystal structure database.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "The root-mean-square value of the Z-scores of bond lengths for the nonpolymer instance in Angstroms\nobtained from a CCDC Mogul survey of bond lengths in the CSD small molecule crystal structure database.", "context" : "dictionary" }, { "text" : "Root-Mean-Aquare Value of the Z-scores for Bond Distances", "context" : "brief" } ], "rcsb_current_maximum_value" : 1047.39, "rcsb_current_minimum_value" : 0.0 }, "natoms_eds" : { "type" : "integer", "description" : "The number of atoms in the non-polymer instance returned by the EDS software.", "rcsb_description" : [ { "text" : "The number of atoms in the non-polymer instance returned by the EDS software.", "context" : "dictionary" } ] }, "num_mogul_angles_RMSZ" : { "type" : "integer", "description" : "The number of bond angles compared to \"standard geometry\" made using the Mogul program.", "rcsb_description" : [ { "text" : "The number of bond angles compared to \"standard geometry\" made using the Mogul program.", "context" : "dictionary" } ] }, "num_mogul_bonds_RMSZ" : { "type" : "integer", "description" : "The number of bond lengths compared to \"standard geometry\" made using the Mogul program.", "rcsb_description" : [ { "text" : "The number of bond lengths compared to \"standard geometry\" made using the Mogul program.", "context" : "dictionary" } ] }, "ranking_model_fit" : { "type" : "number", "examples" : [ 0.9, 0.55 ], "description" : "The ranking of the model fit score component.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The ranking of the model fit score component.", "context" : "dictionary" }, { "text" : "Experimental Model Fit Ranking", "context" : "brief" } ], "rcsb_current_maximum_value" : 1.0, "rcsb_current_minimum_value" : 0.0 }, "ranking_model_geometry" : { "type" : "number", "examples" : [ 0.9, 0.55 ], "description" : "The ranking of the model geometry score component.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The ranking of the model geometry score component.", "context" : "dictionary" }, { "text" : "Model Geometry Ranking", "context" : "brief" } ], "rcsb_current_maximum_value" : 1.0, "rcsb_current_minimum_value" : 0.0 }, "score_model_fit" : { "type" : "number", "examples" : [ -1.5, -0.25 ], "description" : "The value of the model fit score component.", "rcsb_description" : [ { "text" : "The value of the model fit score component.", "context" : "dictionary" } ] }, "score_model_geometry" : { "type" : "number", "examples" : [ -0.79, 0.025 ], "description" : "The value of the model geometry score component.", "rcsb_description" : [ { "text" : "The value of the model geometry score component.", "context" : "dictionary" } ] }, "stereo_outliers" : { "type" : "integer", "description" : "Number of stereochemical/chirality errors.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Number of stereochemical/chirality errors.", "context" : "dictionary" }, { "text" : "Number of Chirality Errors", "context" : "brief" } ], "rcsb_current_maximum_value" : 34.0, "rcsb_current_minimum_value" : 0.0 }, "type" : { "type" : "string", "enum" : [ "RCSB_LIGAND_QUALITY_SCORE_2021" ], "examples" : [ "RCSB_LIGAND_QUALITY_2021" ], "description" : "Score type.", "rcsb_description" : [ { "text" : "Score type.", "context" : "dictionary" } ] } }, "additionalProperties" : false }, "minItems" : 1, "uniqueItems" : true }, "rcsb_nonpolymer_struct_conn" : { "type" : "array", "items" : { "type" : "object", "properties" : { "connect_type" : { "type" : "string", "enum" : [ "covalent bond", "disulfide bridge", "hydrogen bond", "ionic interaction", "metal coordination", "mismatched base pairs" ], "description" : "The connection type.", "rcsb_description" : [ { "text" : "The connection type.", "context" : "dictionary" } ] }, "description" : { "type" : "string", "examples" : [ "Watson-Crick base pair" ], "description" : "A description of special details of the connection.", "rcsb_description" : [ { "text" : "A description of special details of the connection.", "context" : "dictionary" } ] }, "dist_value" : { "type" : "number", "description" : "Distance value for this contact.", "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "Distance value for this contact.", "context" : "dictionary" } ] }, "id" : { "type" : "string", "description" : "The value of _rcsb_nonpolymer_struct_conn.id is an identifier for connection.\n\n Note that this item need not be a number; it can be any unique\n identifier.", "rcsb_description" : [ { "text" : "The value of _rcsb_nonpolymer_struct_conn.id is an identifier for connection.\n\n Note that this item need not be a number; it can be any unique\n identifier.", "context" : "dictionary" } ] }, "ordinal_id" : { "type" : "integer", "description" : "The value of _rcsb_nonpolymer_struct_conn.id must uniquely identify a record in\n the rcsb_nonpolymer_struct_conn list.", "rcsb_description" : [ { "text" : "The value of _rcsb_nonpolymer_struct_conn.id must uniquely identify a record in\n the rcsb_nonpolymer_struct_conn list.", "context" : "dictionary" } ] }, "role" : { "type" : "string", "enum" : [ "C-Mannosylation", "N-Glycosylation", "O-Glycosylation", "S-Glycosylation" ], "examples" : [ "N-Glycosylation", "O-Glycosylation" ], "description" : "The chemical or structural role of the interaction", "rcsb_description" : [ { "text" : "The chemical or structural role of the interaction", "context" : "dictionary" } ] }, "value_order" : { "type" : "string", "enum" : [ "doub", "quad", "sing", "trip" ], "description" : "The chemical bond order associated with the specified atoms in\n this contact.", "rcsb_enum_annotated" : [ { "value" : "doub", "detail" : "double bond" }, { "value" : "quad", "detail" : "quadruple bond" }, { "value" : "sing", "detail" : "single bond" }, { "value" : "trip", "detail" : "triple bond" } ], "rcsb_description" : [ { "text" : "The chemical bond order associated with the specified atoms in\n this contact.", "context" : "dictionary" } ] }, "connect_target" : { "type" : "object", "properties" : { "auth_asym_id" : { "type" : "string", "description" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.auth_asym_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.auth_asym_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "auth_seq_id" : { "type" : "string", "description" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.auth_seq_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.auth_seq_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "label_alt_id" : { "type" : "string", "description" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.label_alt_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.label_alt_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "label_asym_id" : { "type" : "string", "description" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.label_asym_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.label_asym_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "label_atom_id" : { "type" : "string", "description" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.label_atom_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.label_atom_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "label_comp_id" : { "type" : "string", "description" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.label_comp_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.label_comp_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "label_seq_id" : { "type" : "integer", "description" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.connect_target_label_seq_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.connect_target_label_seq_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "symmetry" : { "type" : "string", "examples" : [ "1_555", "7_645" ], "description" : "Describes the symmetry operation that should be applied to the\n atom set specified by _rcsb_nonpolymer_struct_conn.label* to generate the\n target of the structure connection.", "rcsb_description" : [ { "text" : "Describes the symmetry operation that should be applied to the\n atom set specified by _rcsb_nonpolymer_struct_conn.label* to generate the\n target of the structure connection.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "label_asym_id", "label_comp_id" ] }, "connect_partner" : { "type" : "object", "properties" : { "label_alt_id" : { "type" : "string", "description" : "A component of the identifier for the partner in the structure\n connection.\n\n This data item is a pointer to _atom_site.label_alt_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the partner in the structure\n connection.\n\n This data item is a pointer to _atom_site.label_alt_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "label_asym_id" : { "type" : "string", "description" : "A component of the identifier for the partner in the structure\n connection.\n\n This data item is a pointer to _atom_site.label_asym_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the partner in the structure\n connection.\n\n This data item is a pointer to _atom_site.label_asym_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "label_atom_id" : { "type" : "string", "description" : "A component of the identifier for the partner in the structure\n connection.\n\n This data item is a pointer to _chem_comp_atom.atom_id in the\n CHEM_COMP_ATOM category.", "rcsb_description" : [ { "text" : "A component of the identifier for the partner in the structure\n connection.\n\n This data item is a pointer to _chem_comp_atom.atom_id in the\n CHEM_COMP_ATOM category.", "context" : "dictionary" } ] }, "label_comp_id" : { "type" : "string", "description" : "A component of the identifier for the partner in the structure\n connection.\n\n This data item is a pointer to _atom_site.label_comp_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the partner in the structure\n connection.\n\n This data item is a pointer to _atom_site.label_comp_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "label_seq_id" : { "type" : "integer", "description" : "A component of the identifier for the partner in the structure\n connection.\n\n This data item is a pointer to _atom_site.label_seq_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the partner in the structure\n connection.\n\n This data item is a pointer to _atom_site.label_seq_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "symmetry" : { "type" : "string", "examples" : [ "1_555", "7_645" ], "description" : "Describes the symmetry operation that should be applied to the\n atom set specified by _rcsb_nonpolymer_struct_conn.connect_partner_label* to generate the\n partner in the structure connection.", "rcsb_description" : [ { "text" : "Describes the symmetry operation that should be applied to the\n atom set specified by _rcsb_nonpolymer_struct_conn.connect_partner_label* to generate the\n partner in the structure connection.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "label_asym_id", "label_comp_id" ] } }, "additionalProperties" : false, "required" : [ "ordinal_id" ] }, "minItems" : 1, "uniqueItems" : true }, "rcsb_target_neighbors" : { "type" : "array", "items" : { "type" : "object", "properties" : { "alt_id" : { "type" : "string", "description" : "Alternate conformer identifier for the non-polymer entity instance.", "rcsb_description" : [ { "text" : "Alternate conformer identifier for the non-polymer entity instance.", "context" : "dictionary" } ] }, "atom_id" : { "type" : "string", "examples" : [ "O1", "N1", "C1" ], "description" : "The atom identifier for the non-polymer entity instance.", "rcsb_description" : [ { "text" : "The atom identifier for the non-polymer entity instance.", "context" : "dictionary" } ] }, "comp_id" : { "type" : "string", "description" : "Component identifier for the non-polymer entity instance.", "rcsb_description" : [ { "text" : "Component identifier for the non-polymer entity instance.", "context" : "dictionary" } ] }, "distance" : { "type" : "number", "description" : "Distance value for this target interaction.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "Distance value for this target interaction.", "context" : "dictionary" }, { "text" : "Target Neighbor Distance", "context" : "brief" } ], "rcsb_current_maximum_value" : 5.0, "rcsb_current_minimum_value" : 0.0 }, "target_asym_id" : { "type" : "string", "examples" : [ "A", "B" ], "description" : "The entity instance identifier for the target of interaction.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The entity instance identifier for the target of interaction.", "context" : "dictionary" }, { "text" : "Target Entity Instance Identifer", "context" : "brief" } ] }, "target_atom_id" : { "type" : "string", "examples" : [ "OG", "OE1", "CD1" ], "description" : "The atom identifier for the target of interaction.", "rcsb_description" : [ { "text" : "The atom identifier for the target of interaction.", "context" : "dictionary" } ] }, "target_auth_seq_id" : { "type" : "integer", "description" : "The author residue index for the target of interaction.", "rcsb_description" : [ { "text" : "The author residue index for the target of interaction.", "context" : "dictionary" } ] }, "target_comp_id" : { "type" : "string", "examples" : [ "ASN", "TRP", "SER" ], "description" : "The chemical component identifier for the target of interaction.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The chemical component identifier for the target of interaction.", "context" : "dictionary" }, { "text" : "Target Residue Identifier", "context" : "brief" } ] }, "target_entity_id" : { "type" : "string", "examples" : [ "1", "2" ], "description" : "The entity identifier for the target of interaction.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The entity identifier for the target of interaction.", "context" : "dictionary" }, { "text" : "Target Entity Identifier", "context" : "brief" } ] }, "target_is_bound" : { "type" : "string", "enum" : [ "N", "Y" ], "examples" : [ "Y", "N" ], "description" : "A flag to indicate the nature of the target interaction is covalent or metal-coordination.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "N", "detail" : "The target is not bound" }, { "value" : "Y", "detail" : "The target is bound through a covalent or metal-coordination interaction" } ], "rcsb_description" : [ { "text" : "A flag to indicate the nature of the target interaction is covalent or metal-coordination.", "context" : "dictionary" }, { "text" : "Target is Bound to Ligand", "context" : "brief" } ] }, "target_model_id" : { "type" : "integer", "description" : "Model identifier for the target of interaction.", "rcsb_description" : [ { "text" : "Model identifier for the target of interaction.", "context" : "dictionary" } ] }, "target_seq_id" : { "type" : "integer", "description" : "The sequence position for the target of interaction.", "rcsb_description" : [ { "text" : "The sequence position for the target of interaction.", "context" : "dictionary" } ] } }, "additionalProperties" : false }, "minItems" : 1, "uniqueItems" : true }, "struct_asym" : { "type" : "object", "properties" : { "pdbx_PDB_id" : { "type" : "string", "examples" : [ "1ABC" ], "description" : "This data item is a pointer to _atom_site.pdbx_PDB_strand_id the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "This data item is a pointer to _atom_site.pdbx_PDB_strand_id the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "pdbx_alt_id" : { "type" : "string", "description" : "This data item is a pointer to _atom_site.ndb_alias_strand_id the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "This data item is a pointer to _atom_site.ndb_alias_strand_id the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "pdbx_order" : { "type" : "integer", "description" : "This data item gives the order of the structural elements in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "This data item gives the order of the structural elements in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "pdbx_type" : { "type" : "string", "enum" : [ "ATOMN", "ATOMP", "ATOMS", "HETAC", "HETAD", "HETAI", "HETAIN", "HETAS", "HETIC" ], "description" : "This data item describes the general type of the structural elements\n in the ATOM_SITE category.", "rcsb_enum_annotated" : [ { "value" : "ATOMN", "detail" : "nucleic acid" }, { "value" : "ATOMP", "detail" : "protein" }, { "value" : "ATOMS", "detail" : "sugar" }, { "value" : "HETAC", "detail" : "coenzyme" }, { "value" : "HETAD", "detail" : "drug" }, { "value" : "HETAI", "detail" : "ion" }, { "value" : "HETAIN", "detail" : "inhibitor" }, { "value" : "HETAS", "detail" : "solvent" }, { "value" : "HETIC", "detail" : "ion complex" } ], "rcsb_description" : [ { "text" : "This data item describes the general type of the structural elements\n in the ATOM_SITE category.", "context" : "dictionary" } ] } }, "additionalProperties" : false }, "rcsb_uniprot_container_identifiers" : { "type" : "object", "properties" : { "uniprot_id" : { "type" : "string", "description" : "Primary accession number of a given UniProtKB entry." }, "reference_sequence_identifiers" : { "type" : "array", "items" : { "type" : "object", "properties" : { "database_accession" : { "type" : "string", "description" : "Reference database accession code", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 20, "rcsb_description" : [ { "text" : "Reference database accession code", "context" : "dictionary" }, { "text" : "Database Accession (Reference Sequence Identifiers)", "context" : "brief" } ] }, "database_isoform" : { "type" : "string", "description" : "Reference database identifier for the sequence isoform", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Reference database identifier for the sequence isoform", "context" : "dictionary" }, { "text" : "Database Isoform (Reference Sequence Identifiers)", "context" : "brief" } ] }, "database_name" : { "type" : "string", "description" : "Reference database name", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Reference database name", "context" : "dictionary" }, { "text" : "Database Name (Reference Sequence Identifiers)", "context" : "brief" } ] }, "provenance_source" : { "type" : "string", "description" : "Source of the reference database assignment", "rcsb_description" : [ { "text" : "Source of the reference database assignment", "context" : "dictionary" } ] } }, "additionalProperties" : false }, "uniqueItems" : false, "rcsb_nested_indexing" : true } }, "additionalProperties" : false }, "rcsb_uniprot_accession" : { "type" : "array", "items" : { "type" : "string" }, "description" : "List of UniProtKB accession numbers where original accession numbers are retained as ‘secondary’ accession numbers." }, "rcsb_uniprot_entry_name" : { "type" : "array", "items" : { "type" : "string" }, "description" : "A list of unique identifiers (former IDs), often containing biologically relevant information." }, "rcsb_uniprot_keyword" : { "type" : "array", "items" : { "type" : "object", "properties" : { "id" : { "type" : "string", "examples" : [ "KW-0275", "KW-0597" ], "description" : "A unique keyword identifier." }, "value" : { "type" : "string", "examples" : [ "Lipid metabolism", "Phosphoprotein", "Fatty acid biosynthesis" ], "description" : "Human-readable keyword term." } }, "additionalProperties" : false }, "description" : "Keywords constitute a controlled vocabulary that summarises the content of a UniProtKB entry." }, "rcsb_uniprot_protein" : { "type" : "object", "properties" : { "sequence" : { "type" : "string", "description" : "Protein sequence data for canonical protein sequence." }, "name" : { "type" : "object", "required" : [ "value", "provenance_code" ], "properties" : { "value" : { "type" : "string", "description" : "Name that allows to unambiguously identify a protein.", "rcsb_search_context" : [ "exact-match", "full-text", "suggest" ], "examples" : [ "Hemoglobin alpha" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "UniProt Molecule Name", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "ID(s) and Keywords", "priority_order" : 35 } ] }, "provenance_code" : { "type" : "string", "description" : "Historical record of the data attribute." } }, "additionalProperties" : false }, "function" : { "type" : "object", "properties" : { "details" : { "type" : "string", "description" : "General function(s) of a protein." }, "provenance_code" : { "type" : "string", "description" : "Historical record of the data attribute." } } }, "gene" : { "type" : "array", "items" : { "type" : "object", "properties" : { "name" : { "type" : "array", "items" : { "type" : "object", "properties" : { "type" : { "enum" : [ "PRIMARY", "SYNONYM", "ORDERED_LOCUS", "ORF" ], "type" : "string" }, "value" : { "type" : "string" } } } } }, "additionalProperties" : false, "description" : "The name(s) of the gene(s) that code for the protein sequence(s) described in the entry." } }, "source_organism" : { "type" : "object", "required" : [ "scientific_name", "provenance_code" ], "properties" : { "scientific_name" : { "type" : "string", "description" : "The scientific name of the organism in which a protein occurs." }, "taxonomy_id" : { "type" : "integer", "description" : "NCBI Taxonomy identifier for the organism in which a protein occurs." }, "provenance_code" : { "type" : "string", "description" : "Historical record of the data attribute." } }, "additionalProperties" : false, "description" : "Taxonomy information on the organism that is the source of the protein sequence." }, "ec" : { "type" : "array", "items" : { "type" : "object", "properties" : { "number" : { "type" : "string" }, "provenance_code" : { "type" : "string", "description" : "Historical record of the data attribute." } }, "additionalProperties" : false, "description" : "Enzyme Commission (EC) number(s)." }, "minItems" : 1, "uniqueItems" : true } }, "additionalProperties" : false }, "rcsb_uniprot_feature" : { "type" : "array", "items" : { "type" : "object", "properties" : { "assignment_version" : { "type" : "string", "description" : "Identifies the version of the feature assignment." }, "description" : { "type" : "string", "description" : "A description for the feature." }, "feature_id" : { "type" : "string", "description" : "An identifier for the feature." }, "name" : { "type" : "string", "description" : "A name for the feature." }, "provenance_source" : { "type" : "string", "description" : "Code identifying the individual, organization or program that\n assigned the feature." }, "reference_scheme" : { "type" : "string", "description" : "Code residue coordinate system for the assigned feature." }, "type" : { "type" : "string", "enum" : [ "ACTIVE_SITE", "BINDING_SITE", "CALCIUM_BINDING_REGION", "CHAIN", "COMPOSITIONALLY_BIASED_REGION", "CROSS_LINK", "DNA_BINDING_REGION", "DOMAIN", "GLYCOSYLATION_SITE", "INITIATOR_METHIONINE", "LIPID_MOIETY_BINDING_REGION", "METAL_ION_BINDING_SITE", "MODIFIED_RESIDUE", "MUTAGENESIS_SITE", "NON_CONSECUTIVE_RESIDUES", "NON_TERMINAL_RESIDUE", "NUCLEOTIDE_PHOSPHATE_BINDING_REGION", "PEPTIDE", "PROPEPTIDE", "REGION_OF_INTEREST", "REPEAT", "NON_STANDARD_AMINO_ACID", "SEQUENCE_CONFLICT", "SEQUENCE_VARIANT", "SHORT_SEQUENCE_MOTIF", "SIGNAL_PEPTIDE", "SITE", "SPLICE_VARIANT", "TOPOLOGICAL_DOMAIN", "TRANSIT_PEPTIDE", "TRANSMEMBRANE_REGION", "UNSURE_RESIDUE", "ZINC_FINGER_REGION", "INTRAMEMBRANE_REGION" ], "rcsb_enum_annotated" : [ { "value" : "ACTIVE_SITE", "name" : "Active site", "detail" : "Amino acid(s) directly involved in the activity of an enzyme" }, { "value" : "BINDING_SITE", "name" : "Binding site", "detail" : "Binding site for any chemical group (co-enzyme, prosthetic group, etc.)" }, { "value" : "CALCIUM_BINDING_REGION", "name" : "Calcium binding", "detail" : "Position(s) of calcium binding region(s) within the protein (e.g. EF-hand)" }, { "value" : "CHAIN", "name" : "Chain", "detail" : "Extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage" }, { "value" : "COMPOSITIONALLY_BIASED_REGION", "name" : "Compositional bias", "detail" : "Homopolymeric stretches and large regions of compositional bias in the protein" }, { "value" : "CROSS_LINK", "name" : "Cross-link", "detail" : "Residues participating in covalent linkage(s) between proteins" }, { "value" : "DNA_BINDING_REGION", "name" : "DNA binding", "detail" : "Experimentally determined and conserved DNA-binding domains defined by the InterPro resources PROSITE, Pfam and SMART (the AP2/ERF domain, the ETS domain, the Fork-Head domain, etc.)" }, { "value" : "DOMAIN", "name" : "Domain", "detail" : "Modular protein domains which are self-stabilizing and fold independently of the rest of the protein chain" }, { "value" : "GLYCOSYLATION_SITE", "name" : "Glycosylation", "detail" : "Covalently attached glycan group(s) (mono-, di-, or polysaccharide)" }, { "value" : "INITIATOR_METHIONINE", "name" : "Initiator methionine", "detail" : "Cleavage of the initiator methionine from the mature protein" }, { "value" : "LIPID_MOIETY_BINDING_REGION", "name" : "Lipidation", "detail" : "Covalently attached lipid group(s)" }, { "value" : "METAL_ION_BINDING_SITE", "name" : "Metal binding", "detail" : "Binding site for a metal ion" }, { "value" : "MODIFIED_RESIDUE", "name" : "Modified residue", "detail" : "Modified residues excluding lipids, glycans and protein cross-links" }, { "value" : "MUTAGENESIS_SITE", "name" : "Mutagenesis", "detail" : "Site which has been experimentally altered by mutagenesis" }, { "value" : "NON_CONSECUTIVE_RESIDUES", "name" : "Non-adjacent residues", "detail" : "Indicates that two residues in a sequence are not consecutive and that there is an undetermined number of unsequenced residues between them" }, { "value" : "NON_TERMINAL_RESIDUE", "name" : "Non-terminal residue", "detail" : "Indicates that a residue is not the terminal residue of the complete protein (the sequence is incomplete)" }, { "value" : "NUCLEOTIDE_PHOSPHATE_BINDING_REGION", "name" : "Nucleotide binding", "detail" : "Nucleotide phosphate binding region" }, { "value" : "PEPTIDE", "name" : "Peptide", "detail" : "Extent of an active peptide in the mature protein" }, { "value" : "PROPEPTIDE", "name" : "Propeptide", "detail" : "Part of a protein that is cleaved during maturation or activation" }, { "value" : "REGION_OF_INTEREST", "name" : "Region of interest", "detail" : "Region of interest in the sequence (e.g. different regions in multifunctional enzymes or fusion proteins)" }, { "value" : "REPEAT", "name" : "Repeat", "detail" : "Denotes the positions of repeated sequence motifs or repeated domains" }, { "value" : "NON_STANDARD_AMINO_ACID", "name" : "Non-standard residue", "detail" : "Occurrences of non-standard amino acids (selenocysteine and pyrrolysine) in the protein sequence" }, { "value" : "SEQUENCE_CONFLICT", "name" : "Sequence conflict", "detail" : "Description of sequence discrepancies of unknown origin" }, { "value" : "SEQUENCE_VARIANT", "name" : "Natural variant", "detail" : "Description of a natural variant of the protein (polymorphisms, disease-associated mutations, RNA editing events, etc.)" }, { "value" : "SHORT_SEQUENCE_MOTIF", "name" : "Motif", "detail" : "Short (up to 20 amino acids) sequence motif of biological interest" }, { "value" : "SIGNAL_PEPTIDE", "name" : "Signal peptide", "detail" : "Sequence targeting proteins to the secretory pathway or periplasmic space" }, { "value" : "SITE", "name" : "Site", "detail" : "Any interesting single amino acid site on the sequence" }, { "value" : "SPLICE_VARIANT", "name" : "Alternative sequence", "detail" : "Amino acid change(s) producing alternate protein isoforms" }, { "value" : "TOPOLOGICAL_DOMAIN", "name" : "Topological domain", "detail" : "Location of non-membrane regions of membrane-spanning proteins" }, { "value" : "TRANSIT_PEPTIDE", "name" : "Transit peptide", "detail" : "Extent of a transit peptide for organelle targeting" }, { "value" : "TRANSMEMBRANE_REGION", "name" : "Transmembrane", "detail" : "Extent of a membrane-spanning region" }, { "value" : "UNSURE_RESIDUE", "name" : "Sequence uncertainty", "detail" : "Describes region(s) of a sequence for which the authors are unsure about the sequence assignment" }, { "value" : "ZINC_FINGER_REGION", "name" : "Zinc finger", "detail" : "Denotes the position(s) and type(s) of zinc fingers within the protein" }, { "value" : "INTRAMEMBRANE_REGION", "name" : "Intramembrane", "detail" : "Extent of a region located in a membrane without crossing it" } ], "description" : "A type or category of the feature." }, "feature_positions" : { "type" : "array", "items" : { "type" : "object", "properties" : { "beg_comp_id" : { "type" : "string", "description" : "An identifier for the monomer(s) corresponding to the feature assignment." }, "beg_seq_id" : { "type" : "integer", "description" : "An identifier for the monomer at which this segment of the feature begins." }, "end_seq_id" : { "type" : "integer", "description" : "An identifier for the monomer at which this segment of the feature ends." }, "value" : { "type" : "number", "description" : "The value for the feature over this monomer segment." }, "values" : { "type" : "array", "items" : { "type" : "number", "examples" : [ 5, 0.25 ], "description" : "The value(s) for the feature over this monomer segment.", "rcsb_description" : [ { "text" : "The value(s) for the feature over this monomer segment.", "context" : "dictionary" } ] }, "uniqueItems" : false } }, "additionalProperties" : false, "required" : [ "beg_seq_id" ] }, "uniqueItems" : false } }, "additionalProperties" : false }, "minItems" : 1, "uniqueItems" : true }, "rcsb_uniprot_annotation" : { "type" : "array", "items" : { "type" : "object", "properties" : { "annotation_id" : { "type" : "string", "description" : "An identifier for the annotation.", "rcsb_search_context" : [ "exact-match" ], "rcsb_description" : [ { "text" : "An identifier for the annotation.", "context" : "dictionary" }, { "text" : "Identifier", "context" : "brief" } ] }, "assignment_version" : { "type" : "string", "description" : "Identifies the version of the annotation assignment.", "rcsb_description" : [ { "text" : "Identifies the version of the annotation assignment.", "context" : "dictionary" }, { "text" : "Annotation version", "context" : "brief" } ] }, "description" : { "type" : "string", "description" : "A description for the annotation.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "A description for the annotation.", "context" : "dictionary" }, { "text" : "Annotation description", "context" : "brief" } ] }, "name" : { "type" : "string", "description" : "A name for the annotation.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Name", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Polymer Molecular Features", "priority_order" : 108 } ] }, "provenance_source" : { "type" : "string", "description" : "Code identifying the individual, organization or program that\n assigned the annotation.", "rcsb_description" : [ { "text" : "Annotation Source", "context" : "brief" } ] }, "type" : { "type" : "string", "enum" : [ "disease", "phenotype", "GO", "InterPro" ], "description" : "A type or category of the annotation.", "rcsb_search_context" : [ "exact-match" ], "rcsb_enum_annotated" : [ { "value" : "disease", "detail" : "Disease data from OMIM and Disease Ontology represented in Pharos", "name" : "Pharos Disease" }, { "value" : "phenotype", "detail" : "Phenotypic data including mouse phenotypes, mouse/human orthologs and GWAS results represented in IMPC", "name" : "IMPC Phenotype" }, { "value" : "InterPro", "detail" : "InterPro Protein Family", "name" : "InterPro Protein Family" }, { "value" : "GO", "detail" : "Gene Ontology", "name" : "Gene Ontology" } ], "rcsb_description" : [ { "text" : "A type or category of the annotation.", "context" : "dictionary" }, { "text" : "Annotation Type", "context" : "brief" } ] }, "annotation_lineage" : { "type" : "array", "items" : { "type" : "object", "properties" : { "depth" : { "type" : "integer", "description" : "Members of the annotation lineage as parent lineage depth (1-N)", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Lineage Depth", "context" : "brief" } ], "rcsb_current_maximum_value" : 4.0, "rcsb_current_minimum_value" : 1.0 }, "id" : { "type" : "string", "description" : "Members of the annotation lineage as parent class identifiers.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Lineage Identifier", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Polymer Molecular Features", "priority_order" : 111 } ] }, "name" : { "type" : "string", "description" : "Members of the annotation lineage as parent class names.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Lineage Name", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Polymer Molecular Features", "priority_order" : 116 } ] } }, "additionalProperties" : false }, "uniqueItems" : false, "rcsb_nested_indexing" : true }, "additional_properties" : { "type" : "array", "items" : { "type" : "object", "properties" : { "name" : { "type" : "string", "enum" : [ "INTERPRO_TYPE" ], "examples" : [ "INTERPRO_TYPE" ], "description" : "The additional property name", "rcsb_enum_annotated" : [ { "value" : "INTERPRO_TYPE", "detail" : "Describes the type of InterPro annotations: annotations for individual protein families, domains, important sites, etc." } ], "rcsb_description" : [ { "text" : "The additional property name", "context" : "dictionary" } ] }, "values" : { "type" : "array", "items" : { "anyOf" : [ { "type" : "string" }, { "type" : "integer" }, { "type" : "number" } ], "description" : "The value(s) of the additional property", "rcsb_description" : [ { "text" : "The value(s) of the additional property", "context" : "dictionary" } ] }, "uniqueItems" : false } }, "additionalProperties" : false }, "uniqueItems" : false } }, "additionalProperties" : false }, "minItems" : 1, "uniqueItems" : true, "rcsb_nested_indexing" : true, "rcsb_nested_indexing_context" : [ { "category_name" : "annotation_type", "category_path" : "rcsb_uniprot_annotation.type", "context_attributes" : [ { "context_value" : "disease", "attributes" : [ { "examples" : [ "MONDO:0100118", "MONDO:0002051" ], "path" : "rcsb_uniprot_annotation.annotation_lineage.id" }, { "examples" : [ "hepatocellular carcinoma", "tuberculosis" ], "path" : "rcsb_uniprot_annotation.annotation_lineage.name" } ] }, { "context_value" : "phenotype", "attributes" : [ { "examples" : [ "immune system phenotype", "mortality/aging" ], "path" : "rcsb_uniprot_annotation.name" } ] }, { "context_value" : "GO", "attributes" : [ { "examples" : [ "GO:0005575", "GO:0005622" ], "path" : "rcsb_uniprot_annotation.annotation_lineage.id" }, { "examples" : [ "cellular_component", "intracellular" ], "path" : "rcsb_uniprot_annotation.annotation_lineage.name" } ] }, { "context_value" : "InterPro", "attributes" : [ { "examples" : [ "IPR022352", "IPR004825" ], "path" : "rcsb_uniprot_annotation.annotation_lineage.id" }, { "examples" : [ "Insulin family", "Insulin" ], "path" : "rcsb_uniprot_annotation.annotation_lineage.name" } ] } ] } ] }, "rcsb_uniprot_external_reference" : { "type" : "array", "items" : { "type" : "object", "properties" : { "reference_id" : { "type" : "string" }, "reference_name" : { "type" : "string", "enum" : [ "IMPC", "GTEX", "PHAROS" ], "rcsb_search_context" : [ "exact-match" ], "rcsb_enum_annotated" : [ { "value" : "IMPC", "name" : "IMPC", "detail" : "Knockout Mouse Phenotyping Program (IMPC)" }, { "value" : "GTEX", "name" : "GTEx", "detail" : "Genotype-Tissue Expression (GTEx) Project Portal" }, { "value" : "PHAROS", "name" : "Pharos", "detail" : "PHAROS Portal to the Illuminating the Druggable Genome" } ], "rcsb_description" : [ { "text" : "UniProt-mapped Resource", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Linked External Resources", "priority_order" : 10 } ] }, "provenance_source" : { "type" : "string" } } } }, "rcsb_uniprot_alignments" : { "type" : "object", "description" : "UniProt pairwise sequence alignments.", "properties" : { "core_entity_alignments" : { "type" : "array", "description" : "List of alignments with core_entity canonical sequences", "items" : { "type" : "object", "required" : [ "scores", "aligned_regions" ], "properties" : { "scores" : { "type" : "object", "description" : "Alignment scores", "required" : [ "target_coverage", "query_coverage", "target_length", "query_length" ], "properties" : { "target_coverage" : { "type" : "integer" }, "query_coverage" : { "type" : "integer" }, "target_length" : { "type" : "integer" }, "query_length" : { "type" : "integer" } } }, "aligned_regions" : { "type" : "array", "description" : "Aligned sequence regions", "items" : { "type" : "object", "description" : "Aligned region", "required" : [ "target_begin", "query_begin", "length" ], "properties" : { "target_begin" : { "type" : "integer", "description" : "NCBI sequence start position" }, "query_begin" : { "type" : "integer", "description" : "Entity seqeunce start position" }, "length" : { "type" : "integer", "description" : "Aligned region length" } } } }, "core_entity_identifiers" : { "type" : "object", "description" : "core_entity identifiers", "required" : [ "entity_id", "entry_id" ], "properties" : { "entry_id" : { "type" : "string" }, "entity_id" : { "type" : "string" } } } } } } }, "additionalProperties" : false }, "rcsb_branched_entity_instance_container_identifiers" : { "type" : "object", "properties" : { "asym_id" : { "type" : "string", "description" : "Instance identifier for this container.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Instance identifier for this container.", "context" : "dictionary" }, { "text" : "Asym Id (Branched Entity Instance Container Identifiers)", "context" : "brief" } ] }, "auth_asym_id" : { "type" : "string", "description" : "Author instance identifier for this container.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Author instance identifier for this container.", "context" : "dictionary" }, { "text" : "Auth Asym Id (Branched Entity Instance Container Identifiers)", "context" : "brief" } ] }, "entity_id" : { "type" : "string", "description" : "Entity identifier for the container.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Entity identifier for the container.", "context" : "dictionary" }, { "text" : "Entity Id (Branched Entity Instance Container Identifiers)", "context" : "brief" } ] }, "entry_id" : { "type" : "string", "description" : "Entry identifier for the container.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Entry identifier for the container.", "context" : "dictionary" }, { "text" : "Entry Id (Branched Entity Instance Container Identifiers)", "context" : "brief" } ] }, "rcsb_id" : { "type" : "string", "examples" : [ "1KIP.A" ], "description" : "A unique identifier for each object in this entity instance container formed by\n an 'dot' (.) separated concatenation of entry and entity instance identifiers.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "A unique identifier for each object in this entity instance container formed by\n an 'dot' (.) separated concatenation of entry and entity instance identifiers.", "context" : "dictionary" }, { "text" : "Id (Branched Entity Instance Container Identifiers)", "context" : "brief" } ] } }, "additionalProperties" : false, "required" : [ "asym_id", "entry_id" ] }, "rcsb_branched_instance_annotation" : { "type" : "array", "items" : { "type" : "object", "properties" : { "annotation_id" : { "type" : "string", "description" : "An identifier for the annotation.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "An identifier for the annotation.", "context" : "dictionary" }, { "text" : "Identifier", "context" : "brief" } ] }, "assignment_version" : { "type" : "string", "examples" : [ "V4_0_2" ], "description" : "Identifies the version of the annotation assignment.", "rcsb_description" : [ { "text" : "Identifies the version of the annotation assignment.", "context" : "dictionary" }, { "text" : "Annotation Version", "context" : "brief" } ] }, "comp_id" : { "type" : "string", "examples" : [ "ATP" ], "description" : "Chemical component identifier.", "rcsb_description" : [ { "text" : "Chemical component identifier.", "context" : "dictionary" } ] }, "description" : { "type" : "string", "description" : "A description for the annotation.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "A description for the annotation.", "context" : "dictionary" }, { "text" : "Annotation Description", "context" : "brief" } ] }, "name" : { "type" : "string", "description" : "A name for the annotation.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "A name for the annotation.", "context" : "dictionary" }, { "text" : "Name", "context" : "brief" } ] }, "ordinal" : { "type" : "integer", "description" : "Ordinal identifier for this category", "rcsb_description" : [ { "text" : "Ordinal identifier for this category", "context" : "dictionary" } ] }, "provenance_source" : { "type" : "string", "examples" : [ "PDB" ], "description" : "Code identifying the individual, organization or program that\n assigned the annotation.", "rcsb_description" : [ { "text" : "Code identifying the individual, organization or program that\n assigned the annotation.", "context" : "dictionary" }, { "text" : "Annotation Source", "context" : "brief" } ] }, "type" : { "type" : "string", "enum" : [ "CATH", "SCOP" ], "examples" : [ "CATH", "SCOP" ], "description" : "A type or category of the annotation.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "CATH", "detail" : "CATH" }, { "value" : "SCOP", "detail" : "SCOP" } ], "rcsb_description" : [ { "text" : "A type or category of the annotation.", "context" : "dictionary" }, { "text" : "Annotation Type", "context" : "brief" } ] }, "annotation_lineage" : { "type" : "array", "items" : { "type" : "object", "properties" : { "depth" : { "type" : "integer", "description" : "Members of the annotation lineage as parent lineage depth (1-N)", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Members of the annotation lineage as parent lineage depth (1-N)", "context" : "dictionary" }, { "text" : "Lineage Depth", "context" : "brief" } ] }, "id" : { "type" : "string", "description" : "Members of the annotation lineage as parent class identifiers.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Members of the annotation lineage as parent class identifiers.", "context" : "dictionary" }, { "text" : "Lineage Identifier", "context" : "brief" } ] }, "name" : { "type" : "string", "description" : "Members of the annotation lineage as parent class names.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Members of the annotation lineage as parent class names.", "context" : "dictionary" }, { "text" : "Lineage Name", "context" : "brief" } ] } }, "additionalProperties" : false }, "uniqueItems" : false, "rcsb_nested_indexing" : true } }, "additionalProperties" : false, "required" : [ "ordinal" ] }, "minItems" : 1, "uniqueItems" : true, "rcsb_nested_indexing" : true, "rcsb_nested_indexing_context" : [ { "category_name" : "annotation_type", "category_path" : "rcsb_branched_instance_annotation.type" } ] }, "rcsb_branched_instance_feature" : { "type" : "array", "items" : { "type" : "object", "properties" : { "assignment_version" : { "type" : "string", "examples" : [ "V4_0_2" ], "description" : "Identifies the version of the feature assignment.", "rcsb_description" : [ { "text" : "Identifies the version of the feature assignment.", "context" : "dictionary" }, { "text" : "Feature Version", "context" : "brief" } ] }, "description" : { "type" : "string", "description" : "A description for the feature.", "rcsb_description" : [ { "text" : "A description for the feature.", "context" : "dictionary" }, { "text" : "Feature Description", "context" : "brief" } ] }, "feature_id" : { "type" : "string", "description" : "An identifier for the feature.", "rcsb_description" : [ { "text" : "An identifier for the feature.", "context" : "dictionary" } ] }, "name" : { "type" : "string", "description" : "A name for the feature.", "rcsb_description" : [ { "text" : "A name for the feature.", "context" : "dictionary" }, { "text" : "Name", "context" : "brief" } ] }, "ordinal" : { "type" : "integer", "description" : "Ordinal identifier for this category", "rcsb_description" : [ { "text" : "Ordinal identifier for this category", "context" : "dictionary" } ] }, "provenance_source" : { "type" : "string", "examples" : [ "PDB" ], "description" : "Code identifying the individual, organization or program that\n assigned the feature.", "rcsb_description" : [ { "text" : "Code identifying the individual, organization or program that\n assigned the feature.", "context" : "dictionary" }, { "text" : "Feature Source", "context" : "brief" } ] }, "reference_scheme" : { "type" : "string", "enum" : [ "PDB entity", "PDB entry" ], "examples" : [ "PDB entity" ], "description" : "Code residue coordinate system for the assigned feature.", "rcsb_enum_annotated" : [ { "value" : "PDB entity", "detail" : "The reference branched entity in PDB entry" }, { "value" : "PDB entry", "detail" : "The observed branched entity instance in PDB coordinate records" } ], "rcsb_description" : [ { "text" : "Code residue coordinate system for the assigned feature.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "enum" : [ "BINDING_SITE", "CATH", "ECOD", "MOGUL_ANGLE_OUTLIER", "MOGUL_BOND_OUTLIER", "RSCC_OUTLIER", "RSRZ_OUTLIER", "SCOP", "STEREO_OUTLIER", "UNOBSERVED_ATOM_XYZ", "UNOBSERVED_RESIDUE_XYZ", "ZERO_OCCUPANCY_ATOM_XYZ", "ZERO_OCCUPANCY_RESIDUE_XYZ" ], "examples" : [ "UNOBSERVED_ATOM_XYZ", "ZERO_OCCUPANCY_RESIDUE_XYZ" ], "description" : "A type or category of the feature.", "rcsb_enum_annotated" : [ { "value" : "BINDING_SITE", "detail" : "Macromolecular target for ligand binding" }, { "value" : "CATH", "detail" : "CATH - Class, Architecture, Topology, and Homology Protein Structure Database" }, { "value" : "ECOD" }, { "value" : "MOGUL_ANGLE_OUTLIER", "detail" : "Mogul bond angle outlier" }, { "value" : "MOGUL_BOND_OUTLIER", "detail" : "Mogul bond distance outlier" }, { "value" : "RSCC_OUTLIER", "detail" : "Real space density correlation value < 0.65" }, { "value" : "RSRZ_OUTLIER", "detail" : "Real space R-value Z score > 2" }, { "value" : "SCOP", "detail" : "SCOP - Structural Classification of Proteins" }, { "value" : "STEREO_OUTLIER", "detail" : "Stereochemical/chirality outlier" }, { "value" : "UNOBSERVED_ATOM_XYZ", "detail" : "Unobserved atom coordinates" }, { "value" : "UNOBSERVED_RESIDUE_XYZ", "detail" : "Unobserved residue coordinates" }, { "value" : "ZERO_OCCUPANCY_ATOM_XYZ", "detail" : "Atom coordinates with zero occupancy" }, { "value" : "ZERO_OCCUPANCY_RESIDUE_XYZ", "detail" : "Residue coordinates with zero occupancy" } ], "rcsb_description" : [ { "text" : "A type or category of the feature.", "context" : "dictionary" }, { "text" : "Feature Type", "context" : "brief" } ] }, "feature_positions" : { "type" : "array", "items" : { "type" : "object", "properties" : { "beg_comp_id" : { "type" : "string", "examples" : [ "NAG", "MAN" ], "description" : "An identifier for the monomer(s) corresponding to the feature assignment.", "rcsb_description" : [ { "text" : "An identifier for the monomer(s) corresponding to the feature assignment.", "context" : "dictionary" } ] }, "beg_seq_id" : { "type" : "integer", "description" : "An identifier for the leading monomer feature position.", "rcsb_description" : [ { "text" : "An identifier for the leading monomer feature position.", "context" : "dictionary" } ] }, "end_seq_id" : { "type" : "integer", "description" : "An identifier for the terminal monomer feature position.", "rcsb_description" : [ { "text" : "An identifier for the terminal monomer feature position.", "context" : "dictionary" } ] }, "value" : { "type" : "number", "examples" : [ 1.5, 0.25 ], "description" : "The value of the feature at the monomer position.", "rcsb_description" : [ { "text" : "The value of the feature at the monomer position.", "context" : "dictionary" } ] }, "values" : { "type" : "array", "items" : { "type" : "number", "examples" : [ 1.5, 0.25 ], "description" : "The value(s) of the feature at the monomer position.", "rcsb_description" : [ { "text" : "The value(s) of the feature at the monomer position.", "context" : "dictionary" } ] }, "uniqueItems" : false } }, "additionalProperties" : false, "required" : [ "beg_seq_id" ] }, "uniqueItems" : false }, "feature_value" : { "type" : "array", "items" : { "type" : "object", "properties" : { "comp_id" : { "type" : "string", "examples" : [ "ATP,", "STN" ], "description" : "The chemical component identifier for the instance of the feature value.", "rcsb_description" : [ { "text" : "The chemical component identifier for the instance of the feature value.", "context" : "dictionary" } ] }, "details" : { "type" : "string", "examples" : [ "C1,C2", "C1,C2,C3" ], "description" : "Specific details about the feature.", "rcsb_description" : [ { "text" : "Specific details about the feature.", "context" : "dictionary" } ] }, "reference" : { "type" : "number", "examples" : [ 5.0, 0.25 ], "description" : "The reference value of the feature.", "rcsb_description" : [ { "text" : "The reference value of the feature.", "context" : "dictionary" } ] }, "reported" : { "type" : "number", "examples" : [ 5.0, 0.25 ], "description" : "The reported value of the feature.", "rcsb_description" : [ { "text" : "The reported value of the feature.", "context" : "dictionary" } ] }, "uncertainty_estimate" : { "type" : "number", "examples" : [ 1.0, -1.5 ], "description" : "The estimated uncertainty of the reported feature value.", "rcsb_description" : [ { "text" : "The estimated uncertainty of the reported feature value.", "context" : "dictionary" } ] }, "uncertainty_estimate_type" : { "type" : "string", "enum" : [ "Z-Score" ], "examples" : [ "Z-score" ], "description" : "The type of estimated uncertainty for the reported feature value.", "rcsb_enum_annotated" : [ { "value" : "Z-Score", "detail" : "Number of standard deviation units from the reference distribution mean" } ], "rcsb_description" : [ { "text" : "The type of estimated uncertainty for the reported feature value.", "context" : "dictionary" } ] } }, "additionalProperties" : false }, "uniqueItems" : false }, "additional_properties" : { "type" : "array", "items" : { "type" : "object", "properties" : { "name" : { "type" : "string", "examples" : [ "bond_distance", "bond_angle" ], "description" : "The additional property name.", "rcsb_description" : [ { "text" : "The additional property name.", "context" : "dictionary" } ] }, "values" : { "type" : "array", "items" : { "anyOf" : [ { "type" : "string" }, { "type" : "integer" }, { "type" : "number" } ], "examples" : [ "2.54", "300" ], "description" : "The value(s) of the additional property.", "rcsb_description" : [ { "text" : "The value(s) of the additional property.", "context" : "dictionary" } ] }, "uniqueItems" : false } }, "additionalProperties" : false }, "uniqueItems" : false } }, "additionalProperties" : false, "required" : [ "ordinal", "type" ] }, "minItems" : 1, "uniqueItems" : true }, "rcsb_branched_instance_feature_summary" : { "type" : "array", "items" : { "type" : "object", "properties" : { "count" : { "type" : "integer", "description" : "The feature count.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The feature count.", "context" : "dictionary" }, { "text" : "Count (Branched Instance Feature Summary)", "context" : "brief" } ] }, "coverage" : { "type" : "number", "examples" : [ 0.5, 0.95 ], "description" : "The fractional feature coverage relative to the full branched entity.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The fractional feature coverage relative to the full branched entity.", "context" : "dictionary" }, { "text" : "Coverage (Branched Instance Feature Summary)", "context" : "brief" } ] }, "maximum_length" : { "type" : "integer", "description" : "The maximum feature length.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The maximum feature length.", "context" : "dictionary" }, { "text" : "Maximum Length (Branched Instance Feature Summary)", "context" : "brief" } ] }, "maximum_value" : { "type" : "number", "examples" : [ 1.012, 0.813 ], "description" : "The maximum feature value.", "rcsb_description" : [ { "text" : "The maximum feature value.", "context" : "dictionary" } ] }, "minimum_length" : { "type" : "integer", "description" : "The minimum feature length.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The minimum feature length.", "context" : "dictionary" }, { "text" : "Minimum Length (Branched Instance Feature Summary)", "context" : "brief" } ] }, "minimum_value" : { "type" : "number", "examples" : [ 0.012, 0.00132 ], "description" : "The minimum feature value.", "rcsb_description" : [ { "text" : "The minimum feature value.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "enum" : [ "BINDING_SITE", "CATH", "MOGUL_ANGLE_OUTLIER", "MOGUL_BOND_OUTLIER", "RSCC_OUTLIER", "RSRZ_OUTLIER", "SCOP", "STEREO_OUTLIER", "UNOBSERVED_ATOM_XYZ", "UNOBSERVED_RESIDUE_XYZ", "ZERO_OCCUPANCY_ATOM_XYZ", "ZERO_OCCUPANCY_RESIDUE_XYZ" ], "examples" : [ "ZERO_OCCUPANCY_RESIDUE_XYZ", "UNOBSERVED_RESIDUE_XYZ" ], "description" : "Type or category of the feature.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "BINDING_SITE", "detail" : "Macromolecular target for ligand binding" }, { "value" : "CATH", "detail" : "CATH - Class, Architecture, Topology, and Homology Protein Structure Database" }, { "value" : "MOGUL_ANGLE_OUTLIER", "detail" : "Mogul bond angle outlier" }, { "value" : "MOGUL_BOND_OUTLIER", "detail" : "Mogul bond distance outlier" }, { "value" : "RSCC_OUTLIER", "detail" : "Real space density correlation value < 0.65" }, { "value" : "RSRZ_OUTLIER", "detail" : "Real space R-value Z score > 2" }, { "value" : "SCOP", "detail" : "SCOP - Structural Classification of Proteins" }, { "value" : "STEREO_OUTLIER", "detail" : "Stereochemical/chirality outlier" }, { "value" : "UNOBSERVED_ATOM_XYZ", "detail" : "Unobserved atom coordinates" }, { "value" : "UNOBSERVED_RESIDUE_XYZ", "detail" : "Unobserved residue coordinates" }, { "value" : "ZERO_OCCUPANCY_ATOM_XYZ", "detail" : "Atom coordinates with zero occupancy" }, { "value" : "ZERO_OCCUPANCY_RESIDUE_XYZ", "detail" : "Residue coordinates with zero occupancy" } ], "rcsb_description" : [ { "text" : "Type or category of the feature.", "context" : "dictionary" }, { "text" : "Type (Branched Instance Feature Summary)", "context" : "brief" } ] } }, "additionalProperties" : false }, "minItems" : 1, "uniqueItems" : true, "rcsb_nested_indexing" : true, "rcsb_nested_indexing_context" : [ { "category_name" : "feature_summary", "category_path" : "rcsb_branched_instance_feature_summary.type" } ] }, "rcsb_branched_struct_conn" : { "type" : "array", "items" : { "type" : "object", "properties" : { "connect_type" : { "type" : "string", "enum" : [ "covalent bond", "hydrogen bond", "ionic interaction", "metal coordination", "mismatched base pairs" ], "description" : "The connection type.", "rcsb_description" : [ { "text" : "The connection type.", "context" : "dictionary" } ] }, "description" : { "type" : "string", "examples" : [ "Watson-Crick base pair" ], "description" : "A description of special details of the connection.", "rcsb_description" : [ { "text" : "A description of special details of the connection.", "context" : "dictionary" } ] }, "dist_value" : { "type" : "number", "description" : "Distance value for this contact.", "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "Distance value for this contact.", "context" : "dictionary" } ] }, "id" : { "type" : "string", "description" : "The value of _rcsb_branched_struct_conn.id is an identifier for connection.", "rcsb_description" : [ { "text" : "The value of _rcsb_branched_struct_conn.id is an identifier for connection.", "context" : "dictionary" } ] }, "ordinal_id" : { "type" : "integer", "description" : "The value of _rcsb_branched_struct_conn.id must uniquely identify a record in\n the rcsb_branched_struct_conn list.", "rcsb_description" : [ { "text" : "The value of _rcsb_branched_struct_conn.id must uniquely identify a record in\n the rcsb_branched_struct_conn list.", "context" : "dictionary" } ] }, "role" : { "type" : "string", "enum" : [ "C-Mannosylation", "N-Glycosylation", "O-Glycosylation" ], "examples" : [ "N-Glycosylation", "O-Glycosylation" ], "description" : "The chemical or structural role of the interaction", "rcsb_description" : [ { "text" : "The chemical or structural role of the interaction", "context" : "dictionary" } ] }, "value_order" : { "type" : "string", "enum" : [ "doub", "quad", "sing", "trip" ], "description" : "The chemical bond order associated with the specified atoms in\n this contact.", "rcsb_enum_annotated" : [ { "value" : "doub", "detail" : "double bond" }, { "value" : "quad", "detail" : "quadruple bond" }, { "value" : "sing", "detail" : "single bond" }, { "value" : "trip", "detail" : "triple bond" } ], "rcsb_description" : [ { "text" : "The chemical bond order associated with the specified atoms in\n this contact.", "context" : "dictionary" } ] }, "connect_target" : { "type" : "object", "properties" : { "auth_asym_id" : { "type" : "string", "description" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.auth_asym_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.auth_asym_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "auth_seq_id" : { "type" : "string", "description" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.auth_seq_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.auth_seq_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "label_alt_id" : { "type" : "string", "description" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.label_alt_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.label_alt_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "label_asym_id" : { "type" : "string", "description" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.label_asym_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.label_asym_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "label_atom_id" : { "type" : "string", "description" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.label_atom_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.label_atom_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "label_comp_id" : { "type" : "string", "description" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.label_comp_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.label_comp_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "label_seq_id" : { "type" : "integer", "description" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.connect_target_label_seq_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.connect_target_label_seq_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "symmetry" : { "type" : "string", "examples" : [ "1_555", "7_645" ], "description" : "Describes the symmetry operation that should be applied to the\n atom set specified by _rcsb_branched_struct_conn.label* to generate the\n target of the structure connection.", "rcsb_description" : [ { "text" : "Describes the symmetry operation that should be applied to the\n atom set specified by _rcsb_branched_struct_conn.label* to generate the\n target of the structure connection.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "label_asym_id", "label_comp_id" ] }, "connect_partner" : { "type" : "object", "properties" : { "label_alt_id" : { "type" : "string", "description" : "A component of the identifier for the partner in the structure\n connection.\n\n This data item is a pointer to _atom_site.label_alt_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the partner in the structure\n connection.\n\n This data item is a pointer to _atom_site.label_alt_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "label_asym_id" : { "type" : "string", "description" : "A component of the identifier for the partner in the structure\n connection.\n\n This data item is a pointer to _atom_site.label_asym_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the partner in the structure\n connection.\n\n This data item is a pointer to _atom_site.label_asym_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "label_atom_id" : { "type" : "string", "description" : "A component of the identifier for the partner in the structure\n connection.\n\n This data item is a pointer to _chem_comp_atom.atom_id in the\n CHEM_COMP_ATOM category.", "rcsb_description" : [ { "text" : "A component of the identifier for the partner in the structure\n connection.\n\n This data item is a pointer to _chem_comp_atom.atom_id in the\n CHEM_COMP_ATOM category.", "context" : "dictionary" } ] }, "label_comp_id" : { "type" : "string", "description" : "A component of the identifier for the partner in the structure\n connection.\n\n This data item is a pointer to _atom_site.label_comp_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the partner in the structure\n connection.\n\n This data item is a pointer to _atom_site.label_comp_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "label_seq_id" : { "type" : "integer", "description" : "A component of the identifier for the partner in the structure\n connection.\n\n This data item is a pointer to _atom_site.label_seq_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the partner in the structure\n connection.\n\n This data item is a pointer to _atom_site.label_seq_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "symmetry" : { "type" : "string", "examples" : [ "1_555", "7_645" ], "description" : "Describes the symmetry operation that should be applied to the\n atom set specified by _rcsb_branched_struct_conn.connect_partner_label* to generate the\n partner in the structure connection.", "rcsb_description" : [ { "text" : "Describes the symmetry operation that should be applied to the\n atom set specified by _rcsb_branched_struct_conn.connect_partner_label* to generate the\n partner in the structure connection.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "label_asym_id", "label_comp_id" ] } }, "additionalProperties" : false, "required" : [ "ordinal_id" ] }, "minItems" : 1, "uniqueItems" : true }, "rcsb_ligand_neighbors" : { "type" : "array", "items" : { "type" : "object", "properties" : { "alt_id" : { "type" : "string", "description" : "Alternate conformer identifier for the target instance.", "rcsb_description" : [ { "text" : "Alternate conformer identifier for the target instance.", "context" : "dictionary" } ] }, "atom_id" : { "type" : "string", "examples" : [ "O1", "N1", "C1" ], "description" : "The atom identifier for the target instance.", "rcsb_description" : [ { "text" : "The atom identifier for the target instance.", "context" : "dictionary" } ] }, "auth_seq_id" : { "type" : "integer", "description" : "The author residue index for the target instance.", "rcsb_description" : [ { "text" : "The author residue index for the target instance.", "context" : "dictionary" } ] }, "comp_id" : { "type" : "string", "description" : "Component identifier for the target instance.", "rcsb_description" : [ { "text" : "Component identifier for the target instance.", "context" : "dictionary" } ] }, "distance" : { "type" : "number", "description" : "Distance value for this ligand interaction.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "Distance value for this ligand interaction.", "context" : "dictionary" }, { "text" : "Ligand Neighbor Distance", "context" : "brief" } ], "rcsb_current_maximum_value" : 5.0, "rcsb_current_minimum_value" : 0.0 }, "ligand_alt_id" : { "type" : "string", "description" : "Alternate conformer identifier for the ligand interaction.", "rcsb_description" : [ { "text" : "Alternate conformer identifier for the ligand interaction.", "context" : "dictionary" } ] }, "ligand_asym_id" : { "type" : "string", "examples" : [ "A", "B" ], "description" : "The entity instance identifier for the ligand interaction.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The entity instance identifier for the ligand interaction.", "context" : "dictionary" }, { "text" : "Ligand Entity Instance Identifer", "context" : "brief" } ] }, "ligand_atom_id" : { "type" : "string", "examples" : [ "OG", "OE1", "CD1" ], "description" : "The atom identifier for the ligand interaction.", "rcsb_description" : [ { "text" : "The atom identifier for the ligand interaction.", "context" : "dictionary" } ] }, "ligand_comp_id" : { "type" : "string", "examples" : [ "ASN", "TRP", "SER" ], "description" : "The chemical component identifier for the ligand interaction.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The chemical component identifier for the ligand interaction.", "context" : "dictionary" }, { "text" : "Ligand Component Identifier", "context" : "brief" } ] }, "ligand_entity_id" : { "type" : "string", "examples" : [ "1", "2" ], "description" : "The entity identifier for the ligand of interaction.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The entity identifier for the ligand of interaction.", "context" : "dictionary" }, { "text" : "Ligand Entity Identifier", "context" : "brief" } ] }, "ligand_is_bound" : { "type" : "string", "enum" : [ "N", "Y" ], "examples" : [ "Y", "N" ], "description" : "A flag to indicate the nature of the ligand interaction is covalent or metal-coordination.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "N", "detail" : "The target is not bound" }, { "value" : "Y", "detail" : "The target is bound through a covalent or metal-coordination interaction" } ], "rcsb_description" : [ { "text" : "A flag to indicate the nature of the ligand interaction is covalent or metal-coordination.", "context" : "dictionary" }, { "text" : "Ligand is Bound to Ligand", "context" : "brief" } ] }, "ligand_model_id" : { "type" : "integer", "description" : "Model identifier for the ligand interaction.", "rcsb_description" : [ { "text" : "Model identifier for the ligand interaction.", "context" : "dictionary" } ] }, "seq_id" : { "type" : "integer", "description" : "The sequence position for the target instance.", "rcsb_description" : [ { "text" : "The sequence position for the target instance.", "context" : "dictionary" } ] } }, "additionalProperties" : false }, "minItems" : 1, "uniqueItems" : true }, "pdbx_entity_branch" : { "type" : "object", "properties" : { "rcsb_branched_component_count" : { "type" : "integer", "description" : "Number of constituent chemical components in the branched entity.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Number of constituent chemical components in the branched entity.", "context" : "dictionary" }, { "text" : "Oligosaccharide Component Count", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Oligosaccharide/Branched Molecular Features", "priority_order" : 25 } ], "rcsb_current_maximum_value" : 47.0, "rcsb_current_minimum_value" : 2.0 }, "type" : { "type" : "string", "enum" : [ "oligosaccharide" ], "description" : "The type of this branched oligosaccharide.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The type of this branched oligosaccharide.", "context" : "dictionary" }, { "text" : "Branched Entity Type", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Oligosaccharide/Branched Molecular Features", "priority_order" : 5 } ] } }, "additionalProperties" : false }, "pdbx_entity_branch_descriptor" : { "type" : "array", "items" : { "type" : "object", "properties" : { "descriptor" : { "type" : "string", "description" : "This data item contains the descriptor value for this\n entity.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "This data item contains the descriptor value for this\n entity.", "context" : "dictionary" }, { "text" : "Oligosaccharide Linear Descriptor", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Oligosaccharide/Branched Molecular Features", "priority_order" : 20 } ] }, "program" : { "type" : "string", "examples" : [ "PDB-CARE", "OTHER", "GEMS" ], "description" : "This data item contains the name of the program\n or library used to compute the descriptor.", "rcsb_description" : [ { "text" : "This data item contains the name of the program\n or library used to compute the descriptor.", "context" : "dictionary" } ] }, "program_version" : { "type" : "string", "description" : "This data item contains the version of the program\n or library used to compute the descriptor.", "rcsb_description" : [ { "text" : "This data item contains the version of the program\n or library used to compute the descriptor.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "enum" : [ "Glycam Condensed Core Sequence", "Glycam Condensed Sequence", "LINUCS", "WURCS" ], "description" : "This data item contains the descriptor type.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "Glycam Condensed Core Sequence", "detail" : "Linear Notation for Unique description of oligosaccharide core structure" }, { "value" : "Glycam Condensed Sequence", "detail" : "Linear Notation for unique description of an oligosaccharide entity" }, { "value" : "LINUCS", "detail" : "Linear Notation for unique description of an oligosaccharide entity" }, { "value" : "WURCS", "detail" : "Linear Notation for Web3 Unique Representation of Carbohydrate Structures" } ], "rcsb_description" : [ { "text" : "This data item contains the descriptor type.", "context" : "dictionary" }, { "text" : "Oligosaccharide Descriptor Type", "context" : "brief" } ] } }, "additionalProperties" : false }, "minItems" : 1, "uniqueItems" : true, "rcsb_nested_indexing" : true, "rcsb_nested_indexing_context" : [ { "category_name" : "descriptor_type", "category_path" : "pdbx_entity_branch_descriptor.type", "context_attributes" : [ { "context_value" : "LINUCS", "attributes" : [ { "examples" : [ "[][a-D-Manp]{[(2+1)][a-D-Manp]{}}", "[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}" ], "path" : "pdbx_entity_branch_descriptor.descriptor" } ] }, { "context_value" : "Glycam Condensed Sequence", "attributes" : [ { "examples" : [ "DManpa1-2DManpa1-ROH", "DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-" ], "path" : "pdbx_entity_branch_descriptor.descriptor" } ] }, { "context_value" : "WURCS", "attributes" : [ { "examples" : [ "WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a2-b1", "WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1" ], "path" : "pdbx_entity_branch_descriptor.descriptor" } ] } ] } ] }, "rcsb_branched_entity" : { "type" : "object", "properties" : { "details" : { "type" : "string", "description" : "A description of special aspects of the branched entity.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "A description of special aspects of the branched entity.", "context" : "dictionary" }, { "text" : "Details (Branched Entity)", "context" : "brief" } ] }, "formula_weight" : { "type" : "number", "examples" : [ 0.745, 1.2 ], "description" : "Formula mass (KDa) of the branched entity.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "KDa", "rcsb_description" : [ { "text" : "Formula mass (KDa) of the branched entity.", "context" : "dictionary" }, { "text" : "Oligosaccharide Formula Weight", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Oligosaccharide/Branched Molecular Features", "priority_order" : 15 } ], "rcsb_current_maximum_value" : 10.412, "rcsb_current_minimum_value" : 0.268 }, "pdbx_description" : { "type" : "string", "examples" : [ "alpha-D-glucopyranose-(1-6)-beta-D-glucopyranose", "beta-D-xylopyranose-(1-4)-beta-D-xylopyranose" ], "description" : "A description of the branched entity.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "A description of the branched entity.", "context" : "dictionary" }, { "text" : "Oligosaccharide Entity Description", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Oligosaccharide/Branched Molecular Features", "priority_order" : 10 } ] }, "pdbx_number_of_molecules" : { "type" : "integer", "description" : "The number of molecules of the branched entity in the entry.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of molecules of the branched entity in the entry.", "context" : "dictionary" }, { "text" : "Number Of Molecules (Branched Entity)", "context" : "brief" } ], "rcsb_current_maximum_value" : 144.0, "rcsb_current_minimum_value" : 1.0 } }, "additionalProperties" : false }, "rcsb_branched_entity_annotation" : { "type" : "array", "items" : { "type" : "object", "properties" : { "annotation_id" : { "type" : "string", "description" : "An identifier for the annotation.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "An identifier for the annotation.", "context" : "dictionary" }, { "text" : "Identifier", "context" : "brief" } ] }, "assignment_version" : { "type" : "string", "examples" : [ "V4_0_2" ], "description" : "Identifies the version of the annotation assignment.", "rcsb_description" : [ { "text" : "Identifies the version of the annotation assignment.", "context" : "dictionary" }, { "text" : "Annotation Version", "context" : "brief" } ] }, "description" : { "type" : "string", "description" : "A description for the annotation.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "A description for the annotation.", "context" : "dictionary" }, { "text" : "Annotation Description", "context" : "brief" } ] }, "name" : { "type" : "string", "description" : "A name for the annotation.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "A name for the annotation.", "context" : "dictionary" }, { "text" : "Name", "context" : "brief" } ] }, "provenance_source" : { "type" : "string", "examples" : [ "PDB" ], "description" : "Code identifying the individual, organization or program that\n assigned the annotation.", "rcsb_description" : [ { "text" : "Code identifying the individual, organization or program that\n assigned the annotation.", "context" : "dictionary" }, { "text" : "Annotation Source", "context" : "brief" } ] }, "type" : { "type" : "string", "description" : "A type or category of the annotation.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "A type or category of the annotation.", "context" : "dictionary" }, { "text" : "Annotation Type", "context" : "brief" } ] }, "annotation_lineage" : { "type" : "array", "items" : { "type" : "object", "properties" : { "depth" : { "type" : "integer", "description" : "Members of the annotation lineage as parent lineage depth (1-N)", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Members of the annotation lineage as parent lineage depth (1-N)", "context" : "dictionary" }, { "text" : "Lineage Depth", "context" : "brief" } ] }, "id" : { "type" : "string", "description" : "Members of the annotation lineage as parent class identifiers.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Members of the annotation lineage as parent class identifiers.", "context" : "dictionary" }, { "text" : "Lineage Identifier", "context" : "brief" } ] }, "name" : { "type" : "string", "description" : "Members of the annotation lineage as parent class names.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Members of the annotation lineage as parent class names.", "context" : "dictionary" }, { "text" : "Lineage Name", "context" : "brief" } ] } }, "additionalProperties" : false }, "uniqueItems" : false, "rcsb_nested_indexing" : true } }, "additionalProperties" : false }, "minItems" : 1, "uniqueItems" : true, "rcsb_nested_indexing" : true, "rcsb_nested_indexing_context" : [ { "category_name" : "annotation_type", "category_path" : "rcsb_branched_entity_annotation.type" } ] }, "rcsb_branched_entity_container_identifiers" : { "type" : "object", "properties" : { "asym_ids" : { "type" : "array", "items" : { "type" : "string", "examples" : [ "A", "B" ], "description" : "Instance identifiers corresponding to copies of the entity in this container.", "rcsb_description" : [ { "text" : "Instance identifiers corresponding to copies of the entity in this container.", "context" : "dictionary" } ] }, "uniqueItems" : false }, "auth_asym_ids" : { "type" : "array", "items" : { "type" : "string", "examples" : [ "A", "B" ], "description" : "Author instance identifiers corresponding to copies of the entity in this container.", "rcsb_description" : [ { "text" : "Author instance identifiers corresponding to copies of the entity in this container.", "context" : "dictionary" } ] }, "uniqueItems" : false }, "chem_comp_monomers" : { "type" : "array", "items" : { "type" : "string", "examples" : [ "NAG", "MAN", "GAL" ], "description" : "Unique list of monomer chemical component identifiers in the entity in this container.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Unique list of monomer chemical component identifiers in the entity in this container.", "context" : "dictionary" }, { "text" : "Oligosaccharide Component List", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Oligosaccharide/Branched Molecular Features", "priority_order" : 30 } ] }, "uniqueItems" : false }, "chem_ref_def_id" : { "type" : "string", "examples" : [ "PRD_000010" ], "description" : "The chemical reference definition identifier for the entity in this container.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The chemical reference definition identifier for the entity in this container.", "context" : "dictionary" }, { "text" : "Chem Ref Def Id (Branched Entity Container Identifiers)", "context" : "brief" } ] }, "entity_id" : { "type" : "string", "examples" : [ "1", "2" ], "description" : "Entity identifier for the container.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Entity identifier for the container.", "context" : "dictionary" }, { "text" : "Entity Id (Branched Entity Container Identifiers)", "context" : "brief" } ] }, "entry_id" : { "type" : "string", "examples" : [ "1B5F", "2HYV" ], "description" : "Entry identifier for the container.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Entry identifier for the container.", "context" : "dictionary" }, { "text" : "Entry Id (Branched Entity Container Identifiers)", "context" : "brief" } ] }, "prd_id" : { "type" : "string", "examples" : [ "PRD_000010" ], "description" : "The BIRD identifier for the entity in this container.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The BIRD identifier for the entity in this container.", "context" : "dictionary" }, { "text" : "Branched BIRD ID", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Oligosaccharide/Branched Molecular Features", "priority_order" : 35 } ] }, "rcsb_id" : { "type" : "string", "examples" : [ "2HYV_2" ], "description" : "A unique identifier for each object in this entity container formed by\n an underscore separated concatenation of entry and entity identifiers.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "A unique identifier for each object in this entity container formed by\n an underscore separated concatenation of entry and entity identifiers.", "context" : "dictionary" }, { "text" : "Id (Branched Entity Container Identifiers)", "context" : "brief" } ] }, "reference_identifiers" : { "type" : "array", "items" : { "type" : "object", "properties" : { "provenance_source" : { "type" : "string", "enum" : [ "PDB", "RCSB" ], "examples" : [ "RCSB" ], "description" : "Source of the reference resource assignment", "rcsb_description" : [ { "text" : "Source of the reference resource assignment", "context" : "dictionary" } ] }, "resource_accession" : { "type" : "string", "examples" : [ "G07411ON", "G42666HT" ], "description" : "Reference resource accession code", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Reference resource accession code", "context" : "dictionary" }, { "text" : "Resource Accession (Reference Identifiers)", "context" : "brief" } ] }, "resource_name" : { "type" : "string", "enum" : [ "GlyCosmos", "GlyGen", "GlyTouCan" ], "examples" : [ "GlyTouCan", "GlyCosmos" ], "description" : "Reference resource name", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "GlyCosmos", "detail" : "Web portal integrating glycosciences with the life sciences", "name" : "Web portal integrating glycosciences with the life sciences" }, { "value" : "GlyGen", "detail" : "Computational and Informatics Resources for Glycoscience", "name" : "Computational and Informatics Resources for Glycoscience" }, { "value" : "GlyTouCan", "detail" : "International glycan structure repository", "name" : "International glycan structure repository" } ], "rcsb_description" : [ { "text" : "Reference resource name", "context" : "dictionary" }, { "text" : "Resource Name (Reference Identifiers)", "context" : "brief" } ] } }, "additionalProperties" : false }, "uniqueItems" : false, "rcsb_nested_indexing" : true } }, "additionalProperties" : false, "required" : [ "entity_id", "entry_id" ] }, "rcsb_branched_entity_feature" : { "type" : "array", "items" : { "type" : "object", "properties" : { "assignment_version" : { "type" : "string", "examples" : [ "V4_0_2" ], "description" : "Identifies the version of the feature assignment.", "rcsb_description" : [ { "text" : "Identifies the version of the feature assignment.", "context" : "dictionary" }, { "text" : "Feature Version", "context" : "brief" } ] }, "description" : { "type" : "string", "description" : "A description for the feature.", "rcsb_description" : [ { "text" : "A description for the feature.", "context" : "dictionary" }, { "text" : "Feature Description", "context" : "brief" } ] }, "feature_id" : { "type" : "string", "description" : "An identifier for the feature.", "rcsb_description" : [ { "text" : "An identifier for the feature.", "context" : "dictionary" } ] }, "name" : { "type" : "string", "description" : "A name for the feature.", "rcsb_description" : [ { "text" : "A name for the feature.", "context" : "dictionary" }, { "text" : "Name", "context" : "brief" } ] }, "provenance_source" : { "type" : "string", "examples" : [ "PDB" ], "description" : "Code identifying the individual, organization or program that\n assigned the feature.", "rcsb_description" : [ { "text" : "Code identifying the individual, organization or program that\n assigned the feature.", "context" : "dictionary" }, { "text" : "Feature Source", "context" : "brief" } ] }, "reference_scheme" : { "type" : "string", "enum" : [ "PDB entity" ], "examples" : [ "PDB entity" ], "description" : "Code residue coordinate system for the assigned feature.", "rcsb_enum_annotated" : [ { "value" : "PDB entity", "detail" : "The referenced branched entity in PDB entry" } ], "rcsb_description" : [ { "text" : "Code residue coordinate system for the assigned feature.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "enum" : [ "mutation" ], "examples" : [ "mutation" ], "description" : "A type or category of the feature.", "rcsb_enum_annotated" : [ { "value" : "mutation", "detail" : "Engineered mutations and chemical modifications", "name" : "Engineered mutations and chemical modifications" } ], "rcsb_description" : [ { "text" : "A type or category of the feature.", "context" : "dictionary" }, { "text" : "Feature Type", "context" : "brief" } ] }, "feature_positions" : { "type" : "array", "items" : { "type" : "object", "properties" : { "beg_comp_id" : { "type" : "string", "examples" : [ "NAG", "MAN" ], "description" : "An identifier for the leading monomer corresponding to the feature assignment.", "rcsb_description" : [ { "text" : "An identifier for the leading monomer corresponding to the feature assignment.", "context" : "dictionary" } ] }, "beg_seq_id" : { "type" : "integer", "description" : "An identifier for the leading monomer position of the feature.", "rcsb_description" : [ { "text" : "An identifier for the leading monomer position of the feature.", "context" : "dictionary" } ] }, "end_seq_id" : { "type" : "integer", "description" : "An identifier for the leading monomer position of the feature.", "rcsb_description" : [ { "text" : "An identifier for the leading monomer position of the feature.", "context" : "dictionary" } ] }, "value" : { "type" : "number", "examples" : [ 5.0, 0.25 ], "description" : "The value for the feature at this monomer.", "rcsb_description" : [ { "text" : "The value for the feature at this monomer.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "beg_seq_id" ] }, "uniqueItems" : false }, "additional_properties" : { "type" : "array", "items" : { "type" : "object", "properties" : { "name" : { "type" : "string", "description" : "The additional property name.", "rcsb_description" : [ { "text" : "The additional property name.", "context" : "dictionary" } ] }, "values" : { "type" : "array", "items" : { "anyOf" : [ { "type" : "string" }, { "type" : "integer" }, { "type" : "number" } ], "examples" : [ "2.54", "300" ], "description" : "The value(s) of the additional property.", "rcsb_description" : [ { "text" : "The value(s) of the additional property.", "context" : "dictionary" } ] }, "uniqueItems" : false } }, "additionalProperties" : false }, "uniqueItems" : false } }, "additionalProperties" : false }, "minItems" : 1, "uniqueItems" : true }, "rcsb_branched_entity_feature_summary" : { "type" : "array", "items" : { "type" : "object", "properties" : { "count" : { "type" : "integer", "description" : "The feature count.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The feature count.", "context" : "dictionary" }, { "text" : "Count (Branched Entity Feature Summary)", "context" : "brief" } ] }, "coverage" : { "type" : "number", "examples" : [ 0.012, 0.00132 ], "description" : "The fractional feature coverage relative to the full branched entity.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The fractional feature coverage relative to the full branched entity.", "context" : "dictionary" }, { "text" : "Coverage (Branched Entity Feature Summary)", "context" : "brief" } ] }, "maximum_length" : { "type" : "integer", "description" : "The maximum feature length.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The maximum feature length.", "context" : "dictionary" }, { "text" : "Maximum Length (Branched Entity Feature Summary)", "context" : "brief" } ] }, "maximum_value" : { "type" : "number", "examples" : [ 1.012, 0.813 ], "description" : "The maximum feature value.", "rcsb_description" : [ { "text" : "The maximum feature value.", "context" : "dictionary" } ] }, "minimum_length" : { "type" : "integer", "description" : "The minimum feature length.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The minimum feature length.", "context" : "dictionary" }, { "text" : "Minimum Length (Branched Entity Feature Summary)", "context" : "brief" } ] }, "minimum_value" : { "type" : "number", "examples" : [ 0.012, 0.00132 ], "description" : "The minimum feature value.", "rcsb_description" : [ { "text" : "The minimum feature value.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "enum" : [ "mutation" ], "examples" : [ "mutation" ], "description" : "Type or category of the feature.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "mutation", "detail" : "Engineered mutations and chemical modifications", "name" : "Engineered mutations and chemical modifications" } ], "rcsb_description" : [ { "text" : "Type or category of the feature.", "context" : "dictionary" }, { "text" : "Type (Branched Entity Feature Summary)", "context" : "brief" } ] } }, "additionalProperties" : false }, "minItems" : 1, "uniqueItems" : true, "rcsb_nested_indexing" : true, "rcsb_nested_indexing_context" : [ { "category_name" : "feature_summary", "category_path" : "rcsb_branched_entity_feature_summary.type" } ] }, "rcsb_branched_entity_keywords" : { "type" : "object", "properties" : { "text" : { "type" : "string", "description" : "Keywords describing this branched entity.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Keywords describing this branched entity.", "context" : "dictionary" }, { "text" : "Text (Branched Entity Keywords)", "context" : "brief" } ] } }, "additionalProperties" : false }, "rcsb_branched_entity_name_com" : { "type" : "object", "properties" : { "name" : { "type" : "string", "examples" : [ "HIV protease monomer", "hemoglobin alpha chain" ], "description" : "A common name for the branched entity.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "A common name for the branched entity.", "context" : "dictionary" }, { "text" : "Name (Branched Entity Name Com)", "context" : "brief" } ] } }, "additionalProperties" : false }, "rcsb_branched_entity_name_sys" : { "type" : "array", "items" : { "type" : "object", "properties" : { "name" : { "type" : "string", "description" : "The systematic name for the branched entity.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The systematic name for the branched entity.", "context" : "dictionary" }, { "text" : "Name (Branched Entity Name Sys)", "context" : "brief" } ] }, "system" : { "type" : "string", "description" : "The system used to generate the systematic name of the branched entity.", "rcsb_description" : [ { "text" : "The system used to generate the systematic name of the branched entity.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "name" ] }, "minItems" : 1, "uniqueItems" : true }, "rcsb_polymer_entity_instance_container_identifiers" : { "type" : "object", "properties" : { "asym_id" : { "type" : "string", "description" : "Instance identifier for this container.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Instance identifier for this container.", "context" : "dictionary" }, { "text" : "Asym Id (Polymer Entity Instance Container Identifiers)", "context" : "brief" } ] }, "auth_asym_id" : { "type" : "string", "description" : "Author instance identifier for this container.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Author instance identifier for this container.", "context" : "dictionary" }, { "text" : "Auth Asym Id (Polymer Entity Instance Container Identifiers)", "context" : "brief" } ] }, "auth_to_entity_poly_seq_mapping" : { "type" : "array", "items" : { "type" : "string", "description" : "Residue index mappings between author provided and entity polymer sequence positions.\n\n Author residue indices (auth_seq_num) include insertion codes when present.\n The array indices correspond to the indices (1-based) of the deposited sample\n sequence (entity_poly_seq). Unmodelled residues are represented with a \"?\" value.", "rcsb_description" : [ { "text" : "Residue index mappings between author provided and entity polymer sequence positions.\n\n Author residue indices (auth_seq_num) include insertion codes when present.\n The array indices correspond to the indices (1-based) of the deposited sample\n sequence (entity_poly_seq). Unmodelled residues are represented with a \"?\" value.", "context" : "dictionary" } ] }, "uniqueItems" : false }, "entity_id" : { "type" : "string", "description" : "Entity identifier for the container.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Entity identifier for the container.", "context" : "dictionary" }, { "text" : "Entity Id (Polymer Entity Instance Container Identifiers)", "context" : "brief" } ] }, "entry_id" : { "type" : "string", "description" : "Entry identifier for the container.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Entry identifier for the container.", "context" : "dictionary" }, { "text" : "Entry Id (Polymer Entity Instance Container Identifiers)", "context" : "brief" } ] }, "rcsb_id" : { "type" : "string", "examples" : [ "1KIP.A" ], "description" : "A unique identifier for each object in this entity instance container formed by\n an 'dot' (.) separated concatenation of entry and entity instance identifiers.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "A unique identifier for each object in this entity instance container formed by\n an 'dot' (.) separated concatenation of entry and entity instance identifiers.", "context" : "dictionary" }, { "text" : "Id (Polymer Entity Instance Container Identifiers)", "context" : "brief" } ] } }, "additionalProperties" : false, "required" : [ "asym_id", "entry_id" ] }, "rcsb_polymer_instance_annotation" : { "type" : "array", "items" : { "type" : "object", "properties" : { "annotation_id" : { "type" : "string", "description" : "An identifier for the annotation.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "An identifier for the annotation.", "context" : "dictionary" }, { "text" : "Identifier", "context" : "brief" } ] }, "assignment_version" : { "type" : "string", "examples" : [ "V4_0_2" ], "description" : "Identifies the version of the annotation assignment.", "rcsb_description" : [ { "text" : "Identifies the version of the annotation assignment.", "context" : "dictionary" }, { "text" : "Annotation Version", "context" : "brief" } ] }, "description" : { "type" : "string", "description" : "A description for the annotation.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "A description for the annotation.", "context" : "dictionary" }, { "text" : "Annotation Description", "context" : "brief" } ] }, "name" : { "type" : "string", "description" : "A name for the annotation.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "A name for the annotation.", "context" : "dictionary" }, { "text" : "Name", "context" : "brief" } ] }, "ordinal" : { "type" : "integer", "description" : "Ordinal identifier for this category", "rcsb_description" : [ { "text" : "Ordinal identifier for this category", "context" : "dictionary" } ] }, "provenance_source" : { "type" : "string", "examples" : [ "PDB" ], "description" : "Code identifying the individual, organization or program that\n assigned the annotation.", "rcsb_description" : [ { "text" : "Code identifying the individual, organization or program that\n assigned the annotation.", "context" : "dictionary" }, { "text" : "Annotation Source", "context" : "brief" } ] }, "type" : { "type" : "string", "enum" : [ "CATH", "ECOD", "GlyGen", "SCOP", "SCOP2" ], "examples" : [ "CATH", "SCOP" ], "description" : "A type or category of the annotation.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "CATH", "detail" : "CATH - Class, Architecture, Topology, and Homology Protein Structure Database", "name" : "CATH" }, { "value" : "ECOD", "detail" : "ECOD - An Evolutionary Classification of Protein Domains", "name" : "ECOD" }, { "value" : "GlyGen", "detail" : "GlyGen - Computational and Informatics Resources for Glycoscience", "name" : "GlyGen" }, { "value" : "SCOP", "detail" : "SCOP - Structural Classification of Proteins", "name" : "SCOP" }, { "value" : "SCOP2", "detail" : "SCOP2 - Structural Classification of Proteins 2 Family and Superfamilies", "name" : "SCOP2 Family/Superfamily" } ], "rcsb_description" : [ { "text" : "A type or category of the annotation.", "context" : "dictionary" }, { "text" : "Annotation Type", "context" : "brief" } ] }, "annotation_lineage" : { "type" : "array", "items" : { "type" : "object", "properties" : { "depth" : { "type" : "integer", "description" : "Members of the annotation lineage as parent lineage depth (1-N)", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Members of the annotation lineage as parent lineage depth (1-N)", "context" : "dictionary" }, { "text" : "Lineage Depth", "context" : "brief" } ], "rcsb_current_maximum_value" : 5.0, "rcsb_current_minimum_value" : 1.0 }, "id" : { "type" : "string", "description" : "Members of the annotation lineage as parent class identifiers.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Members of the annotation lineage as parent class identifiers.", "context" : "dictionary" }, { "text" : "Lineage Identifier", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Polymer Instance (Chain) Features", "priority_order" : 5 } ] }, "name" : { "type" : "string", "description" : "Members of the annotation lineage as parent class names.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Members of the annotation lineage as parent class names.", "context" : "dictionary" }, { "text" : "Lineage Name", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Polymer Instance (Chain) Features", "priority_order" : 10 } ] } }, "additionalProperties" : false }, "uniqueItems" : false, "rcsb_nested_indexing" : true } }, "additionalProperties" : false, "required" : [ "ordinal", "type" ] }, "minItems" : 1, "uniqueItems" : true, "rcsb_nested_indexing" : true, "rcsb_nested_indexing_context" : [ { "category_name" : "annotation_type", "category_path" : "rcsb_polymer_instance_annotation.type", "context_attributes" : [ { "context_value" : "CATH", "attributes" : [ { "examples" : [ "2.30.30.40", "3.30.420.40" ], "path" : "rcsb_polymer_instance_annotation.annotation_lineage.id" }, { "examples" : [ "SH3 Domains", "ATP Synthase" ], "path" : "rcsb_polymer_instance_annotation.annotation_lineage.name" } ] }, { "context_value" : "SCOP", "attributes" : [ { "examples" : [ 82057, 53067 ], "path" : "rcsb_polymer_instance_annotation.annotation_lineage.id" }, { "examples" : [ "Prokaryotic SH3-related domain", "Actin-like ATPase domain" ], "path" : "rcsb_polymer_instance_annotation.annotation_lineage.name" } ] }, { "context_value" : "SCOP2", "attributes" : [ { "examples" : [ 3001607, 4000551, 2000122, 1000001 ], "path" : "rcsb_polymer_instance_annotation.annotation_lineage.id" }, { "examples" : [ "Sialidases (neuraminidases)", "FAD-dependent thiol oxidase", "Globin-like", "Sialidases" ], "path" : "rcsb_polymer_instance_annotation.annotation_lineage.name" } ] }, { "context_value" : "ECOD", "attributes" : [ { "examples" : [ 100001, 300013 ], "path" : "rcsb_polymer_instance_annotation.annotation_lineage.id" }, { "examples" : [ "F: Evr1_Alr", "F: Peptidase_C30_C" ], "path" : "rcsb_polymer_instance_annotation.annotation_lineage.name" } ] } ] } ] }, "rcsb_polymer_instance_feature" : { "type" : "array", "items" : { "type" : "object", "properties" : { "assignment_version" : { "type" : "string", "examples" : [ "V4_0_2" ], "description" : "Identifies the version of the feature assignment.", "rcsb_description" : [ { "text" : "Identifies the version of the feature assignment.", "context" : "dictionary" }, { "text" : "Feature Version", "context" : "brief" } ] }, "description" : { "type" : "string", "description" : "A description for the feature.", "rcsb_description" : [ { "text" : "A description for the feature.", "context" : "dictionary" }, { "text" : "Feature Description", "context" : "brief" } ] }, "feature_id" : { "type" : "string", "description" : "An identifier for the feature.", "rcsb_description" : [ { "text" : "An identifier for the feature.", "context" : "dictionary" } ] }, "name" : { "type" : "string", "description" : "A name for the feature.", "rcsb_description" : [ { "text" : "A name for the feature.", "context" : "dictionary" }, { "text" : "Name", "context" : "brief" } ] }, "ordinal" : { "type" : "integer", "description" : "Ordinal identifier for this category", "rcsb_description" : [ { "text" : "Ordinal identifier for this category", "context" : "dictionary" } ] }, "provenance_source" : { "type" : "string", "examples" : [ "CATH", "SCOP" ], "description" : "Code identifying the individual, organization or program that\n assigned the feature.", "rcsb_description" : [ { "text" : "Code identifying the individual, organization or program that\n assigned the feature.", "context" : "dictionary" }, { "text" : "Feature Source", "context" : "brief" } ] }, "reference_scheme" : { "type" : "string", "enum" : [ "NCBI", "PDB entity", "PDB entry", "UniProt" ], "examples" : [ "PDB entity", "UniProt", "NCBI" ], "description" : "Code residue coordinate system for the assigned feature.", "rcsb_enum_annotated" : [ { "value" : "NCBI", "detail" : "The reference polymer sequence in NCBI entry" }, { "value" : "PDB entity", "detail" : "The reference polymer entity sequence in PDB entry" }, { "value" : "PDB entry", "detail" : "The observed entity instance sequence in PDB coordinate records" }, { "value" : "UniProt", "detail" : "The reference polymer sequence in UniProt entry" } ], "rcsb_description" : [ { "text" : "Code residue coordinate system for the assigned feature.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "enum" : [ "ANGLE_OUTLIER", "ANGLE_OUTLIERS", "ASA", "AVERAGE_OCCUPANCY", "BEND", "BINDING_SITE", "BOND_OUTLIER", "BOND_OUTLIERS", "C-MANNOSYLATION_SITE", "CATH", "CHIRAL_OUTLIERS", "CIS-PEPTIDE", "CLASHES", "ECOD", "HELIX_P", "HELX_LH_PP_P", "HELX_RH_3T_P", "HELX_RH_AL_P", "HELX_RH_PI_P", "LIGAND_COVALENT_LINKAGE", "LIGAND_INTERACTION", "LIGAND_METAL_COORDINATION_LINKAGE", "MA_QA_METRIC_LOCAL_TYPE_CONTACT_PROBABILITY", "MA_QA_METRIC_LOCAL_TYPE_DISTANCE", "MA_QA_METRIC_LOCAL_TYPE_ENERGY", "MA_QA_METRIC_LOCAL_TYPE_IPTM", "MA_QA_METRIC_LOCAL_TYPE_NORMALIZED_SCORE", "MA_QA_METRIC_LOCAL_TYPE_OTHER", "MA_QA_METRIC_LOCAL_TYPE_PAE", "MA_QA_METRIC_LOCAL_TYPE_PLDDT", "MA_QA_METRIC_LOCAL_TYPE_PLDDT_ALL-ATOM", "MA_QA_METRIC_LOCAL_TYPE_PLDDT_ALL-ATOM_[0,1]", "MA_QA_METRIC_LOCAL_TYPE_PLDDT_[0,1]", "MA_QA_METRIC_LOCAL_TYPE_PTM", "MA_QA_METRIC_LOCAL_TYPE_ZSCORE", "MEMBRANE_SEGMENT", "MOGUL_ANGLE_OUTLIER", "MOGUL_ANGLE_OUTLIERS", "MOGUL_BOND_OUTLIER", "MOGUL_BOND_OUTLIERS", "MOGUL_RING_OUTLIERS", "MOGUL_TORSION_OUTLIERS", "N-GLYCOSYLATION_SITE", "NATOMS_EDS", "O-GLYCOSYLATION_SITE", "OWAB", "PLANE_OUTLIERS", "Q_SCORE", "RAMACHANDRAN_OUTLIER", "ROTAMER_OUTLIER", "RSCC", "RSCC_OUTLIER", "RSR", "RSRZ", "RSRZ_OUTLIER", "S-GLYCOSYLATION_SITE", "SABDAB_ANTIBODY_HEAVY_CHAIN_SUBCLASS", "SABDAB_ANTIBODY_LIGHT_CHAIN_SUBCLASS", "SABDAB_ANTIBODY_LIGHT_CHAIN_TYPE", "SCOP", "SCOP2B_SUPERFAMILY", "SCOP2_FAMILY", "SCOP2_SUPERFAMILY", "SHEET", "STEREO_OUTLIER", "STRN", "SYMM_CLASHES", "TURN_TY1_P", "UNASSIGNED_SEC_STRUCT", "UNOBSERVED_ATOM_XYZ", "UNOBSERVED_RESIDUE_XYZ", "ZERO_OCCUPANCY_ATOM_XYZ", "ZERO_OCCUPANCY_RESIDUE_XYZ" ], "examples" : [ "CATH", "SCOP" ], "description" : "A type or category of the feature.", "rcsb_enum_annotated" : [ { "value" : "ANGLE_OUTLIER", "detail" : "Molprobity bond angle outlier", "name" : "Molprobity bond angle outlier" }, { "value" : "ANGLE_OUTLIERS", "detail" : "Number of atoms with angle outliers", "name" : "ANGLE_OUTLIERS" }, { "value" : "ASA", "detail" : "Accessible Surface Area", "name" : "ASA" }, { "value" : "AVERAGE_OCCUPANCY", "detail" : "The average heavy atom occupancy for coordinate records for the residue", "name" : "AVERAGE_OCCUPANCY" }, { "value" : "BEND", "detail" : "Bend - region with high backbone curvature without specific hydrogen bonding", "name" : "Bend - region with high backbone curvature without specific hydrogen bonding" }, { "value" : "BINDING_SITE", "detail" : "Macromolecular target for ligand binding", "name" : "Ligand Binding Site" }, { "value" : "BOND_OUTLIER", "detail" : "Molprobity bond distance outlier", "name" : "Molprobity bond distance outlier" }, { "value" : "BOND_OUTLIERS", "detail" : "Number of atoms with bond outliers", "name" : "BOND_OUTLIERS" }, { "value" : "C-MANNOSYLATION_SITE", "detail" : "Mannose glycan binding to the first tryptophan (W) residue in the sequence motif WXXW (where X is any amino acid).", "name" : "C-Mannosylation Site" }, { "value" : "CATH", "detail" : "CATH - Class, Architecture, Topology, and Homology Protein Structure Database", "name" : "CATH" }, { "value" : "CHIRAL_OUTLIERS", "detail" : "Number of chiral outliers", "name" : "CHIRAL_OUTLIERS" }, { "value" : "CIS-PEPTIDE", "detail" : "Peptide linkages with CIS configurations", "name" : "CIS Peptide linkages" }, { "value" : "CLASHES", "detail" : "Number of atoms a with clashes", "name" : "CLASHES" }, { "value" : "ECOD", "detail" : "ECOD - An Evolutionary Classification of Protein Domains", "name" : "ECOD" }, { "value" : "HELIX_P", "detail" : "Protein helices", "name" : "Protein helices" }, { "value" : "HELX_LH_PP_P", "detail" : "Left-handed polyproline helix (protein)", "name" : "Left-handed polyproline helix (protein)" }, { "value" : "HELX_RH_3T_P", "detail" : "Right-handed 3-10 helix (protein)", "name" : "Right-handed 3-10 helix (protein)" }, { "value" : "HELX_RH_AL_P", "detail" : "Alpha helix (protein)", "name" : "Alpha helix (protein)" }, { "value" : "HELX_RH_PI_P", "detail" : "Right-handed pi helix (protein)", "name" : "Right-handed pi helix (protein)" }, { "value" : "LIGAND_COVALENT_LINKAGE", "detail" : "Covalent ligand linkages with macromolecular target", "name" : "Covalent Ligand Linkages" }, { "value" : "LIGAND_INTERACTION", "detail" : "Ligand interactions with macromolecular target (includes covalent, metal coordination, and non-bonded interactions)", "name" : "Ligand Interactions" }, { "value" : "LIGAND_METAL_COORDINATION_LINKAGE", "detail" : "Metal coordination ligand linkages with macromolecular target", "name" : "Metal Coordination Ligand Linkages" }, { "value" : "MA_QA_METRIC_LOCAL_TYPE_CONTACT_PROBABILITY", "detail" : "the contact probability of a pairwise interaction", "name" : "MA_QA_METRIC_LOCAL_TYPE" }, { "value" : "MA_QA_METRIC_LOCAL_TYPE_DISTANCE", "detail" : "the lower the distance, the better the quality", "name" : "MA_QA_METRIC_LOCAL_TYPE" }, { "value" : "MA_QA_METRIC_LOCAL_TYPE_ENERGY", "detail" : "the lower the energy, the better the quality", "name" : "MA_QA_METRIC_LOCAL_TYPE" }, { "value" : "MA_QA_METRIC_LOCAL_TYPE_IPTM", "detail" : "confidence score of protein-protein interface based on the template modeling score in [0,1]", "name" : "MA_QA_METRIC_LOCAL_TYPE" }, { "value" : "MA_QA_METRIC_LOCAL_TYPE_NORMALIZED_SCORE", "detail" : "normalized score ranging from 0 to 1", "name" : "MA_QA_METRIC_LOCAL_TYPE" }, { "value" : "MA_QA_METRIC_LOCAL_TYPE_OTHER", "detail" : "other type of QA metric", "name" : "MA_QA_METRIC_LOCAL_TYPE" }, { "value" : "MA_QA_METRIC_LOCAL_TYPE_PAE", "detail" : "predicted aligned error (in Angstroms)", "name" : "MA_QA_METRIC_LOCAL_TYPE" }, { "value" : "MA_QA_METRIC_LOCAL_TYPE_PLDDT", "detail" : "confidence score predicting accuracy according to the CA-only Local Distance Difference Test (lDDT-CA) in [0,100]", "name" : "MA_QA_METRIC_LOCAL_TYPE" }, { "value" : "MA_QA_METRIC_LOCAL_TYPE_PLDDT_ALL-ATOM", "detail" : "confidence score predicting accuracy according to the all-atom Local Distance Difference Test (lDDT) in [0,100]", "name" : "MA_QA_METRIC_LOCAL_TYPE" }, { "value" : "MA_QA_METRIC_LOCAL_TYPE_PLDDT_ALL-ATOM_[0,1]", "detail" : "confidence score predicting accuracy according to the all-atom Local Distance Difference Test (lDDT) in [0,1]", "name" : "MA_QA_METRIC_LOCAL_TYPE" }, { "value" : "MA_QA_METRIC_LOCAL_TYPE_PLDDT_[0,1]", "detail" : "confidence score predicting accuracy according to the CA-only Local Distance Difference Test (lDDT-CA) in [0,1]", "name" : "MA_QA_METRIC_LOCAL_TYPE" }, { "value" : "MA_QA_METRIC_LOCAL_TYPE_PTM", "detail" : "confidence score predicting accuracy according to the template modeling score in [0,1]", "name" : "MA_QA_METRIC_LOCAL_TYPE" }, { "value" : "MA_QA_METRIC_LOCAL_TYPE_ZSCORE", "detail" : "number of standard deviations from optimal/best", "name" : "MA_QA_METRIC_LOCAL_TYPE" }, { "value" : "MEMBRANE_SEGMENT", "detail" : "Extent of a region located in a membrane", "name" : "Extent of a region located in a membrane" }, { "value" : "MOGUL_ANGLE_OUTLIER", "detail" : "Mogul bond angle outlier", "name" : "Mogul bond angle outlier" }, { "value" : "MOGUL_ANGLE_OUTLIERS", "detail" : "Number of angle outliers as reported by MOGUL", "name" : "MOGUL_ANGLE_OUTLIERS" }, { "value" : "MOGUL_BOND_OUTLIER", "detail" : "Mogul bond distance outlier", "name" : "Mogul bond distance outlier" }, { "value" : "MOGUL_BOND_OUTLIERS", "detail" : "Number of bond outliers as reported by MOGUL", "name" : "MOGUL_BOND_OUTLIERS" }, { "value" : "MOGUL_RING_OUTLIERS", "detail" : "Number of atoms with ring outliers as reported by MOGUL", "name" : "MOGUL_RING_OUTLIERS" }, { "value" : "MOGUL_TORSION_OUTLIERS", "detail" : "Number of torsion angle outliers as reported by MOGUL", "name" : "MOGUL_TORSION_OUTLIERS" }, { "value" : "N-GLYCOSYLATION_SITE", "detail" : "Glycan binding to the amide nitrogen of an asparagine (Asn) residue", "name" : "N-Glycosylation Site" }, { "value" : "NATOMS_EDS", "detail" : "Number of atoms in the residue returned by the EDS software", "name" : "NATOMS_EDS" }, { "value" : "O-GLYCOSYLATION_SITE", "detail" : "Glycan binding to the oxygen atom of serine (Ser) or threonine (Thr) residues", "name" : "O-Glycosylation Site" }, { "value" : "OWAB", "detail" : "Occupancy-weighted Average B value", "name" : "OWAB" }, { "value" : "PLANE_OUTLIERS", "detail" : "Number of planar outliers", "name" : "PLANE_OUTLIERS" }, { "value" : "Q_SCORE", "detail" : "Q_score", "name" : "Q_SCORE" }, { "value" : "RAMACHANDRAN_OUTLIER", "detail" : "Molprobity Ramachandran outlier", "name" : "Molprobity Ramachandran outlier" }, { "value" : "ROTAMER_OUTLIER", "detail" : "Molprobity rotamer outlier", "name" : "Molprobity rotamer outlier" }, { "value" : "RSCC", "detail" : "Real space correlation coefficient", "name" : "RSCC" }, { "value" : "RSCC_OUTLIER", "detail" : "Real space density correlation value < 0.65", "name" : "Real space density correlation outlier" }, { "value" : "RSR", "detail" : "Real Space R-value", "name" : "RSR" }, { "value" : "RSRZ", "detail" : "Real Space R-value z-score", "name" : "RSRZ" }, { "value" : "RSRZ_OUTLIER", "detail" : "Real space R-value Z score > 2", "name" : "Real space outlier" }, { "value" : "S-GLYCOSYLATION_SITE", "detail" : "Glycan binding to the sulfur atom of a cysteine (Cys) residue", "name" : "S-Glycosylation Site" }, { "value" : "SABDAB_ANTIBODY_HEAVY_CHAIN_SUBCLASS", "detail" : "Structural Antibody Database (SAbDab) antibody heavy chain subclass (IGHV1, IGHV2,)", "name" : "SAbDab Antibody Heavy Chain Subclass" }, { "value" : "SABDAB_ANTIBODY_LIGHT_CHAIN_SUBCLASS", "detail" : "Structural Antibody Database (SAbDab) antibody light chain subclass (IGLV1, IGLV2, ...)", "name" : "SAbDab Antibody Light Chain Subclass" }, { "value" : "SABDAB_ANTIBODY_LIGHT_CHAIN_TYPE", "detail" : "Structural Antibody Database (SAbDab) antibody light chain type (Kappa or Lambda)", "name" : "SAbDab Antibody Light Chain Type" }, { "value" : "SCOP", "detail" : "SCOP - Structural Classification of Proteins", "name" : "SCOP" }, { "value" : "SCOP2B_SUPERFAMILY", "detail" : "SCOP2B - Structural Classification of Proteins 2 - Superfamily automated assignments", "name" : "SCOP2B Superfamily" }, { "value" : "SCOP2_FAMILY", "detail" : "SCOP2 - Structural Classification of Proteins 2 Family", "name" : "SCOP2 Family" }, { "value" : "SCOP2_SUPERFAMILY", "detail" : "SCOP2 - Structural Classification of Proteins 2 Superfamily", "name" : "SCOP2 Superfamily" }, { "value" : "SHEET", "detail" : "Beta-sheets", "name" : "Beta-sheets" }, { "value" : "STEREO_OUTLIER", "detail" : "Stereochemical/chirality outlier", "name" : "Stereochemical/chirality outlier" }, { "value" : "STRN", "detail" : "Strand or beta-bridge (protein)", "name" : "Strand or beta-bridge (protein)" }, { "value" : "SYMM_CLASHES", "detail" : "Number of symmetry related clashes", "name" : "SYMM_CLASHES" }, { "value" : "TURN_TY1_P", "detail" : "Type I turn (protein)", "name" : "Type I turn (protein)" }, { "value" : "UNASSIGNED_SEC_STRUCT", "detail" : "Unassigned secondary structure", "name" : "Unassigned secondary structure" }, { "value" : "UNOBSERVED_ATOM_XYZ", "detail" : "Unobserved atom coordinates", "name" : "Unobserved Atoms" }, { "value" : "UNOBSERVED_RESIDUE_XYZ", "detail" : "Unobserved residue coordinates", "name" : "Unobserved Residues" }, { "value" : "ZERO_OCCUPANCY_ATOM_XYZ", "detail" : "Atom coordinates with zero occupancy", "name" : "Zero Occupancy Atoms" }, { "value" : "ZERO_OCCUPANCY_RESIDUE_XYZ", "detail" : "Residue coordinates with zero occupancy", "name" : "Zero Occupancy Residues" } ], "rcsb_description" : [ { "text" : "A type or category of the feature.", "context" : "dictionary" }, { "text" : "Feature Type", "context" : "brief" } ] }, "feature_positions" : { "type" : "array", "items" : { "type" : "object", "properties" : { "beg_comp_id" : { "type" : "string", "examples" : [ "TRP", "VAL" ], "description" : "An identifier for the monomer(s) corresponding to the feature assignment.", "rcsb_description" : [ { "text" : "An identifier for the monomer(s) corresponding to the feature assignment.", "context" : "dictionary" } ] }, "beg_seq_id" : { "type" : "integer", "description" : "An identifier for the monomer at which this segment of the feature begins.", "rcsb_description" : [ { "text" : "An identifier for the monomer at which this segment of the feature begins.", "context" : "dictionary" } ] }, "end_seq_id" : { "type" : "integer", "description" : "An identifier for the monomer at which this segment of the feature ends.", "rcsb_description" : [ { "text" : "An identifier for the monomer at which this segment of the feature ends.", "context" : "dictionary" } ] }, "value" : { "type" : "number", "examples" : [ 1.5, 0.25 ], "description" : "The value of the feature over the monomer segment.", "rcsb_description" : [ { "text" : "The value of the feature over the monomer segment.", "context" : "dictionary" } ] }, "values" : { "type" : "array", "items" : { "type" : "number", "examples" : [ 1.5, 0.25 ], "description" : "The value(s) of the feature over the monomer segment.", "rcsb_description" : [ { "text" : "The value(s) of the feature over the monomer segment.", "context" : "dictionary" } ] }, "uniqueItems" : false } }, "additionalProperties" : false, "required" : [ "beg_seq_id" ] }, "uniqueItems" : false }, "additional_properties" : { "type" : "array", "items" : { "type" : "object", "properties" : { "name" : { "type" : "string", "enum" : [ "CATH_DOMAIN_ID", "CATH_NAME", "ECOD_DOMAIN_ID", "ECOD_FAMILY_NAME", "MODELCIF_MODEL_ID", "OMEGA_ANGLE", "PARTNER_ASYM_ID", "PARTNER_BOND_DISTANCE", "PARTNER_COMP_ID", "PDB_MODEL_NUM", "SCOP2_DOMAIN_ID", "SCOP2_FAMILY_ID", "SCOP2_FAMILY_NAME", "SCOP2_SUPERFAMILY_ID", "SCOP2_SUPERFAMILY_NAME", "SCOP_DOMAIN_ID", "SCOP_NAME", "SCOP_SUN_ID", "SHEET_SENSE" ], "examples" : [ "CATH_NAME", "PARTNER_BOND_DISTANCE" ], "description" : "The additional property name.", "rcsb_enum_annotated" : [ { "value" : "CATH_DOMAIN_ID", "detail" : "CATH Domain Identifier" }, { "value" : "CATH_NAME", "detail" : "CATH Classification Name" }, { "value" : "ECOD_DOMAIN_ID", "detail" : "ECOD Domain Identifier" }, { "value" : "ECOD_FAMILY_NAME", "detail" : "ECOD Family Name" }, { "value" : "MODELCIF_MODEL_ID", "detail" : "ModelCIF Model Identifier" }, { "value" : "OMEGA_ANGLE", "detail" : "Cis-Peptide Omega Angle" }, { "value" : "PARTNER_ASYM_ID", "detail" : "Binding Partner Instance Identifier" }, { "value" : "PARTNER_BOND_DISTANCE", "detail" : "Binding Bond Distance" }, { "value" : "PARTNER_COMP_ID", "detail" : "Binding Partner Chemical Component Identifier" }, { "value" : "PDB_MODEL_NUM", "detail" : "PDB Model Number" }, { "value" : "SCOP2_DOMAIN_ID", "detail" : "SCOP2 Domain Identifier" }, { "value" : "SCOP2_FAMILY_ID", "detail" : "SCOP2 Family Identifier" }, { "value" : "SCOP2_FAMILY_NAME", "detail" : "SCOP2 Family Name" }, { "value" : "SCOP2_SUPERFAMILY_ID", "detail" : "SCOP2 Superfamily Identifier" }, { "value" : "SCOP2_SUPERFAMILY_NAME", "detail" : "SCOP2 Superfamily Name" }, { "value" : "SCOP_DOMAIN_ID", "detail" : "SCOP Domain Identifier" }, { "value" : "SCOP_NAME", "detail" : "SCOP Classification Name" }, { "value" : "SCOP_SUN_ID", "detail" : "SCOP Unique Identifier" }, { "value" : "SHEET_SENSE", "detail" : "Secondary Structure Sheet Sense" } ], "rcsb_description" : [ { "text" : "The additional property name.", "context" : "dictionary" } ] }, "values" : { "type" : "array", "items" : { "anyOf" : [ { "type" : "string" }, { "type" : "integer" }, { "type" : "number" } ], "examples" : [ "globin-like", "2.54", "300" ], "description" : "The value(s) of the additional property.", "rcsb_description" : [ { "text" : "The value(s) of the additional property.", "context" : "dictionary" } ] }, "uniqueItems" : false } }, "additionalProperties" : false }, "uniqueItems" : false } }, "additionalProperties" : false, "required" : [ "ordinal", "type" ] }, "minItems" : 1, "uniqueItems" : true }, "rcsb_polymer_instance_feature_summary" : { "type" : "array", "items" : { "type" : "object", "properties" : { "count" : { "type" : "integer", "description" : "The feature count per polymer chain.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The feature count per polymer chain.", "context" : "dictionary" }, { "text" : "Count Per Polymer Chain", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Polymer Instance (Chain) Features", "priority_order" : 15 } ] }, "coverage" : { "type" : "number", "examples" : [ 0.5, 0.95 ], "description" : "The fractional feature coverage relative to the full entity sequence.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The fractional feature coverage relative to the full entity sequence.", "context" : "dictionary" }, { "text" : "Coverage Fraction Per Polymer Chain", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Polymer Instance (Chain) Features", "priority_order" : 20 } ] }, "maximum_length" : { "type" : "integer", "description" : "The maximum feature length.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The maximum feature length.", "context" : "dictionary" }, { "text" : "Maximum Length (Polymer Instance Feature Summary)", "context" : "brief" } ], "rcsb_current_maximum_value" : 43848.0, "rcsb_current_minimum_value" : 1.0 }, "maximum_value" : { "type" : "number", "examples" : [ 1.012, 0.813 ], "description" : "The maximum feature value.", "rcsb_description" : [ { "text" : "The maximum feature value.", "context" : "dictionary" } ] }, "minimum_length" : { "type" : "integer", "description" : "The minimum feature length.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The minimum feature length.", "context" : "dictionary" }, { "text" : "Minimum Length (Polymer Instance Feature Summary)", "context" : "brief" } ], "rcsb_current_maximum_value" : 43848.0, "rcsb_current_minimum_value" : 1.0 }, "minimum_value" : { "type" : "number", "examples" : [ 0.012, 0.00132 ], "description" : "The minimum feature value.", "rcsb_description" : [ { "text" : "The minimum feature value.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "enum" : [ "ANGLE_OUTLIER", "ANGLE_OUTLIERS", "AVERAGE_OCCUPANCY", "BEND", "BINDING_SITE", "BOND_OUTLIER", "BOND_OUTLIERS", "C-MANNOSYLATION_SITE", "CATH", "CHIRAL_OUTLIERS", "CIS-PEPTIDE", "CLASHES", "ECOD", "HELIX_P", "HELX_LH_PP_P", "HELX_RH_3T_P", "HELX_RH_AL_P", "HELX_RH_PI_P", "LIGAND_COVALENT_LINKAGE", "LIGAND_INTERACTION", "LIGAND_METAL_COORDINATION_LINKAGE", "MA_QA_METRIC_LOCAL_TYPE_CONTACT_PROBABILITY", "MA_QA_METRIC_LOCAL_TYPE_DISTANCE", "MA_QA_METRIC_LOCAL_TYPE_ENERGY", "MA_QA_METRIC_LOCAL_TYPE_IPTM", "MA_QA_METRIC_LOCAL_TYPE_NORMALIZED_SCORE", "MA_QA_METRIC_LOCAL_TYPE_OTHER", "MA_QA_METRIC_LOCAL_TYPE_PAE", "MA_QA_METRIC_LOCAL_TYPE_PLDDT", "MA_QA_METRIC_LOCAL_TYPE_PLDDT_ALL-ATOM", "MA_QA_METRIC_LOCAL_TYPE_PLDDT_ALL-ATOM_[0,1]", "MA_QA_METRIC_LOCAL_TYPE_PLDDT_[0,1]", "MA_QA_METRIC_LOCAL_TYPE_PTM", "MA_QA_METRIC_LOCAL_TYPE_ZSCORE", "MEMBRANE_SEGMENT", "MOGUL_ANGLE_OUTLIER", "MOGUL_ANGLE_OUTLIERS", "MOGUL_BOND_OUTLIER", "MOGUL_BOND_OUTLIERS", "MOGUL_RING_OUTLIERS", "MOGUL_TORSION_OUTLIERS", "N-GLYCOSYLATION_SITE", "NATOMS_EDS", "O-GLYCOSYLATION_SITE", "OWAB", "PLANE_OUTLIERS", "Q_SCORE", "RAMACHANDRAN_OUTLIER", "ROTAMER_OUTLIER", "RSCC", "RSCC_OUTLIER", "RSR", "RSRZ", "RSRZ_OUTLIER", "S-GLYCOSYLATION_SITE", "SABDAB_ANTIBODY_HEAVY_CHAIN_SUBCLASS", "SABDAB_ANTIBODY_LIGHT_CHAIN_SUBCLASS", "SABDAB_ANTIBODY_LIGHT_CHAIN_TYPE", "SCOP", "SCOP2B_SUPERFAMILY", "SCOP2_FAMILY", "SCOP2_SUPERFAMILY", "SHEET", "STEREO_OUTLIER", "STRN", "SYMM_CLASHES", "TURN_TY1_P", "UNASSIGNED_SEC_STRUCT", "UNOBSERVED_ATOM_XYZ", "UNOBSERVED_RESIDUE_XYZ", "ZERO_OCCUPANCY_ATOM_XYZ", "ZERO_OCCUPANCY_RESIDUE_XYZ" ], "examples" : [ "CATH", "SCOP" ], "description" : "Type or category of the feature.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "ANGLE_OUTLIER", "detail" : "Molprobity bond angle outlier", "name" : "Molprobity bond angle outlier" }, { "value" : "ANGLE_OUTLIERS", "detail" : "Number of atoms with angle outliers", "name" : "ANGLE_OUTLIERS" }, { "value" : "AVERAGE_OCCUPANCY", "detail" : "The average heavy atom occupancy for coordinate records for the residue", "name" : "AVERAGE_OCCUPANCY" }, { "value" : "BEND", "detail" : "Bend - region with high backbone curvature without specific hydrogen bonding", "name" : "Bend - region with high backbone curvature without specific hydrogen bonding" }, { "value" : "BINDING_SITE", "detail" : "Macromolecular target for ligand binding", "name" : "Ligand Binding Site" }, { "value" : "BOND_OUTLIER", "detail" : "Molprobity bond distance outlier", "name" : "Molprobity bond distance outlier" }, { "value" : "BOND_OUTLIERS", "detail" : "Number of atoms with bond outliers", "name" : "BOND_OUTLIERS" }, { "value" : "C-MANNOSYLATION_SITE", "detail" : "Mannose glycan binding to the first tryptophan (W) residue in the sequence motif WXXW (where X is any amino acid).", "name" : "C-Mannosylation Site" }, { "value" : "CATH", "detail" : "CATH - Class, Architecture, Topology, and Homology Protein Structure Database", "name" : "CATH" }, { "value" : "CHIRAL_OUTLIERS", "detail" : "Number of chiral outliers", "name" : "CHIRAL_OUTLIERS" }, { "value" : "CIS-PEPTIDE", "detail" : "Peptide linkages with CIS configurations", "name" : "CIS Peptide linkages" }, { "value" : "CLASHES", "detail" : "Number of atoms a with clashes", "name" : "CLASHES" }, { "value" : "ECOD", "detail" : "ECOD - An Evolutionary Classification of Protein Domains", "name" : "ECOD" }, { "value" : "HELIX_P", "detail" : "Protein helices", "name" : "Protein helices" }, { "value" : "HELX_LH_PP_P", "detail" : "Left-handed polyproline helix (protein)", "name" : "Left-handed polyproline helix (protein)" }, { "value" : "HELX_RH_3T_P", "detail" : "Right-handed 3-10 helix (protein)", "name" : "Right-handed 3-10 helix (protein)" }, { "value" : "HELX_RH_AL_P", "detail" : "Alpha helix (protein)", "name" : "Alpha helix (protein)" }, { "value" : "HELX_RH_PI_P", "detail" : "Right-handed pi helix (protein)", "name" : "Right-handed pi helix (protein)" }, { "value" : "LIGAND_COVALENT_LINKAGE", "detail" : "Covalent ligand linkages with macromolecular target", "name" : "Covalent Ligand Linkages" }, { "value" : "LIGAND_INTERACTION", "detail" : "Ligand interactions with macromolecular target (includes covalent, metal coordination, and non-bonded interactions)", "name" : "Ligand Interactions" }, { "value" : "LIGAND_METAL_COORDINATION_LINKAGE", "detail" : "Metal coordination ligand linkages with macromolecular target", "name" : "Metal Coordination Ligand Linkages" }, { "value" : "MA_QA_METRIC_LOCAL_TYPE_CONTACT_PROBABILITY", "detail" : "the contact probability of a pairwise interaction", "name" : "MA_QA_METRIC_LOCAL_TYPE" }, { "value" : "MA_QA_METRIC_LOCAL_TYPE_DISTANCE", "detail" : "the lower the distance, the better the quality", "name" : "MA_QA_METRIC_LOCAL_TYPE" }, { "value" : "MA_QA_METRIC_LOCAL_TYPE_ENERGY", "detail" : "the lower the energy, the better the quality", "name" : "MA_QA_METRIC_LOCAL_TYPE" }, { "value" : "MA_QA_METRIC_LOCAL_TYPE_IPTM", "detail" : "confidence score of protein-protein interface based on the template modeling score in [0,1]", "name" : "MA_QA_METRIC_LOCAL_TYPE" }, { "value" : "MA_QA_METRIC_LOCAL_TYPE_NORMALIZED_SCORE", "detail" : "normalized score ranging from 0 to 1", "name" : "MA_QA_METRIC_LOCAL_TYPE" }, { "value" : "MA_QA_METRIC_LOCAL_TYPE_OTHER", "detail" : "other type of QA metric", "name" : "MA_QA_METRIC_LOCAL_TYPE" }, { "value" : "MA_QA_METRIC_LOCAL_TYPE_PAE", "detail" : "predicted aligned error (in Angstroms)", "name" : "MA_QA_METRIC_LOCAL_TYPE" }, { "value" : "MA_QA_METRIC_LOCAL_TYPE_PLDDT", "detail" : "confidence score predicting accuracy according to the CA-only Local Distance Difference Test (lDDT-CA) in [0,100]", "name" : "MA_QA_METRIC_LOCAL_TYPE" }, { "value" : "MA_QA_METRIC_LOCAL_TYPE_PLDDT_ALL-ATOM", "detail" : "confidence score predicting accuracy according to the all-atom Local Distance Difference Test (lDDT) in [0,100]", "name" : "MA_QA_METRIC_LOCAL_TYPE" }, { "value" : "MA_QA_METRIC_LOCAL_TYPE_PLDDT_ALL-ATOM_[0,1]", "detail" : "confidence score predicting accuracy according to the all-atom Local Distance Difference Test (lDDT) in [0,1]", "name" : "MA_QA_METRIC_LOCAL_TYPE" }, { "value" : "MA_QA_METRIC_LOCAL_TYPE_PLDDT_[0,1]", "detail" : "confidence score predicting accuracy according to the CA-only Local Distance Difference Test (lDDT-CA) in [0,1]", "name" : "MA_QA_METRIC_LOCAL_TYPE" }, { "value" : "MA_QA_METRIC_LOCAL_TYPE_PTM", "detail" : "confidence score predicting accuracy according to the template modeling score in [0,1]", "name" : "MA_QA_METRIC_LOCAL_TYPE" }, { "value" : "MA_QA_METRIC_LOCAL_TYPE_ZSCORE", "detail" : "number of standard deviations from optimal/best", "name" : "MA_QA_METRIC_LOCAL_TYPE" }, { "value" : "MEMBRANE_SEGMENT", "detail" : "Extent of a region located in a membrane", "name" : "Extent of a region located in a membrane" }, { "value" : "MOGUL_ANGLE_OUTLIER", "detail" : "Mogul bond angle outlier", "name" : "Mogul bond angle outlier" }, { "value" : "MOGUL_ANGLE_OUTLIERS", "detail" : "Number of angle outliers as reported by MOGUL", "name" : "MOGUL_ANGLE_OUTLIERS" }, { "value" : "MOGUL_BOND_OUTLIER", "detail" : "Mogul bond distance outlier", "name" : "Mogul bond distance outlier" }, { "value" : "MOGUL_BOND_OUTLIERS", "detail" : "Number of bond outliers as reported by MOGUL", "name" : "MOGUL_BOND_OUTLIERS" }, { "value" : "MOGUL_RING_OUTLIERS", "detail" : "Number of atoms with ring outliers as reported by MOGUL", "name" : "MOGUL_RING_OUTLIERS" }, { "value" : "MOGUL_TORSION_OUTLIERS", "detail" : "Number of torsion angle outliers as reported by MOGUL", "name" : "MOGUL_TORSION_OUTLIERS" }, { "value" : "N-GLYCOSYLATION_SITE", "detail" : "Glycan binding to the amide nitrogen of an asparagine (Asn) residue", "name" : "N-Glycosylation Site" }, { "value" : "NATOMS_EDS", "detail" : "Number of atoms in the residue returned by the EDS software", "name" : "NATOMS_EDS" }, { "value" : "O-GLYCOSYLATION_SITE", "detail" : "Glycan binding to the oxygen atom of serine (Ser) or threonine (Thr) residues", "name" : "O-Glycosylation Site" }, { "value" : "OWAB", "detail" : "Occupancy-weighted Average B value", "name" : "OWAB" }, { "value" : "PLANE_OUTLIERS", "detail" : "Number of planar outliers", "name" : "PLANE_OUTLIERS" }, { "value" : "Q_SCORE", "detail" : "Q_score", "name" : "Q_SCORE" }, { "value" : "RAMACHANDRAN_OUTLIER", "detail" : "Molprobity Ramachandran outlier", "name" : "Molprobity Ramachandran outlier" }, { "value" : "ROTAMER_OUTLIER", "detail" : "Molprobity rotamer outlier", "name" : "Molprobity rotamer outlier" }, { "value" : "RSCC", "detail" : "Real space correlation coefficient", "name" : "RSCC" }, { "value" : "RSCC_OUTLIER", "detail" : "Real space density correlation value < 0.65", "name" : "Real space density correlation outlier" }, { "value" : "RSR", "detail" : "Real Space R-value", "name" : "RSR" }, { "value" : "RSRZ", "detail" : "Real Space R-value z-score", "name" : "RSRZ" }, { "value" : "RSRZ_OUTLIER", "detail" : "Real space R-value Z score > 2", "name" : "Real space outlier" }, { "value" : "S-GLYCOSYLATION_SITE", "detail" : "Glycan binding to the sulfur atom of a cysteine (Cys) residue", "name" : "S-Glycosylation Site" }, { "value" : "SABDAB_ANTIBODY_HEAVY_CHAIN_SUBCLASS", "detail" : "Structural Antibody Database (SAbDab) antibody heavy chain subclass (IGHV1, IGHV2,)", "name" : "SAbDab Antibody Heavy Chain Subclass" }, { "value" : "SABDAB_ANTIBODY_LIGHT_CHAIN_SUBCLASS", "detail" : "Structural Antibody Database (SAbDab) antibody light chain subclass (IGLV1, IGLV2, ...)", "name" : "SAbDab Antibody Light Chain Subclass" }, { "value" : "SABDAB_ANTIBODY_LIGHT_CHAIN_TYPE", "detail" : "Structural Antibody Database (SAbDab) antibody light chain type (Kappa or Lambda)", "name" : "SAbDab Antibody Light Chain Type" }, { "value" : "SCOP", "detail" : "SCOP - Structural Classification of Proteins", "name" : "SCOP" }, { "value" : "SCOP2B_SUPERFAMILY", "detail" : "SCOP2B - Structural Classification of Proteins 2 - Superfamily automated assignments", "name" : "SCOP2B Superfamily" }, { "value" : "SCOP2_FAMILY", "detail" : "SCOP2 - Structural Classification of Proteins 2 Family", "name" : "SCOP2 Family" }, { "value" : "SCOP2_SUPERFAMILY", "detail" : "SCOP2 - Structural Classification of Proteins 2 Superfamily", "name" : "SCOP2 Superfamily" }, { "value" : "SHEET", "detail" : "Beta-sheets", "name" : "Beta-sheets" }, { "value" : "STEREO_OUTLIER", "detail" : "Stereochemical/chirality outlier", "name" : "Stereochemical/chirality outlier" }, { "value" : "STRN", "detail" : "Strand or beta-bridge (protein)", "name" : "Strand or beta-bridge (protein)" }, { "value" : "SYMM_CLASHES", "detail" : "Number of symmetry related clashes", "name" : "SYMM_CLASHES" }, { "value" : "TURN_TY1_P", "detail" : "Type I turn (protein)", "name" : "Type I turn (protein)" }, { "value" : "UNASSIGNED_SEC_STRUCT", "detail" : "Unassigned secondary structure", "name" : "Unassigned secondary structure" }, { "value" : "UNOBSERVED_ATOM_XYZ", "detail" : "Unobserved atom coordinates", "name" : "Unobserved Atoms" }, { "value" : "UNOBSERVED_RESIDUE_XYZ", "detail" : "Unobserved residue coordinates", "name" : "Unobserved Residues" }, { "value" : "ZERO_OCCUPANCY_ATOM_XYZ", "detail" : "Atom coordinates with zero occupancy", "name" : "Zero Occupancy Atoms" }, { "value" : "ZERO_OCCUPANCY_RESIDUE_XYZ", "detail" : "Residue coordinates with zero occupancy", "name" : "Zero Occupancy Residues" } ], "rcsb_description" : [ { "text" : "Type or category of the feature.", "context" : "dictionary" }, { "text" : "Type (Polymer Instance Feature Summary)", "context" : "brief" } ] } }, "additionalProperties" : false }, "minItems" : 1, "uniqueItems" : true, "rcsb_nested_indexing" : true, "rcsb_nested_indexing_context" : [ { "category_name" : "feature_summary", "category_path" : "rcsb_polymer_instance_feature_summary.type", "context_attributes" : [ { "context_value" : "CIS-PEPTIDE", "attributes" : [ { "examples" : [ 1, 10 ], "path" : "rcsb_polymer_instance_feature_summary.count", "rcsb_current_minimum_value" : 1.0, "rcsb_current_maximum_value" : 90.0 } ] }, { "context_value" : "HELIX_P", "attributes" : [ { "examples" : [ 1, 10 ], "path" : "rcsb_polymer_instance_feature_summary.count", "rcsb_current_minimum_value" : 1.0, "rcsb_current_maximum_value" : 374.0 }, { "examples" : [ 0.15, 0.45 ], "path" : "rcsb_polymer_instance_feature_summary.coverage", "rcsb_current_minimum_value" : 7.1E-4, "rcsb_current_maximum_value" : 8.06316 } ] }, { "context_value" : "SHEET", "attributes" : [ { "examples" : [ 1, 10 ], "path" : "rcsb_polymer_instance_feature_summary.count", "rcsb_current_minimum_value" : 1.0, "rcsb_current_maximum_value" : 295.0 }, { "examples" : [ 0.15, 0.45 ], "path" : "rcsb_polymer_instance_feature_summary.coverage", "rcsb_current_minimum_value" : 4.1E-4, "rcsb_current_maximum_value" : 19.54641 } ] }, { "context_value" : "RSCC_OUTLIER", "attributes" : [ { "examples" : [ 1, 10 ], "path" : "rcsb_polymer_instance_feature_summary.count" } ] }, { "context_value" : "RSRZ_OUTLIER", "attributes" : [ { "examples" : [ 1, 10 ], "path" : "rcsb_polymer_instance_feature_summary.count" } ] }, { "context_value" : "UNOBSERVED_RESIDUE_XYZ", "attributes" : [ { "examples" : [ 0.15, 0.45 ], "path" : "rcsb_polymer_instance_feature_summary.coverage", "rcsb_current_minimum_value" : 2.2E-4, "rcsb_current_maximum_value" : 0.99964 } ] }, { "context_value" : "UNOBSERVED_ATOM_XYZ", "attributes" : [ { "examples" : [ 0.15, 0.45 ], "path" : "rcsb_polymer_instance_feature_summary.coverage", "rcsb_current_minimum_value" : 1.9E-4, "rcsb_current_maximum_value" : 1.0 } ] } ] } ] }, "rcsb_polymer_instance_info" : { "type" : "object", "properties" : { "modeled_residue_count" : { "type" : "integer", "description" : "The number of modeled residues in the polymer instance.", "rcsb_description" : [ { "text" : "The number of modeled residues in the polymer instance.", "context" : "dictionary" } ] } }, "additionalProperties" : false }, "rcsb_polymer_struct_conn" : { "type" : "array", "items" : { "type" : "object", "properties" : { "connect_type" : { "type" : "string", "enum" : [ "covalent bond", "covalent modification of a nucleotide base", "covalent modification of a nucleotide phosphate", "covalent modification of a nucleotide sugar", "covalent residue modification", "disulfide bridge", "hydrogen bond", "ionic interaction", "metal coordination", "mismatched base pairs" ], "description" : "The connection type.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The connection type.", "context" : "dictionary" }, { "text" : "Connect Type (Polymer Struct Conn)", "context" : "brief" } ] }, "description" : { "type" : "string", "examples" : [ "Watson-Crick base pair" ], "description" : "A description of special details of the connection.", "rcsb_description" : [ { "text" : "A description of special details of the connection.", "context" : "dictionary" } ] }, "dist_value" : { "type" : "number", "description" : "Distance value for this contact.", "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "Distance value for this contact.", "context" : "dictionary" } ] }, "id" : { "type" : "string", "description" : "The value of _rcsb_polymer_struct_conn.id is an identifier for connection.\n\n Note that this item need not be a number; it can be any unique\n identifier.", "rcsb_description" : [ { "text" : "The value of _rcsb_polymer_struct_conn.id is an identifier for connection.\n\n Note that this item need not be a number; it can be any unique\n identifier.", "context" : "dictionary" } ] }, "ordinal_id" : { "type" : "integer", "description" : "The value of _rcsb_polymer_struct_conn.id must uniquely identify a record in\n the rcsb_polymer_struct_conn list.", "rcsb_description" : [ { "text" : "The value of _rcsb_polymer_struct_conn.id must uniquely identify a record in\n the rcsb_polymer_struct_conn list.", "context" : "dictionary" } ] }, "role" : { "type" : "string", "enum" : [ "C-Mannosylation", "N-Glycosylation", "O-Glycosylation", "S-Glycosylation" ], "examples" : [ "N-Glycosylation", "O-Glycosylation" ], "description" : "The chemical or structural role of the interaction", "rcsb_search_context" : [ "exact-match", "suggest" ], "rcsb_full_text_priority" : 20, "rcsb_description" : [ { "text" : "The chemical or structural role of the interaction", "context" : "dictionary" }, { "text" : "Glycosylation Site", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Polymer Molecular Features", "priority_order" : 45 } ] }, "value_order" : { "type" : "string", "enum" : [ "doub", "quad", "sing", "trip" ], "description" : "The chemical bond order associated with the specified atoms in\n this contact.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "doub", "detail" : "double bond" }, { "value" : "quad", "detail" : "quadruple bond" }, { "value" : "sing", "detail" : "single bond" }, { "value" : "trip", "detail" : "triple bond" } ], "rcsb_description" : [ { "text" : "The chemical bond order associated with the specified atoms in\n this contact.", "context" : "dictionary" }, { "text" : "Value Order (Polymer Struct Conn)", "context" : "brief" } ] }, "connect_target" : { "type" : "object", "properties" : { "auth_asym_id" : { "type" : "string", "description" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.auth_asym_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.auth_asym_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "auth_seq_id" : { "type" : "string", "description" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.auth_seq_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.auth_seq_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "label_alt_id" : { "type" : "string", "description" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.label_alt_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.label_alt_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "label_asym_id" : { "type" : "string", "description" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.label_asym_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.label_asym_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "label_atom_id" : { "type" : "string", "description" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.label_atom_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.label_atom_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "label_comp_id" : { "type" : "string", "description" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.label_comp_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.label_comp_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "label_seq_id" : { "type" : "integer", "description" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.connect_target_label_seq_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the target of the structure\n connection.\n\n This data item is a pointer to _atom_site.connect_target_label_seq_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "symmetry" : { "type" : "string", "examples" : [ "1_555", "7_645" ], "description" : "Describes the symmetry operation that should be applied to the\n atom set specified by _rcsb_polymer_struct_conn.label* to generate the\n target of the structure connection.", "rcsb_description" : [ { "text" : "Describes the symmetry operation that should be applied to the\n atom set specified by _rcsb_polymer_struct_conn.label* to generate the\n target of the structure connection.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "label_asym_id", "label_comp_id" ] }, "connect_partner" : { "type" : "object", "properties" : { "label_alt_id" : { "type" : "string", "description" : "A component of the identifier for the partner in the structure\n connection.\n\n This data item is a pointer to _atom_site.label_alt_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the partner in the structure\n connection.\n\n This data item is a pointer to _atom_site.label_alt_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "label_asym_id" : { "type" : "string", "description" : "A component of the identifier for the partner in the structure\n connection.\n\n This data item is a pointer to _atom_site.label_asym_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the partner in the structure\n connection.\n\n This data item is a pointer to _atom_site.label_asym_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "label_atom_id" : { "type" : "string", "description" : "A component of the identifier for the partner in the structure\n connection.\n\n This data item is a pointer to _chem_comp_atom.atom_id in the\n CHEM_COMP_ATOM category.", "rcsb_description" : [ { "text" : "A component of the identifier for the partner in the structure\n connection.\n\n This data item is a pointer to _chem_comp_atom.atom_id in the\n CHEM_COMP_ATOM category.", "context" : "dictionary" } ] }, "label_comp_id" : { "type" : "string", "description" : "A component of the identifier for the partner in the structure\n connection.\n\n This data item is a pointer to _atom_site.label_comp_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the partner in the structure\n connection.\n\n This data item is a pointer to _atom_site.label_comp_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "label_seq_id" : { "type" : "integer", "description" : "A component of the identifier for the partner in the structure\n connection.\n\n This data item is a pointer to _atom_site.label_seq_id in the\n ATOM_SITE category.", "rcsb_description" : [ { "text" : "A component of the identifier for the partner in the structure\n connection.\n\n This data item is a pointer to _atom_site.label_seq_id in the\n ATOM_SITE category.", "context" : "dictionary" } ] }, "symmetry" : { "type" : "string", "examples" : [ "1_555", "7_645" ], "description" : "Describes the symmetry operation that should be applied to the\n atom set specified by _rcsb_polymer_struct_conn.connect_partner_label* to generate the\n partner in the structure connection.", "rcsb_description" : [ { "text" : "Describes the symmetry operation that should be applied to the\n atom set specified by _rcsb_polymer_struct_conn.connect_partner_label* to generate the\n partner in the structure connection.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "label_asym_id", "label_comp_id" ] } }, "additionalProperties" : false, "required" : [ "ordinal_id" ] }, "minItems" : 1, "uniqueItems" : true }, "audit_author" : { "type" : "array", "items" : { "type" : "object", "properties" : { "identifier_ORCID" : { "type" : "string", "examples" : [ "0000-0002-6681-547X" ], "description" : "The Open Researcher and Contributor ID (ORCID).", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The Open Researcher and Contributor ID (ORCID).", "context" : "dictionary" }, { "text" : "Structure Author ORCID", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Structure Details", "priority_order" : 15 } ] }, "name" : { "type" : "string", "examples" : [ "Jones, T.J.", "Bleary, Percival R.", "O'Neil, F.K.", "Van den Bossche, G.", "Yang, D.-L.", "Simonov, Yu.A" ], "description" : "The name of an author of this data block. If there are multiple\n authors, _audit_author.name is looped with _audit_author.address.\n The family name(s), followed by a comma and including any\n dynastic components, precedes the first name(s) or initial(s).", "rcsb_search_context" : [ "exact-match", "full-text", "suggest" ], "rcsb_full_text_priority" : 20, "rcsb_description" : [ { "text" : "The name of an author of this data block. If there are multiple\n authors, _audit_author.name is looped with _audit_author.address.\n The family name(s), followed by a comma and including any\n dynastic components, precedes the first name(s) or initial(s).", "context" : "dictionary" }, { "text" : "List people responsible for the contents of this entry. Hyphens, apostrophes and blank spaces are allowed in the last names. Special characters and character modifiers should not be used.", "context" : "deposition" }, { "text" : "Structure Author", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Structure Details", "priority_order" : 10 } ] }, "pdbx_ordinal" : { "type" : "integer", "description" : "This data item defines the order of the author's name in the\n list of audit authors.", "rcsb_description" : [ { "text" : "This data item defines the order of the author's name in the\n list of audit authors.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "pdbx_ordinal" ] }, "minItems" : 1, "uniqueItems" : true }, "cell" : { "type" : "object", "properties" : { "Z_PDB" : { "type" : "integer", "description" : "The number of the polymeric chains in a unit cell. In the case\n of heteropolymers, Z is the number of occurrences of the most\n populous chain.\n\n This data item is provided for compatibility with the original\n Protein Data Bank format, and only for that purpose.", "rcsb_description" : [ { "text" : "The number of the polymeric chains in a unit cell. In the case\n of heteropolymers, Z is the number of occurrences of the most\n populous chain.\n\n This data item is provided for compatibility with the original\n Protein Data Bank format, and only for that purpose.", "context" : "dictionary" } ] }, "angle_alpha" : { "type" : "number", "description" : "Unit-cell angle alpha of the reported structure in degrees.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "degrees", "rcsb_description" : [ { "text" : "Unit-cell angle alpha of the reported structure in degrees.", "context" : "dictionary" }, { "text" : "Angle alpha", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Cell Dimensions and Space Group", "priority_order" : 20 } ], "rcsb_current_maximum_value" : 124.813, "rcsb_current_minimum_value" : 58.8 }, "angle_beta" : { "type" : "number", "description" : "Unit-cell angle beta of the reported structure in degrees.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "degrees", "rcsb_description" : [ { "text" : "Unit-cell angle beta of the reported structure in degrees.", "context" : "dictionary" }, { "text" : "Angle beta", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Cell Dimensions and Space Group", "priority_order" : 25 } ], "rcsb_current_maximum_value" : 164.339, "rcsb_current_minimum_value" : 45.4 }, "angle_gamma" : { "type" : "number", "description" : "Unit-cell angle gamma of the reported structure in degrees.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "degrees", "rcsb_description" : [ { "text" : "Unit-cell angle gamma of the reported structure in degrees.", "context" : "dictionary" }, { "text" : "Angle gamma", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Cell Dimensions and Space Group", "priority_order" : 30 } ], "rcsb_current_maximum_value" : 125.0, "rcsb_current_minimum_value" : 57.76 }, "formula_units_Z" : { "type" : "integer", "description" : "The number of the formula units in the unit cell as specified\n by _chemical_formula.structural, _chemical_formula.moiety or\n _chemical_formula.sum.", "rcsb_description" : [ { "text" : "The number of the formula units in the unit cell as specified\n by _chemical_formula.structural, _chemical_formula.moiety or\n _chemical_formula.sum.", "context" : "dictionary" } ] }, "length_a" : { "type" : "number", "description" : "Unit-cell length a corresponding to the structure reported in\nangstroms.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "Unit-cell length a corresponding to the structure reported in\nangstroms.", "context" : "dictionary" }, { "text" : "Length a", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Cell Dimensions and Space Group", "priority_order" : 5 } ], "rcsb_current_maximum_value" : 1255.0, "rcsb_current_minimum_value" : 1.0 }, "length_b" : { "type" : "number", "description" : "Unit-cell length b corresponding to the structure reported in\n angstroms.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "Unit-cell length b corresponding to the structure reported in\n angstroms.", "context" : "dictionary" }, { "text" : "Length b", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Cell Dimensions and Space Group", "priority_order" : 10 } ], "rcsb_current_maximum_value" : 1255.0, "rcsb_current_minimum_value" : 1.0 }, "length_c" : { "type" : "number", "description" : "Unit-cell length c corresponding to the structure reported in\nangstroms.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "Unit-cell length c corresponding to the structure reported in\nangstroms.", "context" : "dictionary" }, { "text" : "Length c", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Cell Dimensions and Space Group", "priority_order" : 15 } ], "rcsb_current_maximum_value" : 1933.3, "rcsb_current_minimum_value" : 1.0 }, "pdbx_unique_axis" : { "type" : "string", "description" : "To further identify unique axis if necessary. E.g., P 21 with\n an unique C axis will have 'C' in this field.", "rcsb_description" : [ { "text" : "To further identify unique axis if necessary. E.g., P 21 with\n an unique C axis will have 'C' in this field.", "context" : "dictionary" } ] }, "volume" : { "type" : "number", "description" : "Cell volume V in angstroms cubed.\n\n V = a b c (1 - cos^2^~alpha~ - cos^2^~beta~ - cos^2^~gamma~\n + 2 cos~alpha~ cos~beta~ cos~gamma~)^1/2^\n\n a = _cell.length_a\n b = _cell.length_b\n c = _cell.length_c\n alpha = _cell.angle_alpha\n beta = _cell.angle_beta\n gamma = _cell.angle_gamma", "rcsb_units" : "angstroms_cubed", "rcsb_description" : [ { "text" : "Cell volume V in angstroms cubed.\n\n V = a b c (1 - cos^2^~alpha~ - cos^2^~beta~ - cos^2^~gamma~\n + 2 cos~alpha~ cos~beta~ cos~gamma~)^1/2^\n\n a = _cell.length_a\n b = _cell.length_b\n c = _cell.length_c\n alpha = _cell.angle_alpha\n beta = _cell.angle_beta\n gamma = _cell.angle_gamma", "context" : "dictionary" } ] } }, "additionalProperties" : false }, "citation" : { "type" : "array", "items" : { "type" : "object", "properties" : { "book_id_ISBN" : { "type" : "string", "description" : "The International Standard Book Number (ISBN) code assigned to\n the book cited; relevant for books or book chapters.", "rcsb_description" : [ { "text" : "The International Standard Book Number (ISBN) code assigned to\n the book cited; relevant for books or book chapters.", "context" : "dictionary" } ] }, "book_publisher" : { "type" : "string", "examples" : [ "John Wiley and Sons" ], "description" : "The name of the publisher of the citation; relevant\n for books or book chapters.", "rcsb_description" : [ { "text" : "The name of the publisher of the citation; relevant\n for books or book chapters.", "context" : "dictionary" } ] }, "book_publisher_city" : { "type" : "string", "examples" : [ "London" ], "description" : "The location of the publisher of the citation; relevant\n for books or book chapters.", "rcsb_description" : [ { "text" : "The location of the publisher of the citation; relevant\n for books or book chapters.", "context" : "dictionary" } ] }, "book_title" : { "type" : "string", "description" : "The title of the book in which the citation appeared; relevant\n for books or book chapters.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The title of the book in which the citation appeared; relevant\n for books or book chapters.", "context" : "dictionary" }, { "text" : "Book Title (Citation)", "context" : "brief" } ] }, "coordinate_linkage" : { "type" : "string", "enum" : [ "n", "no", "y", "yes" ], "description" : "_citation.coordinate_linkage states whether this citation\n is concerned with precisely the set of coordinates given in the\n data block. If, for instance, the publication described the same\n structure, but the coordinates had undergone further refinement\n prior to the creation of the data block, the value of this data\n item would be 'no'.", "rcsb_enum_annotated" : [ { "value" : "n", "detail" : "abbreviation for \"no\"" }, { "value" : "no", "detail" : "citation unrelated to current coordinates" }, { "value" : "y", "detail" : "abbreviation for \"yes\"" }, { "value" : "yes", "detail" : "citation related to current coordinates" } ], "rcsb_description" : [ { "text" : "_citation.coordinate_linkage states whether this citation\n is concerned with precisely the set of coordinates given in the\n data block. If, for instance, the publication described the same\n structure, but the coordinates had undergone further refinement\n prior to the creation of the data block, the value of this data\n item would be 'no'.", "context" : "dictionary" } ] }, "country" : { "type" : "string", "description" : "The country/region of publication; relevant for books\n and book chapters.", "rcsb_description" : [ { "text" : "The country/region of publication; relevant for books\n and book chapters.", "context" : "dictionary" } ] }, "id" : { "type" : "string", "examples" : [ "primary", "1", "2" ], "description" : "The value of _citation.id must uniquely identify a record in the\n CITATION list.\n\n The _citation.id 'primary' should be used to indicate the\n citation that the author(s) consider to be the most pertinent to\n the contents of the data block.\n\n Note that this item need not be a number; it can be any unique\n identifier.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The value of _citation.id must uniquely identify a record in the\n CITATION list.\n\n The _citation.id 'primary' should be used to indicate the\n citation that the author(s) consider to be the most pertinent to\n the contents of the data block.\n\n Note that this item need not be a number; it can be any unique\n identifier.", "context" : "dictionary" }, { "text" : "Id (Citation)", "context" : "brief" } ] }, "journal_abbrev" : { "type" : "string", "examples" : [ "J.Mol.Biol.", "J. Mol. Biol." ], "description" : "Abbreviated name of the cited journal as given in the\n Chemical Abstracts Service Source Index.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Abbreviated name of the cited journal as given in the\n Chemical Abstracts Service Source Index.", "context" : "dictionary" }, { "text" : "The PDB (i.e., the Chemical Abstracts) abbreviation for a journal. If you do not know the abbreviation, then give the complete name of the journal and we will try and find it for you. If it is a book or other monographic work, state the full title.", "context" : "deposition" }, { "text" : "Citation Journal Name", "context" : "brief" } ] }, "journal_full" : { "type" : "string", "examples" : [ "Journal of Molecular Biology" ], "description" : "Full name of the cited journal; relevant for journal articles.", "rcsb_description" : [ { "text" : "Full name of the cited journal; relevant for journal articles.", "context" : "dictionary" } ] }, "journal_id_ASTM" : { "type" : "string", "description" : "The American Society for Testing and Materials (ASTM) code\n assigned to the journal cited (also referred to as the CODEN\n designator of the Chemical Abstracts Service); relevant for\n journal articles.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The American Society for Testing and Materials (ASTM) code\n assigned to the journal cited (also referred to as the CODEN\n designator of the Chemical Abstracts Service); relevant for\n journal articles.", "context" : "dictionary" }, { "text" : "Journal Id Astm (Citation)", "context" : "brief" } ] }, "journal_id_CSD" : { "type" : "string", "examples" : [ "0070" ], "description" : "The Cambridge Structural Database (CSD) code assigned to the\n journal cited; relevant for journal articles. This is also the\n system used at the Protein Data Bank (PDB).", "rcsb_description" : [ { "text" : "The Cambridge Structural Database (CSD) code assigned to the\n journal cited; relevant for journal articles. This is also the\n system used at the Protein Data Bank (PDB).", "context" : "dictionary" } ] }, "journal_id_ISSN" : { "type" : "string", "description" : "The International Standard Serial Number (ISSN) code assigned to\n the journal cited; relevant for journal articles.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The International Standard Serial Number (ISSN) code assigned to\n the journal cited; relevant for journal articles.", "context" : "dictionary" }, { "text" : "Journal Id Issn (Citation)", "context" : "brief" } ] }, "journal_issue" : { "type" : "string", "examples" : [ "2" ], "description" : "Issue number of the journal cited; relevant for journal\n articles.", "rcsb_description" : [ { "text" : "Issue number of the journal cited; relevant for journal\n articles.", "context" : "dictionary" } ] }, "journal_volume" : { "type" : "string", "examples" : [ "174" ], "description" : "Volume number of the journal cited; relevant for journal\n articles.", "rcsb_description" : [ { "text" : "Volume number of the journal cited; relevant for journal\n articles.", "context" : "dictionary" }, { "text" : "The volume number of the journal in which the article appeared. Example: 317", "context" : "deposition" } ] }, "language" : { "type" : "string", "examples" : [ "German" ], "description" : "Language in which the cited article is written.", "rcsb_description" : [ { "text" : "Language in which the cited article is written.", "context" : "dictionary" } ] }, "page_first" : { "type" : "string", "description" : "The first page of the citation; relevant for journal\n articles, books and book chapters.", "rcsb_description" : [ { "text" : "The first page of the citation; relevant for journal\n articles, books and book chapters.", "context" : "dictionary" }, { "text" : "The starting page number of this article.", "context" : "deposition" } ] }, "page_last" : { "type" : "string", "description" : "The last page of the citation; relevant for journal\n articles, books and book chapters.", "rcsb_description" : [ { "text" : "The last page of the citation; relevant for journal\n articles, books and book chapters.", "context" : "dictionary" }, { "text" : "The last page number of this article.", "context" : "deposition" } ] }, "pdbx_database_id_DOI" : { "type" : "string", "examples" : [ "10.2345/S1384107697000225" ], "description" : "Document Object Identifier used by doi.org to uniquely\n specify bibliographic entry.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Document Object Identifier used by doi.org to uniquely\n specify bibliographic entry.", "context" : "dictionary" }, { "text" : "The document Object Identifier used by doi.org to uniquely specify bibliographic entry", "context" : "deposition" }, { "text" : "Citation DOI", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Publications All", "priority_order" : 25 } ] }, "pdbx_database_id_PubMed" : { "type" : "integer", "description" : "Ascession number used by PubMed to categorize a specific\n bibliographic entry.", "rcsb_description" : [ { "text" : "Ascession number used by PubMed to categorize a specific\n bibliographic entry.", "context" : "dictionary" }, { "text" : "The accession number used by PubMed to categorize a specific bibliographic entry", "context" : "deposition" } ] }, "rcsb_authors" : { "type" : "array", "items" : { "type" : "string", "examples" : [ "Bleary, Percival R." ], "description" : "Names of the authors of the citation; relevant for journal\n articles, books and book chapters. Names are separated by vertical bars.\n\n The family name(s), followed by a comma and including any\n dynastic components, precedes the first name(s) or initial(s).", "rcsb_search_context" : [ "exact-match", "full-text", "suggest" ], "rcsb_full_text_priority" : 20, "rcsb_description" : [ { "text" : "Names of the authors of the citation; relevant for journal\n articles, books and book chapters. Names are separated by vertical bars.\n\n The family name(s), followed by a comma and including any\n dynastic components, precedes the first name(s) or initial(s).", "context" : "dictionary" }, { "text" : "Citation Author", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Publications All", "priority_order" : 5 } ] }, "uniqueItems" : false }, "rcsb_is_primary" : { "type" : "string", "enum" : [ "N", "Y" ], "examples" : [ "Y" ], "description" : "Flag to indicate a primary citation.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Flag to indicate a primary citation.", "context" : "dictionary" }, { "text" : "Is Primary (Citation)", "context" : "brief" } ] }, "rcsb_journal_abbrev" : { "type" : "string", "examples" : [ "Nat Struct Mol Biol" ], "description" : "Normalized journal abbreviation.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Normalized journal abbreviation.", "context" : "dictionary" }, { "text" : "Citation Journal Name (Abbreviated)", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Publications All", "priority_order" : 15 } ] }, "title" : { "type" : "string", "examples" : [ "Structure of diferric duck ovotransferrin\n at 2.35 Angstroms resolution." ], "description" : "The title of the citation; relevant for journal articles, books\n and book chapters.", "rcsb_search_context" : [ "full-text", "suggest" ], "rcsb_full_text_priority" : 20, "rcsb_description" : [ { "text" : "The title of the citation; relevant for journal articles, books\n and book chapters.", "context" : "dictionary" }, { "text" : "Title of the article or chapter or part of a book. This should be marked NULL if the author(s) listed wrote the entire book (or other work) and no sub-section of the book is being cited. Example: The Structure of Crystalline Profilin-Beta-Actin", "context" : "deposition" }, { "text" : "Citation Title", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Publications All", "priority_order" : 10 } ] }, "unpublished_flag" : { "type" : "string", "enum" : [ "N", "Y" ], "description" : "Flag to indicate that this citation will not be published.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Flag to indicate that this citation will not be published.", "context" : "dictionary" }, { "text" : "Unpublished Flag (Citation)", "context" : "brief" } ] }, "year" : { "type" : "integer", "description" : "The year of the citation; relevant for journal articles, books\n and book chapters.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The year of the citation; relevant for journal articles, books\n and book chapters.", "context" : "dictionary" }, { "text" : "The year of publication of the article. Example: 2002", "context" : "deposition" }, { "text" : "Citation Publication Year", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Publications All", "priority_order" : 20 } ], "rcsb_current_maximum_value" : 2026.0, "rcsb_current_minimum_value" : 1947.0 } }, "additionalProperties" : false, "required" : [ "id" ] }, "minItems" : 1, "uniqueItems" : true, "rcsb_nested_indexing" : true }, "database_2" : { "type" : "array", "items" : { "type" : "object", "properties" : { "database_code" : { "type" : "string", "examples" : [ "4HHB", "3LTQ" ], "description" : "The code assigned by the database identified in\n _database_2.database_id.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The code assigned by the database identified in\n _database_2.database_id.", "context" : "dictionary" }, { "text" : "Database Code", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "ID(s) and Keywords", "priority_order" : 15 } ] }, "database_id" : { "type" : "string", "enum" : [ "AlphaFoldDB", "BMRB", "EBI", "EMDB", "MODBASE", "ModelArchive", "NDB", "PDB", "PDB-Dev", "PDBE", "PDB_ACC", "RCSB", "SWISS-MODEL_REPOSITORY", "WWPDB" ], "description" : "An abbreviation that identifies the database.", "rcsb_enum_annotated" : [ { "value" : "AlphaFoldDB", "detail" : " AlphaFoldDB" }, { "value" : "BMRB", "detail" : " Biological Magnetic Reference Data Bank" }, { "value" : "EBI", "detail" : " European Bioinformatics Institute" }, { "value" : "EMDB", "detail" : " Electron Microscopy Data Bank" }, { "value" : "MODBASE", "detail" : " Database of Comparative Protein Structure Models" }, { "value" : "ModelArchive", "detail" : " ModelArchive" }, { "value" : "NDB", "detail" : " Nucleic Acid Database" }, { "value" : "PDB", "detail" : " Protein Data Bank" }, { "value" : "PDB-Dev", "detail" : " PDB-Dev integrative/hybrid methods" }, { "value" : "PDBE", "detail" : " Protein Data Bank Europe" }, { "value" : "PDB_ACC", "detail" : " Protein Data Bank Versioned Accession" }, { "value" : "RCSB", "detail" : " Research Collaboratory for Structural Bioinformatics" }, { "value" : "SWISS-MODEL_REPOSITORY", "detail" : " Swiss-Model Repository" }, { "value" : "WWPDB", "detail" : " Worldwide Protein Data Bank" } ], "rcsb_description" : [ { "text" : "An abbreviation that identifies the database.", "context" : "dictionary" } ] }, "pdbx_DOI" : { "type" : "string", "examples" : [ "10.2210/pdb6lu7/pdb" ], "description" : "Document Object Identifier (DOI) for this entry registered\nwith http://crossref.org.", "rcsb_description" : [ { "text" : "Document Object Identifier (DOI) for this entry registered\nwith http://crossref.org.", "context" : "dictionary" } ] }, "pdbx_database_accession" : { "type" : "string", "examples" : [ "pdb_00006lu7" ], "description" : "Extended accession code issued for for _database_2.database_code assigned by the database identified in\n _database_2.database_id.", "rcsb_search_context" : [ "exact-match", "suggest" ], "rcsb_full_text_priority" : 20, "rcsb_description" : [ { "text" : "Extended accession code issued for for _database_2.database_code assigned by the database identified in\n _database_2.database_id.", "context" : "dictionary" }, { "text" : "Database Accession", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "ID(s) and Keywords", "priority_order" : 10 } ] } }, "additionalProperties" : false, "required" : [ "database_code", "database_id" ] }, "minItems" : 1, "uniqueItems" : true }, "diffrn" : { "type" : "array", "items" : { "type" : "object", "properties" : { "ambient_pressure" : { "type" : "number", "description" : "The mean hydrostatic pressure in kilopascals at which the\n intensities were measured.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "kilopascals", "rcsb_description" : [ { "text" : "The mean hydrostatic pressure in kilopascals at which the\n intensities were measured.", "context" : "dictionary" }, { "text" : "Ambient Pressure (Diffrn)", "context" : "brief" } ], "rcsb_current_maximum_value" : 430000.0, "rcsb_current_minimum_value" : 101.0 }, "ambient_temp" : { "type" : "number", "description" : "The mean temperature in kelvins at which the intensities were\n measured.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "kelvins", "rcsb_description" : [ { "text" : "The mean temperature in kelvins at which the intensities were\n measured.", "context" : "dictionary" }, { "text" : "The usual temperature when using cold nitrogen gas stream is around T=100 K", "context" : "deposition" }, { "text" : "Diffraction Source Temperature", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "X-ray Data Collection Details", "priority_order" : 50 } ], "rcsb_current_maximum_value" : 446.15, "rcsb_current_minimum_value" : 0.0 }, "ambient_temp_details" : { "type" : "string", "description" : "A description of special aspects of temperature control during\n data collection.", "rcsb_description" : [ { "text" : "A description of special aspects of temperature control during\n data collection.", "context" : "dictionary" } ] }, "crystal_id" : { "type" : "string", "description" : "This data item is a pointer to _exptl_crystal.id in the\n EXPTL_CRYSTAL category.", "rcsb_description" : [ { "text" : "This data item is a pointer to _exptl_crystal.id in the\n EXPTL_CRYSTAL category.", "context" : "dictionary" } ] }, "crystal_support" : { "type" : "string", "examples" : [ "glass capillary", "quartz capillary", "fiber", "metal loop" ], "description" : "The physical device used to support the crystal during data\n collection.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The physical device used to support the crystal during data\n collection.", "context" : "dictionary" }, { "text" : "Crystal Support (Diffrn)", "context" : "brief" } ] }, "details" : { "type" : "string", "description" : "Special details of the diffraction measurement process. Should\n include information about source instability, crystal motion,\n degradation and so on.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Special details of the diffraction measurement process. Should\n include information about source instability, crystal motion,\n degradation and so on.", "context" : "dictionary" }, { "text" : "Indicate anything special or unique about the data collection", "context" : "deposition" }, { "text" : "Details (Diffrn)", "context" : "brief" } ] }, "id" : { "type" : "string", "description" : "This data item uniquely identifies a set of diffraction\n data.", "rcsb_description" : [ { "text" : "This data item uniquely identifies a set of diffraction\n data.", "context" : "dictionary" } ] }, "pdbx_serial_crystal_experiment" : { "type" : "string", "enum" : [ "N", "Y" ], "examples" : [ "Y", "N" ], "description" : "Y/N if using serial crystallography experiment in which multiple crystals contribute to each diffraction frame in the experiment.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "N", "detail" : "No" }, { "value" : "Y", "detail" : "Yes" } ], "rcsb_description" : [ { "text" : "Y/N if using serial crystallography experiment in which multiple crystals contribute to each diffraction frame in the experiment.", "context" : "dictionary" }, { "text" : "Diffraction Serial Crystal Experiment", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "X-ray Data Collection Details", "priority_order" : 55 } ] } }, "additionalProperties" : false, "required" : [ "id" ] }, "minItems" : 1, "uniqueItems" : true }, "diffrn_detector" : { "type" : "array", "items" : { "type" : "object", "properties" : { "details" : { "type" : "string", "description" : "A description of special aspects of the radiation detector.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "A description of special aspects of the radiation detector.", "context" : "dictionary" }, { "text" : "Decribe the optics used in the experiment", "context" : "deposition" }, { "text" : "Details (Diffrn Detector)", "context" : "brief" } ] }, "detector" : { "type" : "string", "examples" : [ "photographic film", "scintillation counter", "CCD plate", "BF~3~ counter" ], "description" : "The general class of the radiation detector.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The general class of the radiation detector.", "context" : "dictionary" }, { "text" : "Describe the detector used from the pulldown list", "context" : "deposition" }, { "text" : "Detector (Diffrn Detector)", "context" : "brief" } ] }, "diffrn_id" : { "type" : "string", "description" : "This data item is a pointer to _diffrn.id in the DIFFRN\n category.", "rcsb_description" : [ { "text" : "This data item is a pointer to _diffrn.id in the DIFFRN\n category.", "context" : "dictionary" } ] }, "pdbx_collection_date" : { "type" : "string", "format" : "date-time", "examples" : [ "1996-12-25" ], "description" : "The date of data collection.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The date of data collection.", "context" : "dictionary" }, { "text" : "Please provide the date that the experiment was carried out. Use the format YYYY-MM-DD.", "context" : "deposition" }, { "text" : "Collection Date (Diffrn Detector)", "context" : "brief" } ], "rcsb_current_maximum_value" : 1.7813088E12, "rcsb_current_minimum_value" : -3.00475872E13 }, "pdbx_frequency" : { "type" : "number", "description" : "The operating frequency of the detector (Hz) used in data collection.", "rcsb_description" : [ { "text" : "The operating frequency of the detector (Hz) used in data collection.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "examples" : [ "DECTRIS PILATUS 12M", "RAYONIX MX-325" ], "description" : "The make, model or name of the detector device used.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The make, model or name of the detector device used.", "context" : "dictionary" }, { "text" : "The type of detector used. Such values include CCD, image plate, ....", "context" : "deposition" }, { "text" : "Diffraction Detector", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "X-ray Data Collection Details", "priority_order" : 30 } ] } }, "additionalProperties" : false, "required" : [ "diffrn_id" ] }, "minItems" : 1, "uniqueItems" : true }, "diffrn_radiation" : { "type" : "array", "items" : { "type" : "object", "properties" : { "collimation" : { "type" : "string", "examples" : [ "0.3 mm double-pinhole", "0.5 mm", "focusing mirrors" ], "description" : "The collimation or focusing applied to the radiation.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The collimation or focusing applied to the radiation.", "context" : "dictionary" }, { "text" : "Collimation (Diffrn Radiation)", "context" : "brief" } ] }, "diffrn_id" : { "type" : "string", "description" : "This data item is a pointer to _diffrn.id in the DIFFRN\n category.", "rcsb_description" : [ { "text" : "This data item is a pointer to _diffrn.id in the DIFFRN\n category.", "context" : "dictionary" } ] }, "monochromator" : { "type" : "string", "examples" : [ "Zr filter", "Ge 220", "none", "equatorial mounted graphite" ], "description" : "The method used to obtain monochromatic radiation. If a mono-\n chromator crystal is used, the material and the indices of the\n Bragg reflection are specified.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The method used to obtain monochromatic radiation. If a mono-\n chromator crystal is used, the material and the indices of the\n Bragg reflection are specified.", "context" : "dictionary" }, { "text" : "Specify the type of monochromator used. Types may include: GOBEL MIRRORS GRAPHITE GRAPHIC CRYSTAL SI(111) SILICON CRYSTAL NI FILTER SUPER DOUBLE MIRRORS SUPER LONG MIRRORS YALE MIRRORS", "context" : "deposition" }, { "text" : "Monochromator (Diffrn Radiation)", "context" : "brief" } ] }, "pdbx_diffrn_protocol" : { "type" : "string", "examples" : [ "SINGLE WAVELENGTH", "MONOCHROMATIC", "LAUE", "MAD", "OTHER" ], "description" : "SINGLE WAVELENGTH, LAUE, or MAD.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "SINGLE WAVELENGTH, LAUE, or MAD.", "context" : "dictionary" }, { "text" : "Give the experimental protocol used for data collection.", "context" : "deposition" }, { "text" : "Diffrn Protocol (Diffrn Radiation)", "context" : "brief" } ] }, "pdbx_monochromatic_or_laue_m_l" : { "type" : "string", "enum" : [ "L", "M" ], "examples" : [ "M", "L" ], "description" : "Monochromatic or Laue.", "rcsb_description" : [ { "text" : "Monochromatic or Laue.", "context" : "dictionary" }, { "text" : "Indicate whether monochromatic or Laue radiation was used for the experiment", "context" : "deposition" } ] }, "pdbx_scattering_type" : { "type" : "string", "enum" : [ "electron", "neutron", "x-ray" ], "description" : "The radiation scattering type for this diffraction data set.", "rcsb_description" : [ { "text" : "The radiation scattering type for this diffraction data set.", "context" : "dictionary" } ] }, "pdbx_wavelength" : { "type" : "string", "description" : "Wavelength of radiation.", "rcsb_description" : [ { "text" : "Wavelength of radiation.", "context" : "dictionary" } ] }, "pdbx_wavelength_list" : { "type" : "string", "description" : "Comma separated list of wavelengths or wavelength range.", "rcsb_description" : [ { "text" : "Comma separated list of wavelengths or wavelength range.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "examples" : [ "CuK\\a", "Cu K\\a~1~", "Cu K-L~2,3~", "white-beam" ], "description" : "The nature of the radiation. This is typically a description\n of the X-ray wavelength in Siegbahn notation.", "rcsb_description" : [ { "text" : "The nature of the radiation. This is typically a description\n of the X-ray wavelength in Siegbahn notation.", "context" : "dictionary" } ] }, "wavelength_id" : { "type" : "string", "description" : "This data item is a pointer to _diffrn_radiation_wavelength.id\n in the DIFFRN_RADIATION_WAVELENGTH category.", "rcsb_description" : [ { "text" : "This data item is a pointer to _diffrn_radiation_wavelength.id\n in the DIFFRN_RADIATION_WAVELENGTH category.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "diffrn_id" ] }, "minItems" : 1, "uniqueItems" : true }, "diffrn_source" : { "type" : "array", "items" : { "type" : "object", "properties" : { "details" : { "type" : "string", "description" : "A description of special aspects of the radiation source used.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "A description of special aspects of the radiation source used.", "context" : "dictionary" }, { "text" : "Details (Diffrn Source)", "context" : "brief" } ] }, "diffrn_id" : { "type" : "string", "description" : "This data item is a pointer to _diffrn.id in the DIFFRN\n category.", "rcsb_description" : [ { "text" : "This data item is a pointer to _diffrn.id in the DIFFRN\n category.", "context" : "dictionary" } ] }, "pdbx_synchrotron_beamline" : { "type" : "string", "examples" : [ "17-ID-1", "19-ID" ], "description" : "Synchrotron beamline.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Synchrotron beamline.", "context" : "dictionary" }, { "text" : "If synchrotron radition was used, use the pulldown to specificy the site", "context" : "deposition" }, { "text" : "Diffraction Source Synchrotron Beamline", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "X-ray Data Collection Details", "priority_order" : 40 } ] }, "pdbx_synchrotron_site" : { "type" : "string", "examples" : [ "APS", "NSLS-II" ], "description" : "Synchrotron site.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Synchrotron site.", "context" : "dictionary" }, { "text" : "If synchrotron radiation was used, please use the pulldown to specify the site and beamline", "context" : "deposition" }, { "text" : "Diffraction Source Synchrotron Site", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "X-ray Data Collection Details", "priority_order" : 35 } ] }, "pdbx_wavelength" : { "type" : "string", "description" : "Wavelength of radiation.", "rcsb_description" : [ { "text" : "Wavelength of radiation.", "context" : "dictionary" } ] }, "pdbx_wavelength_list" : { "type" : "string", "examples" : [ "0.987 or 0.987, 0.988, 1.0 or 0.99-1.5" ], "description" : "Comma separated list of wavelengths or wavelength range.", "rcsb_description" : [ { "text" : "Comma separated list of wavelengths or wavelength range.", "context" : "dictionary" }, { "text" : "Provide the wavelength(s) in angstrom used for data collection. Multiple wavelengths should be comma separated. For Laue experiments, indicate the range with a hyphen.", "context" : "deposition" } ] }, "source" : { "type" : "string", "examples" : [ "sealed X-ray tube", "nuclear reactor", "spallation source", "electron microscope", "rotating-anode X-ray tube", "synchrotron" ], "description" : "The general class of the radiation source.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The general class of the radiation source.", "context" : "dictionary" }, { "text" : "If an X-ray generator was used, please specify the name and model of the generator. If your particular model is not found, use other.", "context" : "deposition" }, { "text" : "Diffraction Source General Class", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "X-ray Data Collection Details", "priority_order" : 45 } ] }, "type" : { "type" : "string", "examples" : [ "NSLS beamline X8C", "Rigaku RU200" ], "description" : "The make, model or name of the source of radiation.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The make, model or name of the source of radiation.", "context" : "dictionary" }, { "text" : "Type (Diffrn Source)", "context" : "brief" } ] } }, "additionalProperties" : false, "required" : [ "diffrn_id" ] }, "minItems" : 1, "uniqueItems" : true }, "em_2d_crystal_entity" : { "type" : "array", "items" : { "type" : "object", "properties" : { "angle_gamma" : { "type" : "number", "description" : "Unit-cell angle gamma in degrees.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "degrees", "rcsb_description" : [ { "text" : "Unit-cell angle gamma in degrees.", "context" : "dictionary" }, { "text" : "Angle Gamma (Em 2d Crystal Entity)", "context" : "brief" } ], "rcsb_current_maximum_value" : 120.0, "rcsb_current_minimum_value" : 1.0 }, "c_sampling_length" : { "type" : "number", "description" : "Length used to sample the reciprocal lattice lines in the c-direction.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "Length used to sample the reciprocal lattice lines in the c-direction.", "context" : "dictionary" }, { "text" : "C Sampling Length (Em 2d Crystal Entity)", "context" : "brief" } ], "rcsb_current_maximum_value" : 320.0, "rcsb_current_minimum_value" : 10.0 }, "id" : { "type" : "string", "description" : "PRIMARY KEY", "rcsb_description" : [ { "text" : "PRIMARY KEY", "context" : "dictionary" } ] }, "image_processing_id" : { "type" : "string", "description" : "pointer to _em_image_processing.id in the EM_IMAGE_PROCESSING category.", "rcsb_description" : [ { "text" : "pointer to _em_image_processing.id in the EM_IMAGE_PROCESSING category.", "context" : "dictionary" } ] }, "length_a" : { "type" : "number", "examples" : [ 62.4 ], "description" : "Unit-cell length a in angstroms.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "Unit-cell length a in angstroms.", "context" : "dictionary" }, { "text" : "Length A (Em 2d Crystal Entity)", "context" : "brief" } ], "rcsb_current_maximum_value" : 220.0, "rcsb_current_minimum_value" : 1.0 }, "length_b" : { "type" : "number", "examples" : [ 62.4 ], "description" : "Unit-cell length b in angstroms.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "Unit-cell length b in angstroms.", "context" : "dictionary" }, { "text" : "Length B (Em 2d Crystal Entity)", "context" : "brief" } ], "rcsb_current_maximum_value" : 304.0, "rcsb_current_minimum_value" : 1.0 }, "length_c" : { "type" : "number", "examples" : [ 62.4 ], "description" : "Thickness of 2D crystal", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "Thickness of 2D crystal", "context" : "dictionary" }, { "text" : "Length C (Em 2d Crystal Entity)", "context" : "brief" } ], "rcsb_current_maximum_value" : 320.0, "rcsb_current_minimum_value" : 1.0 }, "space_group_name_H_M" : { "type" : "string", "enum" : [ "C 1 2", "C 2 2 2", "P 1", "P 1 2", "P 1 21", "P 2", "P 2 2 2", "P 2 2 21", "P 2 21 21", "P 3", "P 3 1 2", "P 3 2 1", "P 4", "P 4 2 2", "P 4 21 2", "P 6", "P 6 2 2" ], "description" : "There are 17 plane groups classified as oblique, rectangular, square, and hexagonal.\n To describe the symmetry of 2D crystals of biological molecules,\n plane groups are expanded to equivalent noncentrosymmetric space groups.\n The 2D crystal plane corresponds to the 'ab' plane of the space group.\n\n Enumerated space group descriptions include the plane group number in parentheses,\n the H-M plane group symbol, and the plane group class.", "rcsb_enum_annotated" : [ { "value" : "C 1 2", "detail" : "(5) cm, rectangular" }, { "value" : "C 2 2 2", "detail" : "(9) c2mm, rectangular" }, { "value" : "P 1", "detail" : "(1) p1, oblique" }, { "value" : "P 1 2", "detail" : "(3) pm, rectangular" }, { "value" : "P 1 21", "detail" : "(4) pg, rectangular" }, { "value" : "P 2", "detail" : "(2) p2, oblique" }, { "value" : "P 2 2 2", "detail" : "(6) 2mm, rectangular" }, { "value" : "P 2 2 21", "detail" : "(7) p2mg, rectangular" }, { "value" : "P 2 21 21", "detail" : "(8) p2gg, rectangular" }, { "value" : "P 3", "detail" : "(13) p3, hexagonal" }, { "value" : "P 3 1 2", "detail" : "(14) p3m1, hexagonal" }, { "value" : "P 3 2 1", "detail" : "(15) p31m, hexagonal" }, { "value" : "P 4", "detail" : "(10) p4, square" }, { "value" : "P 4 2 2", "detail" : "(11) p4mm, square" }, { "value" : "P 4 21 2", "detail" : "(12) p4gm, square" }, { "value" : "P 6", "detail" : "(16) p6, hexagonal" }, { "value" : "P 6 2 2", "detail" : "(17) p6mm, hexagonal" } ], "rcsb_description" : [ { "text" : "There are 17 plane groups classified as oblique, rectangular, square, and hexagonal.\n To describe the symmetry of 2D crystals of biological molecules,\n plane groups are expanded to equivalent noncentrosymmetric space groups.\n The 2D crystal plane corresponds to the 'ab' plane of the space group.\n\n Enumerated space group descriptions include the plane group number in parentheses,\n the H-M plane group symbol, and the plane group class.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "id", "image_processing_id" ] }, "minItems" : 1, "uniqueItems" : true }, "em_3d_crystal_entity" : { "type" : "array", "items" : { "type" : "object", "properties" : { "angle_alpha" : { "type" : "number", "examples" : [ 120.0 ], "description" : "Unit-cell angle alpha in degrees.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "degrees", "rcsb_description" : [ { "text" : "Unit-cell angle alpha in degrees.", "context" : "dictionary" }, { "text" : "Angle Alpha (Em 3d Crystal Entity)", "context" : "brief" } ], "rcsb_current_maximum_value" : 109.52, "rcsb_current_minimum_value" : 62.8 }, "angle_beta" : { "type" : "number", "examples" : [ 120.0 ], "description" : "Unit-cell angle beta in degrees.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "degrees", "rcsb_description" : [ { "text" : "Unit-cell angle beta in degrees.", "context" : "dictionary" }, { "text" : "Angle Beta (Em 3d Crystal Entity)", "context" : "brief" } ], "rcsb_current_maximum_value" : 116.15, "rcsb_current_minimum_value" : 77.16 }, "angle_gamma" : { "type" : "number", "examples" : [ 120.0 ], "description" : "Unit-cell angle gamma in degrees.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "degrees", "rcsb_description" : [ { "text" : "Unit-cell angle gamma in degrees.", "context" : "dictionary" }, { "text" : "Angle Gamma (Em 3d Crystal Entity)", "context" : "brief" } ], "rcsb_current_maximum_value" : 120.0, "rcsb_current_minimum_value" : 81.124 }, "id" : { "type" : "string", "description" : "PRIMARY KEY", "rcsb_description" : [ { "text" : "PRIMARY KEY", "context" : "dictionary" } ] }, "image_processing_id" : { "type" : "string", "description" : "pointer to _em_image_processing.id in the EM_IMAGE_PROCESSING category.", "rcsb_description" : [ { "text" : "pointer to _em_image_processing.id in the EM_IMAGE_PROCESSING category.", "context" : "dictionary" } ] }, "length_a" : { "type" : "number", "examples" : [ 62.4 ], "description" : "Unit-cell length a in angstroms.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "Unit-cell length a in angstroms.", "context" : "dictionary" }, { "text" : "Length A (Em 3d Crystal Entity)", "context" : "brief" } ], "rcsb_current_maximum_value" : 600.0, "rcsb_current_minimum_value" : 1.0 }, "length_b" : { "type" : "number", "examples" : [ 62.4 ], "description" : "Unit-cell length b in angstroms.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "Unit-cell length b in angstroms.", "context" : "dictionary" }, { "text" : "Length B (Em 3d Crystal Entity)", "context" : "brief" } ], "rcsb_current_maximum_value" : 600.0, "rcsb_current_minimum_value" : 1.0 }, "length_c" : { "type" : "number", "examples" : [ 62.4 ], "description" : "Unit-cell length c in angstroms.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "Unit-cell length c in angstroms.", "context" : "dictionary" }, { "text" : "Length C (Em 3d Crystal Entity)", "context" : "brief" } ], "rcsb_current_maximum_value" : 600.0, "rcsb_current_minimum_value" : 1.0 }, "space_group_name" : { "type" : "string", "examples" : [ "P 1", "P 21 21 2", "I 4", "H 3" ], "description" : "Space group name.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Space group name.", "context" : "dictionary" }, { "text" : "Space Group Name (Em 3d Crystal Entity)", "context" : "brief" } ] }, "space_group_num" : { "type" : "integer", "description" : "Space group number.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Space group number.", "context" : "dictionary" }, { "text" : "Space Group Num (Em 3d Crystal Entity)", "context" : "brief" } ], "rcsb_current_maximum_value" : 197.0, "rcsb_current_minimum_value" : 1.0 } }, "additionalProperties" : false, "required" : [ "id", "image_processing_id" ] }, "minItems" : 1, "uniqueItems" : true }, "em_3d_fitting" : { "type" : "array", "items" : { "type" : "object", "properties" : { "details" : { "type" : "string", "examples" : [ "Initial local fitting was done using Chimera and then NMFF was used for flexible fitting." ], "description" : "Any additional details regarding fitting of atomic coordinates into\n the 3DEM volume, including data and considerations from other\n methods used in computation of the model.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Any additional details regarding fitting of atomic coordinates into\n the 3DEM volume, including data and considerations from other\n methods used in computation of the model.", "context" : "dictionary" }, { "text" : "Details (Em 3d Fitting)", "context" : "brief" } ] }, "id" : { "type" : "string", "description" : "The value of _em_3d_fitting.id must uniquely identify\n a fitting procedure of atomic coordinates\n into 3dem reconstructed map volume.", "rcsb_description" : [ { "text" : "The value of _em_3d_fitting.id must uniquely identify\n a fitting procedure of atomic coordinates\n into 3dem reconstructed map volume.", "context" : "dictionary" } ] }, "method" : { "type" : "string", "description" : "The method used to fit atomic coordinates\n into the 3dem reconstructed map.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The method used to fit atomic coordinates\n into the 3dem reconstructed map.", "context" : "dictionary" }, { "text" : "Method (Em 3d Fitting)", "context" : "brief" } ] }, "overall_b_value" : { "type" : "number", "description" : "The overall B (temperature factor) value for the 3d-em volume.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The overall B (temperature factor) value for the 3d-em volume.", "context" : "dictionary" }, { "text" : "Overall B Value (Em 3d Fitting)", "context" : "brief" } ], "rcsb_current_maximum_value" : 1000.0, "rcsb_current_minimum_value" : 0.836 }, "ref_protocol" : { "type" : "string", "enum" : [ "AB INITIO MODEL", "BACKBONE TRACE", "FLEXIBLE FIT", "OTHER", "RIGID BODY FIT" ], "description" : "The refinement protocol used.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The refinement protocol used.", "context" : "dictionary" }, { "text" : "Ref Protocol (Em 3d Fitting)", "context" : "brief" } ] }, "ref_space" : { "type" : "string", "enum" : [ "REAL", "RECIPROCAL" ], "description" : "A flag to indicate whether fitting was carried out in real\n or reciprocal refinement space.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "A flag to indicate whether fitting was carried out in real\n or reciprocal refinement space.", "context" : "dictionary" }, { "text" : "Ref Space (Em 3d Fitting)", "context" : "brief" } ] }, "target_criteria" : { "type" : "string", "examples" : [ "Cross-correlation coefficient" ], "description" : "The measure used to assess quality of fit of the atomic coordinates in the\n 3DEM map volume.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The measure used to assess quality of fit of the atomic coordinates in the\n 3DEM map volume.", "context" : "dictionary" }, { "text" : "Target Criteria (Em 3d Fitting)", "context" : "brief" } ] } }, "additionalProperties" : false, "required" : [ "id" ] }, "minItems" : 1, "uniqueItems" : true }, "em_3d_fitting_list" : { "type" : "array", "items" : { "type" : "object", "properties" : { "3d_fitting_id" : { "type" : "string", "description" : "The value of _em_3d_fitting_list.3d_fitting_id is a pointer\n to _em_3d_fitting.id in the 3d_fitting category", "rcsb_description" : [ { "text" : "The value of _em_3d_fitting_list.3d_fitting_id is a pointer\n to _em_3d_fitting.id in the 3d_fitting category", "context" : "dictionary" } ] }, "details" : { "type" : "string", "examples" : [ "The initial model consisted of the complete biological assembly for PDB entry 2GTL." ], "description" : "Details about the model used in fitting.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Details about the model used in fitting.", "context" : "dictionary" }, { "text" : "Details (Em 3d Fitting List)", "context" : "brief" } ] }, "id" : { "type" : "string", "description" : "PRIMARY KEY", "rcsb_description" : [ { "text" : "PRIMARY KEY", "context" : "dictionary" } ] }, "pdb_chain_id" : { "type" : "string", "examples" : [ "The ID of the biopolymer chain used for fitting, e.g., A. Please note that only one chain can be specified per instance. If all chains of a particular structure have been used for fitting, this field can be left blank." ], "description" : "The ID of the biopolymer chain used for fitting, e.g., A. Please note that\nonly one chain can be specified per instance. If all chains of a particular\nstructure have been used for fitting, this field can be left blank.", "rcsb_description" : [ { "text" : "The ID of the biopolymer chain used for fitting, e.g., A. Please note that\nonly one chain can be specified per instance. If all chains of a particular\nstructure have been used for fitting, this field can be left blank.", "context" : "dictionary" } ] }, "pdb_chain_residue_range" : { "type" : "string", "description" : "Residue range for the identified chain.", "rcsb_description" : [ { "text" : "Residue range for the identified chain.", "context" : "dictionary" } ] }, "pdb_entry_id" : { "type" : "string", "examples" : [ "1EHZ" ], "description" : "The PDB code for the entry used in fitting.", "rcsb_description" : [ { "text" : "The PDB code for the entry used in fitting.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "3d_fitting_id", "id" ] }, "minItems" : 1, "uniqueItems" : true }, "em_3d_reconstruction" : { "type" : "array", "items" : { "type" : "object", "properties" : { "actual_pixel_size" : { "type" : "number", "examples" : [ 2.8, 5.76 ], "description" : "The actual pixel size of the projection set of images in Angstroms.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The actual pixel size of the projection set of images in Angstroms.", "context" : "dictionary" }, { "text" : "Actual Pixel Size (Em 3d Reconstruction)", "context" : "brief" } ], "rcsb_current_maximum_value" : 11.4, "rcsb_current_minimum_value" : 0.5 }, "algorithm" : { "type" : "string", "description" : "The reconstruction algorithm/technique used to generate the map.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The reconstruction algorithm/technique used to generate the map.", "context" : "dictionary" }, { "text" : "Algorithm (Em 3d Reconstruction)", "context" : "brief" } ] }, "details" : { "type" : "string", "examples" : [ "a modified version of SPIDER program was used for the reconstruction" ], "description" : "Any additional details used in the 3d reconstruction.", "rcsb_description" : [ { "text" : "Any additional details used in the 3d reconstruction.", "context" : "dictionary" } ] }, "id" : { "type" : "string", "description" : "PRIMARY KEY", "rcsb_description" : [ { "text" : "PRIMARY KEY", "context" : "dictionary" } ] }, "image_processing_id" : { "type" : "string", "description" : "Foreign key to the EM_IMAGE_PROCESSING category", "rcsb_description" : [ { "text" : "Foreign key to the EM_IMAGE_PROCESSING category", "context" : "dictionary" } ] }, "magnification_calibration" : { "type" : "string", "examples" : [ "TMV images" ], "description" : "The magnification calibration method for the 3d reconstruction.", "rcsb_description" : [ { "text" : "The magnification calibration method for the 3d reconstruction.", "context" : "dictionary" } ] }, "method" : { "type" : "string", "examples" : [ "cross-common lines", "polar Fourier transform (PFT)" ], "description" : "The algorithm method used for the 3d-reconstruction.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The algorithm method used for the 3d-reconstruction.", "context" : "dictionary" }, { "text" : "Method (Em 3d Reconstruction)", "context" : "brief" } ] }, "nominal_pixel_size" : { "type" : "number", "examples" : [ 3.11, 6.78 ], "description" : "The nominal pixel size of the projection set of images in Angstroms.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The nominal pixel size of the projection set of images in Angstroms.", "context" : "dictionary" }, { "text" : "Nominal Pixel Size (Em 3d Reconstruction)", "context" : "brief" } ], "rcsb_current_maximum_value" : 15.5, "rcsb_current_minimum_value" : 0.41 }, "num_class_averages" : { "type" : "integer", "description" : "The number of classes used in the final 3d reconstruction", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of classes used in the final 3d reconstruction", "context" : "dictionary" }, { "text" : "Num Class Averages (Em 3d Reconstruction)", "context" : "brief" } ], "rcsb_current_maximum_value" : 1246669.0, "rcsb_current_minimum_value" : 1.0 }, "num_particles" : { "type" : "integer", "description" : "The number of 2D projections or 3D subtomograms used in the 3d reconstruction", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of 2D projections or 3D subtomograms used in the 3d reconstruction", "context" : "dictionary" }, { "text" : "Num Particles (Em 3d Reconstruction)", "context" : "brief" } ], "rcsb_current_maximum_value" : 1.937076E7, "rcsb_current_minimum_value" : 1.0 }, "refinement_type" : { "type" : "string", "enum" : [ "HALF-MAPS REFINED AGAINST SAME DATA", "HALF-MAPS REFINED INDEPENDENTLY", "HALF-MAPS REFINED INDEPENDENTLY WITH FREQUENCY RANGE OMITTED", "HALF-MAPS REFINED WITH FREQUENCY RANGE OMITTED", "OTHER" ], "description" : "Indicates details on how the half-map used for resolution determination (usually by FSC) have been generated.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Indicates details on how the half-map used for resolution determination (usually by FSC) have been generated.", "context" : "dictionary" }, { "text" : "Refinement Type (Em 3d Reconstruction)", "context" : "brief" } ] }, "resolution" : { "type" : "number", "examples" : [ 8.9, 10.0 ], "description" : "The final resolution (in angstroms) of the 3D reconstruction.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "The final resolution (in angstroms) of the 3D reconstruction.", "context" : "dictionary" }, { "text" : "Reconstruction Resolution", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "EM Method Details", "priority_order" : 5 } ], "rcsb_current_maximum_value" : 70.0, "rcsb_current_minimum_value" : 0.6 }, "resolution_method" : { "type" : "string", "examples" : [ "FSC at 0.5 cut-off" ], "description" : "The method used to determine the final resolution\n of the 3d reconstruction.\n The Fourier Shell Correlation criterion as a measure of\n resolution is based on the concept of splitting the (2D)\n data set into two halves; averaging each and comparing them\n using the Fourier Ring Correlation (FRC) technique.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The method used to determine the final resolution\n of the 3d reconstruction.\n The Fourier Shell Correlation criterion as a measure of\n resolution is based on the concept of splitting the (2D)\n data set into two halves; averaging each and comparing them\n using the Fourier Ring Correlation (FRC) technique.", "context" : "dictionary" }, { "text" : "Resolution Method (Em 3d Reconstruction)", "context" : "brief" } ] }, "symmetry_type" : { "type" : "string", "enum" : [ "2D CRYSTAL", "3D CRYSTAL", "HELICAL", "POINT" ], "description" : "The type of symmetry applied to the reconstruction", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The type of symmetry applied to the reconstruction", "context" : "dictionary" }, { "text" : "Symmetry Type (Em 3d Reconstruction)", "context" : "brief" } ] } }, "additionalProperties" : false, "required" : [ "id", "image_processing_id" ] }, "minItems" : 1, "uniqueItems" : true }, "em_ctf_correction" : { "type" : "array", "items" : { "type" : "object", "properties" : { "details" : { "type" : "string", "examples" : [ "CTF amplitude correction was performed following 3D reconstruction" ], "description" : "Any additional details about CTF correction", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Any additional details about CTF correction", "context" : "dictionary" }, { "text" : "Details (Em Ctf Correction)", "context" : "brief" } ] }, "em_image_processing_id" : { "type" : "string", "description" : "Foreign key to the EM_IMAGE_PROCESSING category", "rcsb_description" : [ { "text" : "Foreign key to the EM_IMAGE_PROCESSING category", "context" : "dictionary" } ] }, "id" : { "type" : "string", "description" : "PRIMARY KEY", "rcsb_description" : [ { "text" : "PRIMARY KEY", "context" : "dictionary" } ] }, "type" : { "type" : "string", "description" : "Type of CTF correction applied", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Type of CTF correction applied", "context" : "dictionary" }, { "text" : "Type (Em Ctf Correction)", "context" : "brief" } ] } }, "additionalProperties" : false, "required" : [ "id" ] }, "minItems" : 1, "uniqueItems" : true }, "em_diffraction" : { "type" : "array", "items" : { "type" : "object", "properties" : { "camera_length" : { "type" : "number", "description" : "The camera length (in millimeters). The camera length is the\n product of the objective focal length and the combined magnification\n of the intermediate and projector lenses when the microscope is\n operated in the diffraction mode.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "millimetres", "rcsb_description" : [ { "text" : "The camera length (in millimeters). The camera length is the\n product of the objective focal length and the combined magnification\n of the intermediate and projector lenses when the microscope is\n operated in the diffraction mode.", "context" : "dictionary" }, { "text" : "Camera Length (Em Diffraction)", "context" : "brief" } ], "rcsb_current_maximum_value" : 4705.0, "rcsb_current_minimum_value" : 0.1 }, "id" : { "type" : "string", "description" : "PRIMARY KEY", "rcsb_description" : [ { "text" : "PRIMARY KEY", "context" : "dictionary" } ] }, "imaging_id" : { "type" : "string", "description" : "Foreign key to the EM_IMAGING category", "rcsb_description" : [ { "text" : "Foreign key to the EM_IMAGING category", "context" : "dictionary" } ] }, "tilt_angle_list" : { "type" : "string", "examples" : [ "20,40,50,55" ], "description" : "Comma-separated list of tilt angles (in degrees) used in the electron diffraction experiment.", "rcsb_description" : [ { "text" : "Comma-separated list of tilt angles (in degrees) used in the electron diffraction experiment.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "id" ] }, "minItems" : 1, "uniqueItems" : true }, "em_diffraction_shell" : { "type" : "array", "items" : { "type" : "object", "properties" : { "em_diffraction_stats_id" : { "type" : "string", "description" : "Pointer to EM CRYSTALLOGRAPHY STATS", "rcsb_description" : [ { "text" : "Pointer to EM CRYSTALLOGRAPHY STATS", "context" : "dictionary" } ] }, "fourier_space_coverage" : { "type" : "number", "examples" : [ 93.2 ], "description" : "Completeness of the structure factor data within this resolution shell, in percent", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Completeness of the structure factor data within this resolution shell, in percent", "context" : "dictionary" }, { "text" : "Fourier Space Coverage (Em Diffraction Shell)", "context" : "brief" } ], "rcsb_current_maximum_value" : 100.0, "rcsb_current_minimum_value" : 0.001 }, "high_resolution" : { "type" : "number", "examples" : [ 3.0 ], "description" : "High resolution limit for this shell (angstroms)", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "High resolution limit for this shell (angstroms)", "context" : "dictionary" }, { "text" : "High Resolution (Em Diffraction Shell)", "context" : "brief" } ], "rcsb_current_maximum_value" : 55.79, "rcsb_current_minimum_value" : 0.6 }, "id" : { "type" : "string", "description" : "PRIMARY KEY", "rcsb_description" : [ { "text" : "PRIMARY KEY", "context" : "dictionary" } ] }, "low_resolution" : { "type" : "number", "examples" : [ 5.5 ], "description" : "Low resolution limit for this shell (angstroms)", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "Low resolution limit for this shell (angstroms)", "context" : "dictionary" }, { "text" : "Low Resolution (Em Diffraction Shell)", "context" : "brief" } ], "rcsb_current_maximum_value" : 200.0, "rcsb_current_minimum_value" : 0.1 }, "multiplicity" : { "type" : "number", "examples" : [ 2.5 ], "description" : "Multiplicity (average number of measurements) for the structure factors in this resolution shell", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Multiplicity (average number of measurements) for the structure factors in this resolution shell", "context" : "dictionary" }, { "text" : "Multiplicity (Em Diffraction Shell)", "context" : "brief" } ], "rcsb_current_maximum_value" : 983.44, "rcsb_current_minimum_value" : 0.1 }, "num_structure_factors" : { "type" : "integer", "description" : "Number of measured structure factors in this resolution shell", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Number of measured structure factors in this resolution shell", "context" : "dictionary" }, { "text" : "Num Structure Factors (Em Diffraction Shell)", "context" : "brief" } ], 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details about the structure factor measurements", "context" : "dictionary" } ] }, "fourier_space_coverage" : { "type" : "number", "examples" : [ 89.3 ], "description" : "Completeness of the structure factor data within the defined space group\n at the reported resolution (percent).", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Completeness of the structure factor data within the defined space group\n at the reported resolution (percent).", "context" : "dictionary" }, { "text" : "Fourier Space Coverage (Em Diffraction Stats)", "context" : "brief" } ], "rcsb_current_maximum_value" : 100.0, "rcsb_current_minimum_value" : 0.1 }, "high_resolution" : { "type" : "number", "examples" : [ 7.5 ], "description" : "High resolution limit of the structure factor data, in angstroms", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "High resolution limit of the structure factor data, in angstroms", "context" : "dictionary" }, { "text" : "High Resolution (Em Diffraction Stats)", "context" : "brief" } ], "rcsb_current_maximum_value" : 18.25, "rcsb_current_minimum_value" : 0.6 }, "id" : { "type" : "string", "description" : "PRIMARY KEY", "rcsb_description" : [ { "text" : "PRIMARY KEY", "context" : "dictionary" } ] }, "image_processing_id" : { "type" : "string", "description" : "Pointer to _em_image_processing.id", "rcsb_description" : [ { "text" : "Pointer to _em_image_processing.id", "context" : "dictionary" } ] }, "num_intensities_measured" : { "type" : "integer", "description" : "Total number of diffraction intensities measured (before averaging)", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Total number of diffraction intensities measured (before averaging)", "context" : "dictionary" }, { "text" : "Num Intensities Measured (Em Diffraction Stats)", "context" : "brief" } ], "rcsb_current_maximum_value" : 2.582955E7, "rcsb_current_minimum_value" : 943.0 }, "num_structure_factors" : { "type" : "integer", "description" : "Number of structure factors obtained (merged amplitudes + phases)", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Number of structure factors obtained (merged amplitudes + phases)", "context" : "dictionary" }, { "text" : "Num Structure Factors (Em Diffraction Stats)", "context" : "brief" } ], "rcsb_current_maximum_value" : 6901357.0, "rcsb_current_minimum_value" : 325.0 }, "overall_phase_error" : { "type" : "number", "examples" : [ 17.5 ], "description" : "Overall phase error in degrees", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "degrees", "rcsb_description" : [ { "text" : "Overall phase error in degrees", "context" : "dictionary" }, { "text" : "Overall Phase Error (Em Diffraction Stats)", "context" : "brief" } ], "rcsb_current_maximum_value" : 179.9, "rcsb_current_minimum_value" : 0.0 }, "overall_phase_residual" : { "type" : "number", "examples" : [ 17.5 ], "description" : "Overall phase residual in degrees", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "degrees", "rcsb_description" : [ { "text" : "Overall phase residual in degrees", "context" : "dictionary" }, { "text" : "Overall Phase Residual (Em Diffraction Stats)", "context" : "brief" } ], "rcsb_current_maximum_value" : 179.9, "rcsb_current_minimum_value" : 1.0E-10 }, "phase_error_rejection_criteria" : { "type" : "string", "examples" : [ "Structure factors with phase errors higher than 20 degrees were omitted from refinement" ], "description" : "Criteria used to reject phases", "rcsb_description" : [ { "text" : "Criteria used to reject phases", "context" : "dictionary" } ] }, "r_merge" : { "type" : "number", "examples" : [ 19.8 ], "description" : "Rmerge value (percent)", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Rmerge value (percent)", "context" : "dictionary" }, { "text" : "R Merge (Em Diffraction Stats)", "context" : "brief" } ], "rcsb_current_maximum_value" : 99.0, "rcsb_current_minimum_value" : 0.093 }, "r_sym" : { "type" : "number", "examples" : [ 24.4 ], "description" : "Rsym value (percent)", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Rsym value (percent)", "context" : "dictionary" }, { "text" : "R Sym (Em Diffraction Stats)", "context" : "brief" } ], "rcsb_current_maximum_value" : 100.0, "rcsb_current_minimum_value" : 0.073 } }, "additionalProperties" : false, "required" : [ "id" ] }, "minItems" : 1, "uniqueItems" : true }, "em_embedding" : { "type" : "array", "items" : { "type" : "object", "properties" : { "details" : { "type" : "string", "examples" : [ "The crystal suspension was injected into the lens of a drop of buffer containing\n 1 % tannin sitting on a carbon film supported by a molybdenum grid. An equal volume\n of 1% glucose was then added and the solution thoroughly but gently mixed. The grid\n was then blotted, air dried, and frozen in LN2." ], "description" : "Staining procedure used in the specimen preparation.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Staining procedure used in the specimen preparation.", "context" : "dictionary" }, { "text" : "Details (Em Embedding)", "context" : "brief" } ] }, "id" : { "type" : "string", "description" : "PRIMARY KEY", "rcsb_description" : [ { "text" : "PRIMARY KEY", "context" : "dictionary" } ] }, "material" : { "type" : "string", "examples" : [ "tannin and glucose" ], "description" : "The embedding material.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The embedding material.", "context" : "dictionary" }, { "text" : "Material (Em Embedding)", "context" : "brief" } ] }, "specimen_id" : { "type" : "string", "description" : "Foreign key relationship to the EM SPECIMEN category", "rcsb_description" : [ { "text" : "Foreign key relationship to the EM SPECIMEN category", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "id" ] }, "minItems" : 1, "uniqueItems" : true }, "em_entity_assembly" : { "type" : "array", "items" : { "type" : "object", "properties" : { "details" : { "type" : "string", "examples" : [ "Fab fragment generated by proteolytic cleavage of LA2 IgG antibody." ], "description" : "Additional details about the sample or sample subcomponent.", "rcsb_description" : [ { "text" : "Additional details about the sample or sample subcomponent.", "context" : "dictionary" } ] }, "entity_id_list" : { "type" : "array", "items" : { "type" : "string", "examples" : [ "1,2,3,4" ], "description" : "macromolecules associated with this component, if defined\n as comma separated list of entity ids (integers).", "rcsb_description" : [ { "text" : "macromolecules associated with this component, if defined\n as comma separated list of entity ids (integers).", "context" : "dictionary" } ] }, "uniqueItems" : false }, "id" : { "type" : "string", "description" : "PRIMARY KEY", "rcsb_description" : [ { "text" : "PRIMARY KEY", "context" : "dictionary" } ] }, "name" : { "type" : "string", "examples" : [ "Ternary complex of alpha-tubulin with tubulin folding cofactors TBCE and TBCB", "80S Ribosome bound to emetine", "messenger RNA", "initiation factor 2", "GroEL", "antibody Fab fragment" ], "description" : "The name of the sample or sample subcomponent.", "rcsb_description" : [ { "text" : "The name of the sample or sample subcomponent.", "context" : "dictionary" } ] }, "oligomeric_details" : { "type" : "string", "description" : "oligomeric details", "rcsb_description" : [ { "text" : "oligomeric details", "context" : "dictionary" } ] }, "parent_id" : { "type" : "integer", "description" : "The parent of this assembly.\n This data item is an internal category pointer to _em_entity_assembly.id.\n By convention, the full assembly (top of hierarchy) is assigned parent id 0 (zero).", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The parent of this assembly.\n This data item is an internal category pointer to _em_entity_assembly.id.\n By convention, the full assembly (top of hierarchy) is assigned parent id 0 (zero).", "context" : "dictionary" }, { "text" : "Parent Id (Em Entity Assembly)", "context" : "brief" } ], "rcsb_current_maximum_value" : 12.0, "rcsb_current_minimum_value" : 0.0 }, "source" : { "type" : "string", "enum" : [ "MULTIPLE SOURCES", "NATURAL", "RECOMBINANT", "SYNTHETIC" ], "description" : "The type of source (e.g., natural source) for the component (sample or sample\nsubcomponent)", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The type of source (e.g., natural source) for the component (sample or sample\nsubcomponent)", "context" : "dictionary" }, { "text" : "Source (Em Entity Assembly)", "context" : "brief" } ] }, "synonym" : { "type" : "string", "examples" : [ "FADV-1" ], "description" : "Alternative name of the component.", "rcsb_description" : [ { "text" : "Alternative name of the component.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "description" : "The general type of the sample or sample subcomponent.", "rcsb_description" : [ { "text" : "The general type of the sample or sample subcomponent.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "id" ] }, "minItems" : 1, "uniqueItems" : true }, "em_experiment" : { "type" : "object", "properties" : { "aggregation_state" : { "type" : "string", "enum" : [ "2D ARRAY", "3D ARRAY", "CELL", "FILAMENT", "HELICAL ARRAY", "PARTICLE", "TISSUE" ], "description" : "The aggregation/assembly state of the imaged specimen.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The aggregation/assembly state of the imaged specimen.", "context" : "dictionary" }, { "text" : "EM Specimen Aggregation State", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "EM Method Details", "priority_order" : 15 } ] }, "entity_assembly_id" : { "type" : "string", "description" : "Foreign key to the EM_ENTITY_ASSEMBLY category", "rcsb_description" : [ { "text" : "Foreign key to the EM_ENTITY_ASSEMBLY category", "context" : "dictionary" } ] }, "id" : { "type" : "string", "description" : "PRIMARY KEY", "rcsb_description" : [ { "text" : "PRIMARY KEY", "context" : "dictionary" } ] }, "reconstruction_method" : { "type" : "string", "enum" : [ "CRYSTALLOGRAPHY", "HELICAL", "SINGLE PARTICLE", "SUBTOMOGRAM AVERAGING", "TOMOGRAPHY" ], "description" : "The reconstruction method used in the EM experiment.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The reconstruction method used in the EM experiment.", "context" : "dictionary" }, { "text" : "EM Reconstruction Method", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "EM Method Details", "priority_order" : 20 } ] } }, "additionalProperties" : false }, "em_helical_entity" : { "type" : "array", "items" : { "type" : "object", "properties" : { "angular_rotation_per_subunit" : { "type" : "number", "examples" : [ -34.616 ], "description" : "The angular rotation per helical subunit in degrees. Negative values indicate left-handed helices; positive values indicate right handed helices.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "degrees", "rcsb_description" : [ { "text" : "The angular rotation per helical subunit in degrees. Negative values indicate left-handed helices; positive values indicate right handed helices.", "context" : "dictionary" }, { "text" : "Angular Rotation Per Subunit (Em Helical Entity)", "context" : "brief" } ], "rcsb_current_maximum_value" : 180.0, "rcsb_current_minimum_value" : -179.9 }, "axial_rise_per_subunit" : { "type" : "number", "examples" : [ 17.4 ], "description" : "The axial rise per subunit in the helical assembly.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "The axial rise per subunit in the helical assembly.", "context" : "dictionary" }, { "text" : "Axial Rise Per Subunit (Em Helical Entity)", "context" : "brief" } ], "rcsb_current_maximum_value" : 430.0, "rcsb_current_minimum_value" : 0.001 }, "axial_symmetry" : { "type" : "string", "examples" : [ "C1", "D2", "C7" ], "description" : "Symmetry of the helical axis, either cyclic (Cn) or dihedral (Dn), where n>=1.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Symmetry of the helical axis, either cyclic (Cn) or dihedral (Dn), where n>=1.", "context" : "dictionary" }, { "text" : "Axial Symmetry (Em Helical Entity)", "context" : "brief" } ] }, "details" : { "type" : "string", "examples" : [ "Dihedral symmetry" ], "description" : "Any other details regarding the helical assembly", "rcsb_description" : [ { "text" : "Any other details regarding the helical assembly", "context" : "dictionary" } ] }, "id" : { "type" : "string", "description" : "PRIMARY KEY", "rcsb_description" : [ { "text" : "PRIMARY KEY", "context" : "dictionary" } ] }, "image_processing_id" : { "type" : "string", "description" : "This data item is a pointer to _em_image_processing.id.", "rcsb_description" : [ { "text" : "This data item is a pointer to _em_image_processing.id.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "id", "image_processing_id" ] }, "minItems" : 1, "uniqueItems" : true }, "em_image_recording" : { "type" : "array", "items" : { "type" : "object", "properties" : { "average_exposure_time" : { "type" : "number", "examples" : [ 2.0 ], "description" : "The average exposure time for each image.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "seconds", "rcsb_description" : [ { "text" : "The average exposure time for each image.", "context" : "dictionary" }, { "text" : "Average Exposure Time (Em Image Recording)", "context" : "brief" } ], "rcsb_current_maximum_value" : 150.0, "rcsb_current_minimum_value" : 0.00313 }, "avg_electron_dose_per_image" : { "type" : "number", "examples" : [ 30.0 ], "description" : "The electron dose received by the specimen per image (electrons per square angstrom).", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "electrons_angstrom_squared", "rcsb_description" : [ { "text" : "The electron dose received by the specimen per image (electrons per square angstrom).", "context" : "dictionary" }, { "text" : "Avg Electron Dose Per Image (Em Image Recording)", "context" : "brief" } ], "rcsb_current_maximum_value" : 1200.0, "rcsb_current_minimum_value" : 2.5E-4 }, "details" : { "type" : "string", "examples" : [ "Images were collected in movie-mode at 17 frames per second" ], "description" : "Any additional details about image recording.", "rcsb_description" : [ { "text" : "Any additional details about image recording.", "context" : "dictionary" } ] }, "detector_mode" : { "type" : "string", "enum" : [ "COUNTING", "INTEGRATING", "OTHER", "SUPER-RESOLUTION" ], "description" : "The detector mode used during image recording.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The detector mode used during image recording.", "context" : "dictionary" }, { "text" : "Detector Mode (Em Image Recording)", "context" : "brief" } ] }, "film_or_detector_model" : { "type" : "string", "description" : "The detector type used for recording images.\n Usually film , CCD camera or direct electron detector.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The detector type used for recording images.\n Usually film , CCD camera or direct electron detector.", "context" : "dictionary" }, { "text" : "EM Imaging Detector", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "EM Method Details", "priority_order" : 45 } ] }, "id" : { "type" : "string", "description" : "PRIMARY KEY", "rcsb_description" : [ { "text" : "PRIMARY KEY", "context" : "dictionary" } ] }, "imaging_id" : { "type" : "string", "description" : "This data item the id of the microscopy settings used in the imaging.", "rcsb_description" : [ { "text" : "This data item the id of the microscopy settings used in the imaging.", "context" : "dictionary" } ] }, "num_diffraction_images" : { "type" : "integer", "description" : "The number of diffraction images collected.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of diffraction images collected.", "context" : "dictionary" }, { "text" : "Num Diffraction Images (Em Image Recording)", "context" : "brief" } ], "rcsb_current_maximum_value" : 130000.0, "rcsb_current_minimum_value" : 22.0 }, "num_grids_imaged" : { "type" : "integer", "description" : "Number of grids in the microscopy session", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Number of grids in the microscopy session", "context" : "dictionary" }, { "text" : "Num Grids Imaged (Em Image Recording)", "context" : "brief" } ], "rcsb_current_maximum_value" : 16184.0, "rcsb_current_minimum_value" : 1.0 }, "num_real_images" : { "type" : "integer", "description" : "The number of micrograph images collected.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of micrograph images collected.", "context" : "dictionary" }, { "text" : "Num Real Images (Em Image Recording)", "context" : "brief" } ], "rcsb_current_maximum_value" : 9080999.0, "rcsb_current_minimum_value" : 1.0 } }, "additionalProperties" : false, "required" : [ "id", "imaging_id" ] }, "minItems" : 1, "uniqueItems" : true }, "em_imaging" : { "type" : "array", "items" : { "type" : "object", "properties" : { "accelerating_voltage" : { "type" : "integer", "description" : "A value of accelerating voltage (in kV) used for imaging.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "kilovolts", "rcsb_description" : [ { "text" : "A value of accelerating voltage (in kV) used for imaging.", "context" : "dictionary" }, { "text" : "EM Accelerating Voltage", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "EM Method Details", "priority_order" : 40 } ], "rcsb_current_maximum_value" : 300300.0, "rcsb_current_minimum_value" : 30.0 }, "alignment_procedure" : { "type" : "string", "enum" : [ "BASIC", "COMA FREE", "NONE", "OTHER", "ZEMLIN TABLEAU" ], "description" : "The type of procedure used to align the microscope electron beam.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The type of procedure used to align the microscope electron beam.", "context" : "dictionary" }, { "text" : "Alignment Procedure (Em Imaging)", "context" : "brief" } ] }, "astigmatism" : { "type" : "string", "description" : "astigmatism", "rcsb_description" : [ { "text" : "astigmatism", "context" : "dictionary" } ] }, "c2_aperture_diameter" : { "type" : "number", "description" : "The open diameter of the c2 condenser lens,\n in microns.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "microns", "rcsb_description" : [ { "text" : "The open diameter of the c2 condenser lens,\n in microns.", "context" : "dictionary" }, { "text" : "C2 Aperture Diameter (Em Imaging)", "context" : "brief" } ], "rcsb_current_maximum_value" : 150.0, "rcsb_current_minimum_value" : 2.0 }, "calibrated_defocus_max" : { "type" : "number", "description" : "The maximum calibrated defocus value of the objective lens (in nanometres) used\n to obtain the recorded images. Negative values refer to overfocus.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "nanometres", "rcsb_description" : [ { "text" : "The maximum calibrated defocus value of the objective lens (in nanometres) used\n to obtain the recorded images. Negative values refer to overfocus.", "context" : "dictionary" }, { "text" : "Calibrated Defocus Max (Em Imaging)", "context" : "brief" } ], "rcsb_current_maximum_value" : 30000.0, "rcsb_current_minimum_value" : -7000.0 }, "calibrated_defocus_min" : { "type" : "number", "description" : "The minimum calibrated defocus value of the objective lens (in nanometres) used\n to obtain the recorded images. Negative values refer to overfocus.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "nanometres", "rcsb_description" : [ { "text" : "The minimum calibrated defocus value of the objective lens (in nanometres) used\n to obtain the recorded images. Negative values refer to overfocus.", "context" : "dictionary" }, { "text" : "Calibrated Defocus Min (Em Imaging)", "context" : "brief" } ], "rcsb_current_maximum_value" : 15000.0, "rcsb_current_minimum_value" : -2000.0 }, "calibrated_magnification" : { "type" : "integer", "description" : "The magnification value obtained for a known standard just\n prior to, during or just after the imaging experiment.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The magnification value obtained for a known standard just\n prior to, during or just after the imaging experiment.", "context" : "dictionary" }, { "text" : "Calibrated Magnification (Em Imaging)", "context" : "brief" } ], "rcsb_current_maximum_value" : 587963.0, "rcsb_current_minimum_value" : 2250.0 }, "cryogen" : { "type" : "string", "enum" : [ "HELIUM", "NITROGEN" ], "description" : "Cryogen type used to maintain the specimen stage temperature during imaging\n in the microscope.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Cryogen type used to maintain the specimen stage temperature during imaging\n in the microscope.", "context" : "dictionary" }, { "text" : "Cryogen (Em Imaging)", "context" : "brief" } ] }, "date" : { "type" : "string", "format" : "date", "examples" : [ "2001-05-08" ], "description" : "Date (YYYY-MM-DD) of imaging experiment or the date at which\n a series of experiments began.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Date (YYYY-MM-DD) of imaging experiment or the date at which\n a series of experiments began.", "context" : "dictionary" }, { "text" : "Date (Em Imaging)", "context" : "brief" } ], "rcsb_current_maximum_value" : 1.5770592E12, "rcsb_current_minimum_value" : 6.862752E11 }, "details" : { "type" : "string", "examples" : [ "Preliminary grid screening was performed manually." ], "description" : "Any additional imaging details.", "rcsb_description" : [ { "text" : "Any additional imaging details.", "context" : "dictionary" } ] }, "detector_distance" : { "type" : "number", "description" : "The camera length (in millimeters). The camera length is the\n product of the objective focal length and the combined magnification\n of the intermediate and projector lenses when the microscope is\n operated in the diffraction mode.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "millimetres", "rcsb_description" : [ { "text" : "The camera length (in millimeters). The camera length is the\n product of the objective focal length and the combined magnification\n of the intermediate and projector lenses when the microscope is\n operated in the diffraction mode.", "context" : "dictionary" }, { "text" : "Detector Distance (Em Imaging)", "context" : "brief" } ], "rcsb_current_maximum_value" : 800.0, "rcsb_current_minimum_value" : 0.0 }, "electron_beam_tilt_params" : { "type" : "string", "description" : "electron beam tilt params", "rcsb_description" : [ { "text" : "electron beam tilt params", "context" : "dictionary" } ] }, "electron_source" : { "type" : "string", "description" : "The source of electrons. The electron gun.", "rcsb_description" : [ { "text" : "The source of electrons. The electron gun.", "context" : "dictionary" } ] }, "id" : { "type" : "string", "description" : "PRIMARY KEY", "rcsb_description" : [ { "text" : "PRIMARY KEY", "context" : "dictionary" } ] }, "illumination_mode" : { "type" : "string", "enum" : [ "FLOOD BEAM", "OTHER", "SPOT SCAN" ], "description" : "The mode of illumination.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The mode of illumination.", "context" : "dictionary" }, { "text" : "Illumination Mode (Em Imaging)", "context" : "brief" } ] }, "microscope_model" : { "type" : "string", "enum" : [ "FEI MORGAGNI", "FEI POLARA 300", "FEI TALOS ARCTICA", "FEI TECNAI 10", "FEI TECNAI 12", "FEI TECNAI 20", "FEI TECNAI ARCTICA", "FEI TECNAI F20", "FEI TECNAI F30", "FEI TECNAI SPHERA", "FEI TECNAI SPIRIT", "FEI TITAN", "FEI TITAN KRIOS", "FEI/PHILIPS CM10", "FEI/PHILIPS CM12", "FEI/PHILIPS CM120T", "FEI/PHILIPS CM200FEG", "FEI/PHILIPS CM200FEG/SOPHIE", "FEI/PHILIPS CM200FEG/ST", "FEI/PHILIPS CM200FEG/UT", "FEI/PHILIPS CM200T", "FEI/PHILIPS CM300FEG/HE", "FEI/PHILIPS CM300FEG/ST", "FEI/PHILIPS CM300FEG/T", "FEI/PHILIPS EM400", "FEI/PHILIPS EM420", "HITACHI EF2000", "HITACHI EF3000", "HITACHI H-9500SD", "HITACHI H3000 UHVEM", "HITACHI H7600", "HITACHI HF2000", "HITACHI HF3000", "JEOL 1000EES", "JEOL 100B", "JEOL 100CX", "JEOL 1010", "JEOL 1200", "JEOL 1200EX", "JEOL 1200EXII", "JEOL 1230", "JEOL 1400", "JEOL 1400/HR + YPS FEG", "JEOL 2000EX", "JEOL 2000EXII", "JEOL 2010", "JEOL 2010F", "JEOL 2010HC", "JEOL 2010HT", "JEOL 2010UHR", "JEOL 2011", "JEOL 2100", "JEOL 2100F", "JEOL 2200FS", "JEOL 2200FSC", "JEOL 3000SFF", "JEOL 3100FEF", "JEOL 3100FFC", "JEOL 3200FS", "JEOL 3200FSC", "JEOL 4000", "JEOL 4000EX", "JEOL CRYO ARM 200", "JEOL CRYO ARM 300", "JEOL KYOTO-3000SFF", "SHUIMU TOTEM 120S", "SHUIMU TOTEM 200S", "SHUIMU TOTEM 300S", "SIEMENS SULEIKA", "TFS GLACIOS", "TFS KRIOS", "TFS TALOS", "TFS TALOS F200C", "TFS TALOS L120C", "TFS TITAN THEMIS", "TFS TUNDRA", "ZEISS LEO912", "ZEISS LIBRA120PLUS" ], "description" : "The name of the model of microscope.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The name of the model of microscope.", "context" : "dictionary" }, { "text" : "EM Microscope Model", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "EM Method Details", "priority_order" : 35 } ] }, "mode" : { "type" : "string", "enum" : [ "4D-STEM", "BRIGHT FIELD", "DARK FIELD", "DIFFRACTION", "OTHER" ], "description" : "The mode of imaging.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The mode of imaging.", "context" : "dictionary" }, { "text" : "Mode (Em Imaging)", "context" : "brief" } ] }, "nominal_cs" : { "type" : "number", "examples" : [ 2.0 ], "description" : "The spherical aberration coefficient (Cs) in millimeters,\n of the objective lens.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "millimetres", "rcsb_description" : [ { "text" : "The spherical aberration coefficient (Cs) in millimeters,\n of the objective lens.", "context" : "dictionary" }, { "text" : "Nominal Cs (Em Imaging)", "context" : "brief" } ], "rcsb_current_maximum_value" : 6.3, "rcsb_current_minimum_value" : 0.0 }, "nominal_defocus_max" : { "type" : "number", "description" : "The maximum defocus value of the objective lens (in nanometres) used\n to obtain the recorded images. Negative values refer to overfocus.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "nanometres", "rcsb_description" : [ { "text" : "The maximum defocus value of the objective lens (in nanometres) used\n to obtain the recorded images. Negative values refer to overfocus.", "context" : "dictionary" }, { "text" : "Nominal Defocus Max (Em Imaging)", "context" : "brief" } ], "rcsb_current_maximum_value" : 50000.0, "rcsb_current_minimum_value" : -25000.0 }, "nominal_defocus_min" : { "type" : "number", "description" : "The minimum defocus value of the objective lens (in nanometres) used\n to obtain the recorded images. Negative values refer to overfocus.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "nanometres", "rcsb_description" : [ { "text" : "The minimum defocus value of the objective lens (in nanometres) used\n to obtain the recorded images. Negative values refer to overfocus.", "context" : "dictionary" }, { "text" : "Nominal Defocus Min (Em Imaging)", "context" : "brief" } ], "rcsb_current_maximum_value" : 16000.0, "rcsb_current_minimum_value" : -15000.0 }, "nominal_magnification" : { "type" : "integer", "description" : "The magnification indicated by the microscope readout.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The magnification indicated by the microscope readout.", "context" : "dictionary" }, { "text" : "Nominal Magnification (Em Imaging)", "context" : "brief" } ], "rcsb_current_maximum_value" : 310000.0, "rcsb_current_minimum_value" : 2250.0 }, "recording_temperature_maximum" : { "type" : "number", "description" : "The specimen temperature maximum (kelvin) for the duration\n of imaging.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "kelvins", "rcsb_description" : [ { "text" : "The specimen temperature maximum (kelvin) for the duration\n of imaging.", "context" : "dictionary" }, { "text" : "Recording Temperature Maximum (Em Imaging)", "context" : "brief" } ], "rcsb_current_maximum_value" : 310.0, "rcsb_current_minimum_value" : 4.2 }, "recording_temperature_minimum" : { "type" : "number", "description" : "The specimen temperature minimum (kelvin) for the duration\n of imaging.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "kelvins", "rcsb_description" : [ { "text" : "The specimen temperature minimum (kelvin) for the duration\n of imaging.", "context" : "dictionary" }, { "text" : "Recording Temperature Minimum (Em Imaging)", "context" : "brief" } ], "rcsb_current_maximum_value" : 293.0, "rcsb_current_minimum_value" : 4.2 }, "residual_tilt" : { "type" : "number", "description" : "Residual tilt of the electron beam (in miliradians)", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "milliradians", "rcsb_description" : [ { "text" : "Residual tilt of the electron beam (in miliradians)", "context" : "dictionary" }, { "text" : "Residual Tilt (Em Imaging)", "context" : "brief" } ], "rcsb_current_maximum_value" : 350.0, "rcsb_current_minimum_value" : 0.001 }, "specimen_holder_model" : { "type" : "string", "enum" : [ "FEI TITAN KRIOS AUTOGRID HOLDER", "FISCHIONE 2550", "FISCHIONE INSTRUMENTS DUAL AXIS TOMOGRAPHY HOLDER", "GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER", "GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER", "GATAN 914 HIGH TILT LIQUID NITROGEN CRYO TRANSFER TOMOGRAPHY HOLDER", "GATAN 915 DOUBLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER", "GATAN CHDT 3504 DOUBLE TILT HIGH RESOLUTION NITROGEN COOLING HOLDER", "GATAN CT3500 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER", "GATAN CT3500TR SINGLE TILT ROTATION LIQUID NITROGEN CRYO TRANSFER HOLDER", "GATAN ELSA 698 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER", "GATAN HC 3500 SINGLE TILT HEATING/NITROGEN COOLING HOLDER", "GATAN HCHDT 3010 DOUBLE TILT HIGH RESOLUTION HELIUM COOLING HOLDER", "GATAN HCHST 3008 SINGLE TILT HIGH RESOLUTION HELIUM COOLING HOLDER", "GATAN HELIUM", "GATAN LIQUID NITROGEN", "GATAN UHRST 3500 SINGLE TILT ULTRA HIGH RESOLUTION NITROGEN COOLING HOLDER", "GATAN ULTDT ULTRA LOW TEMPERATURE DOUBLE TILT HELIUM COOLING HOLDER", "GATAN ULTST ULTRA LOW TEMPERATURE SINGLE TILT HELIUM COOLING HOLDER", "HOME BUILD", "JEOL", "JEOL 3200FSC CRYOHOLDER", "JEOL CRYOSPECPORTER", "OTHER", "PHILIPS ROTATION HOLDER", "SIDE ENTRY, EUCENTRIC" ], "description" : "The name of the model of specimen holder used during imaging.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The name of the model of specimen holder used during imaging.", "context" : "dictionary" }, { "text" : "Specimen Holder Model (Em Imaging)", "context" : "brief" } ] }, "specimen_holder_type" : { "type" : "string", "examples" : [ "cryo" ], "description" : "The type of specimen holder used during imaging.", "rcsb_description" : [ { "text" : "The type of specimen holder used during imaging.", "context" : "dictionary" } ] }, "specimen_id" : { "type" : "string", "description" : "Foreign key to the EM_SPECIMEN category", "rcsb_description" : [ { "text" : "Foreign key to the EM_SPECIMEN category", "context" : "dictionary" } ] }, "temperature" : { "type" : "number", "description" : "The mean specimen stage temperature (in kelvin) during imaging\n in the microscope.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "kelvins", "rcsb_description" : [ { "text" : "The mean specimen stage temperature (in kelvin) during imaging\n in the microscope.", "context" : "dictionary" }, { "text" : "Temperature (Em Imaging)", "context" : "brief" } ], "rcsb_current_maximum_value" : 300.0, "rcsb_current_minimum_value" : 4.0 }, "tilt_angle_max" : { "type" : "number", "description" : "The maximum angle at which the specimen was tilted to obtain\n recorded images.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "degrees", "rcsb_description" : [ { "text" : "The maximum angle at which the specimen was tilted to obtain\n recorded images.", "context" : "dictionary" }, { "text" : "Tilt Angle Max (Em Imaging)", "context" : "brief" } ], "rcsb_current_maximum_value" : 79.0, "rcsb_current_minimum_value" : -9999.0 }, "tilt_angle_min" : { "type" : "number", "description" : "The minimum angle at which the specimen was tilted to obtain\n recorded images.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "degrees", "rcsb_description" : [ { "text" : "The minimum angle at which the specimen was tilted to obtain\n recorded images.", "context" : "dictionary" }, { "text" : "Tilt Angle Min (Em Imaging)", "context" : "brief" } ], "rcsb_current_maximum_value" : 60.0, "rcsb_current_minimum_value" : -9999.0 } }, "additionalProperties" : false, "required" : [ "id" ] }, "minItems" : 1, "uniqueItems" : true }, "em_particle_selection" : { "type" : "array", "items" : { "type" : "object", "properties" : { "details" : { "type" : "string", "examples" : [ "negative monitor contrast facilitated particle picking" ], "description" : "Additional detail such as description of filters used, if selection was\nmanual or automated, and/or template details.", "rcsb_description" : [ { "text" : "Additional detail such as description of filters used, if selection was\nmanual or automated, and/or template details.", "context" : "dictionary" } ] }, "id" : { "type" : "string", "description" : "PRIMARY KEY", "rcsb_description" : [ { "text" : "PRIMARY KEY", "context" : "dictionary" } ] }, "image_processing_id" : { "type" : "string", "description" : "The value of _em_particle_selection.image_processing_id points to\n the EM_IMAGE_PROCESSING category.", "rcsb_description" : [ { "text" : "The value of _em_particle_selection.image_processing_id points to\n the EM_IMAGE_PROCESSING category.", "context" : "dictionary" } ] }, "num_particles_selected" : { "type" : "integer", "description" : "The number of particles selected from the projection set of images.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of particles selected from the projection set of images.", "context" : "dictionary" }, { "text" : "Num Particles Selected (Em Particle Selection)", "context" : "brief" } ], "rcsb_current_maximum_value" : 1.5E8, "rcsb_current_minimum_value" : 1.0 } }, "additionalProperties" : false, "required" : [ "id", "image_processing_id" ] }, "minItems" : 1, "uniqueItems" : true }, "em_single_particle_entity" : { "type" : "array", "items" : { "type" : "object", "properties" : { "id" : { "type" : "integer", "description" : "PRIMARY KEY", "rcsb_description" : [ { "text" : "PRIMARY KEY", "context" : "dictionary" } ] }, "image_processing_id" : { "type" : "string", "description" : "pointer to _em_image_processing.id.", "rcsb_description" : [ { "text" : "pointer to _em_image_processing.id.", "context" : "dictionary" } ] }, "point_symmetry" : { "type" : "string", "examples" : [ "C1", "C5", "C4" ], "description" : "Point symmetry symbol, either Cn, Dn, T, O, or I", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Point symmetry symbol, either Cn, Dn, T, O, or I", "context" : "dictionary" }, { "text" : "EM Point Symmetry Imposed", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "EM Method Details", "priority_order" : 50 } ] } }, "additionalProperties" : false, "required" : [ "id", "image_processing_id" ] }, "minItems" : 1, "uniqueItems" : true }, "em_software" : { "type" : "array", "items" : { "type" : "object", "properties" : { "category" : { "type" : "string", "enum" : [ "CLASSIFICATION", "CRYSTALLOGRAPHY MERGING", "CTF CORRECTION", "DIFFRACTION INDEXING", "EWALD SPHERE CORRECTION", "FINAL EULER ASSIGNMENT", "IMAGE ACQUISITION", "INITIAL EULER ASSIGNMENT", "LATTICE DISTORTION CORRECTION", "LAYERLINE INDEXING", "MASKING", "MODEL FITTING", "MODEL REFINEMENT", "MOLECULAR REPLACEMENT", "OTHER", "PARTICLE SELECTION", "RECONSTRUCTION", "SERIES ALIGNMENT", "SYMMETRY DETERMINATION", "VOLUME SELECTION" ], "description" : "The purpose of the software.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The purpose of the software.", "context" : "dictionary" }, { "text" : "Category (Em Software)", "context" : "brief" } ] }, "details" : { "type" : "string", "examples" : [ "EMAN2 e2boxer.py was used to automatically select particle images." ], "description" : "Details about the software used.", "rcsb_description" : [ { "text" : "Details about the software used.", "context" : "dictionary" } ] }, "fitting_id" : { "type" : "string", "description" : "pointer to _em_3d_fitting.id in the EM_3D_FITTING category.", "rcsb_description" : [ { "text" : "pointer to _em_3d_fitting.id in the EM_3D_FITTING category.", "context" : "dictionary" } ] }, "id" : { "type" : "string", "description" : "PRIMARY KEY", "rcsb_description" : [ { "text" : "PRIMARY KEY", "context" : "dictionary" } ] }, "image_processing_id" : { "type" : "string", "description" : "pointer to _em_image_processing.id in the EM_IMAGE_PROCESSING category.", "rcsb_description" : [ { "text" : "pointer to _em_image_processing.id in the EM_IMAGE_PROCESSING category.", "context" : "dictionary" } ] }, "imaging_id" : { "type" : "string", "description" : "pointer to _em_imaging.id in the EM_IMAGING category.", "rcsb_description" : [ { "text" : "pointer to _em_imaging.id in the EM_IMAGING category.", "context" : "dictionary" } ] }, "name" : { "type" : "string", "examples" : [ "EMAN", "Imagic", "Spider", "Bsoft", "UCSF-Chimera" ], "description" : "The name of the software package used, e.g., RELION. Depositors are strongly\n encouraged to provide a value in this field.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The name of the software package used, e.g., RELION. Depositors are strongly\n encouraged to provide a value in this field.", "context" : "dictionary" }, { "text" : "EM Software", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "EM Method Details", "priority_order" : 25 } ] }, "version" : { "type" : "string", "examples" : [ "9.03", "2.1" ], "description" : "The version of the software.", "rcsb_description" : [ { "text" : "The version of the software.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "id" ] }, "minItems" : 1, "uniqueItems" : true }, "em_specimen" : { "type" : "array", "items" : { "type" : "object", "properties" : { "concentration" : { "type" : "number", "examples" : [ 1.35 ], "description" : "The concentration (in milligrams per milliliter, mg/ml)\n of the complex in the sample.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "mg_per_ml", "rcsb_description" : [ { "text" : "The concentration (in milligrams per milliliter, mg/ml)\n of the complex in the sample.", "context" : "dictionary" }, { "text" : "Concentration (Em Specimen)", "context" : "brief" } ], "rcsb_current_maximum_value" : 1000000.0, "rcsb_current_minimum_value" : 7.5E-5 }, "details" : { "type" : "string", "examples" : [ "This sample was monodisperse.", "Au was deposited at a 30 degree angle to 15 nm thickness.", "Colloidal gold particles were deposited by dipping into dilute solution.", "The specimen was frozen at high pressure using the bal-tec hpm 010 instrument.", "The embedded sample was sectioned at 100 K to 50 nm final thickness." ], "description" : "A description of any additional details of the specimen preparation.", "rcsb_description" : [ { "text" : "A description of any additional details of the specimen preparation.", "context" : "dictionary" } ] }, "embedding_applied" : { "type" : "string", "enum" : [ "NO", "YES" ], "description" : "'YES' indicates that the specimen has been embedded.", "rcsb_description" : [ { "text" : "'YES' indicates that the specimen has been embedded.", "context" : "dictionary" } ] }, "experiment_id" : { "type" : "string", "description" : "Pointer to _em_experiment.id.", "rcsb_description" : [ { "text" : "Pointer to _em_experiment.id.", "context" : "dictionary" } ] }, "id" : { "type" : "string", "description" : "PRIMARY KEY", "rcsb_description" : [ { "text" : "PRIMARY KEY", "context" : "dictionary" } ] }, "shadowing_applied" : { "type" : "string", "enum" : [ "NO", "YES" ], "description" : "'YES' indicates that the specimen has been shadowed.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "'YES' indicates that the specimen has been shadowed.", "context" : "dictionary" }, { "text" : "Shadowing Applied (Em Specimen)", "context" : "brief" } ] }, "staining_applied" : { "type" : "string", "enum" : [ "NO", "YES" ], "description" : "'YES' indicates that the specimen has been stained.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "'YES' indicates that the specimen has been stained.", "context" : "dictionary" }, { "text" : "Staining Applied (Em Specimen)", "context" : "brief" } ] }, "vitrification_applied" : { "type" : "string", "enum" : [ "NO", "YES" ], "description" : "'YES' indicates that the specimen was vitrified by cryopreservation.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "'YES' indicates that the specimen was vitrified by cryopreservation.", "context" : "dictionary" }, { "text" : "Vitrification Applied (Em Specimen)", "context" : "brief" } ] } }, "additionalProperties" : false, "required" : [ "experiment_id", "id" ] }, "minItems" : 1, "uniqueItems" : true }, "em_staining" : { "type" : "array", "items" : { "type" : "object", "properties" : { "details" : { "type" : "string", "examples" : [ "Negatively stained EM specimens were prepared using a carbon-sandwich technique\n and uranyl-formate stain." ], "description" : "Staining procedure used in the specimen preparation.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Staining procedure used in the specimen preparation.", "context" : "dictionary" }, { "text" : "EM Staining Details", "context" : "brief" } ] }, "id" : { "type" : "string", "description" : "PRIMARY KEY", "rcsb_description" : [ { "text" : "PRIMARY KEY", "context" : "dictionary" } ] }, "material" : { "type" : "string", "examples" : [ "Uranyl Acetate" ], "description" : "The staining material.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The staining material.", "context" : "dictionary" }, { "text" : "EM Staining Material", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "EM Method Details", "priority_order" : 55 } ] }, "specimen_id" : { "type" : "string", "description" : "Foreign key relationship to the EM SPECIMEN category", "rcsb_description" : [ { "text" : "Foreign key relationship to the EM SPECIMEN category", "context" : "dictionary" } ] }, "type" : { "type" : "string", "enum" : [ "NEGATIVE", "NONE", "POSITIVE" ], "description" : "type of staining", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "type of staining", "context" : "dictionary" }, { "text" : "EM Staining Type", "context" : "brief" } ] } }, "additionalProperties" : false, "required" : [ "id" ] }, "minItems" : 1, "uniqueItems" : true }, "em_vitrification" : { "type" : "array", "items" : { "type" : "object", "properties" : { "chamber_temperature" : { "type" : "number", "description" : "The temperature (in kelvin) of the sample just prior to vitrification.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "kelvins", "rcsb_description" : [ { "text" : "The temperature (in kelvin) of the sample just prior to vitrification.", "context" : "dictionary" }, { "text" : "Chamber Temperature (Em Vitrification)", "context" : "brief" } ], "rcsb_current_maximum_value" : 2881.0, "rcsb_current_minimum_value" : 4.0 }, "cryogen_name" : { "type" : "string", "enum" : [ "ETHANE", "ETHANE-PROPANE", "FREON 12", "FREON 22", "HELIUM", "METHANE", "NITROGEN", "OTHER", "PROPANE" ], "description" : "This is the name of the cryogen.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "This is the name of the cryogen.", "context" : "dictionary" }, { "text" : "Cryogen Name (Em Vitrification)", "context" : "brief" } ] }, "details" : { "type" : "string", "examples" : [ "Vitrification carried out in argon atmosphere." ], "description" : "Any additional details relating to vitrification.", "rcsb_description" : [ { "text" : "Any additional details relating to vitrification.", "context" : "dictionary" } ] }, "humidity" : { "type" : "number", "description" : "Relative humidity (%) of air surrounding the specimen just prior to\nvitrification.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Relative humidity (%) of air surrounding the specimen just prior to\nvitrification.", "context" : "dictionary" }, { "text" : "Humidity (Em Vitrification)", "context" : "brief" } ], "rcsb_current_maximum_value" : 100.0, "rcsb_current_minimum_value" : 0.0 }, "id" : { "type" : "string", "description" : "PRIMARY KEY", "rcsb_description" : [ { "text" : "PRIMARY KEY", "context" : "dictionary" } ] }, "instrument" : { "type" : "string", "enum" : [ "CRYOSOL VITROJET", "EMS-002 RAPID IMMERSION FREEZER", "FEI VITROBOT MARK I", "FEI VITROBOT MARK II", "FEI VITROBOT MARK III", "FEI VITROBOT MARK IV", "GATAN CRYOPLUNGE 3", "HOMEMADE PLUNGER", "LEICA EM CPC", "LEICA EM GP", "LEICA KF80", "LEICA PLUNGER", "REICHERT-JUNG PLUNGER", "SPOTITON", "SPT LABTECH CHAMELEON", "ZEISS PLUNGE FREEZER CRYOBOX" ], "description" : "The type of instrument used in the vitrification process.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The type of instrument used in the vitrification process.", "context" : "dictionary" }, { "text" : "EM Vitrification Instrument", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "EM Method Details", "priority_order" : 30 } ] }, "method" : { "type" : "string", "examples" : [ "plunge freezing" ], "description" : "The procedure for vitrification.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The procedure for vitrification.", "context" : "dictionary" }, { "text" : "Method (Em Vitrification)", "context" : "brief" } ] }, "specimen_id" : { "type" : "string", "description" : "This data item is a pointer to _em_specimen.id", "rcsb_description" : [ { "text" : "This data item is a pointer to _em_specimen.id", "context" : "dictionary" } ] }, "temp" : { "type" : "number", "description" : "The vitrification temperature (in kelvin), e.g.,\n temperature of the plunge instrument cryogen bath.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "kelvins", "rcsb_description" : [ { "text" : "The vitrification temperature (in kelvin), e.g.,\n temperature of the plunge instrument cryogen bath.", "context" : "dictionary" }, { "text" : "Temp (Em Vitrification)", "context" : "brief" } ], "rcsb_current_maximum_value" : 277.0, "rcsb_current_minimum_value" : 76.0 }, "time_resolved_state" : { "type" : "string", "examples" : [ "plunge 30 msec after spraying with effector" ], "description" : "The length of time after an event effecting the sample that\n vitrification was induced and a description of the event.", "rcsb_description" : [ { "text" : "The length of time after an event effecting the sample that\n vitrification was induced and a description of the event.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "id", "specimen_id" ] }, "minItems" : 1, "uniqueItems" : true }, "entry" : { "type" : "object", "properties" : { "id" : { "type" : "string", "description" : "The value of _entry.id identifies the data block.\n\n Note that this item need not be a number; it can be any unique\n identifier.", "rcsb_description" : [ { "text" : "The value of _entry.id identifies the data block.\n\n Note that this item need not be a number; it can be any unique\n identifier.", "context" : "dictionary" } ] }, "ma_collection_id" : { "type" : "string", "description" : "An identifier for the model collection associated with the entry.", "rcsb_description" : [ { "text" : "An identifier for the model collection associated with the entry.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "id" ] }, "exptl" : { "type" : "array", "items" : { "type" : "object", "properties" : { "crystals_number" : { "type" : "integer", "description" : "The total number of crystals used in the measurement of\n intensities.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The total number of crystals used in the measurement of\n intensities.", "context" : "dictionary" }, { "text" : "Indicate the number of crystals used in your experiments", "context" : "deposition" }, { "text" : "Crystals Number (Exptl)", "context" : "brief" } ], "rcsb_current_maximum_value" : 1029868.0, "rcsb_current_minimum_value" : 1.0 }, "details" : { "type" : "string", "description" : "Any special information about the experimental work prior to the\n intensity measurement. See also _exptl_crystal.preparation.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Any special information about the experimental work prior to the\n intensity measurement. See also _exptl_crystal.preparation.", "context" : "dictionary" }, { "text" : "Details (Exptl)", "context" : "brief" } ] }, "method" : { "type" : "string", "enum" : [ "ELECTRON CRYSTALLOGRAPHY", "ELECTRON MICROSCOPY", "EPR", "FIBER DIFFRACTION", "FLUORESCENCE TRANSFER", "INFRARED SPECTROSCOPY", "NEUTRON DIFFRACTION", "POWDER DIFFRACTION", "SOLID-STATE NMR", "SOLUTION NMR", "SOLUTION SCATTERING", "THEORETICAL MODEL", "X-RAY DIFFRACTION" ], "examples" : [ "X-RAY DIFFRACTION", "NEUTRON DIFFRACTION", "FIBER DIFFRACTION", "ELECTRON CRYSTALLOGRAPHY", "ELECTRON MICROSCOPY", "SOLUTION NMR", "SOLID-STATE NMR", "SOLUTION SCATTERING", "POWDER DIFFRACTION" ], "description" : "The method used in the experiment.", "rcsb_search_context" : [ "exact-match", "suggest" ], "rcsb_full_text_priority" : 20, "rcsb_enum_annotated" : [ { "value" : "ELECTRON CRYSTALLOGRAPHY" }, { "value" : "ELECTRON MICROSCOPY" }, { "value" : "EPR", "detail" : "EPR only as a supporting method" }, { "value" : "FIBER DIFFRACTION" }, { "value" : "FLUORESCENCE TRANSFER", "detail" : "FLUORESCENCE TRANSFER only as a supporting method" }, { "value" : "INFRARED SPECTROSCOPY", "detail" : "IR and FTIR only as supporting methods" }, { "value" : "NEUTRON DIFFRACTION" }, { "value" : "POWDER DIFFRACTION" }, { "value" : "SOLID-STATE NMR" }, { "value" : "SOLUTION NMR" }, { "value" : "SOLUTION SCATTERING" }, { "value" : "THEORETICAL MODEL", "detail" : "THEORETICAL MODEL only as a supporting method" }, { "value" : "X-RAY DIFFRACTION" } ], "rcsb_description" : [ { "text" : "The method used in the experiment.", "context" : "dictionary" }, { "text" : "The method(s) used in the experiment", "context" : "deposition" }, { "text" : "Experimental Method", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Methods", "priority_order" : 10 } ] }, "method_details" : { "type" : "string", "examples" : [ "29 structures", "minimized average structure" ], "description" : "A description of special aspects of the experimental method.", "rcsb_description" : [ { "text" : "A description of special aspects of the experimental method.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "method" ] }, "minItems" : 1, "uniqueItems" : true }, "exptl_crystal" : { "type" : "array", "items" : { "type" : "object", "properties" : { "colour" : { "type" : "string", "examples" : [ "dark green" ], "description" : "The colour of the crystal.", "rcsb_description" : [ { "text" : "The colour of the crystal.", "context" : "dictionary" } ] }, "density_Matthews" : { "type" : "number", "examples" : [ 3.1 ], "description" : "The density of the crystal, expressed as the ratio of the\n volume of the asymmetric unit to the molecular mass of a\n monomer of the structure, in units of angstroms^3^ per dalton.\n\n Ref: Matthews, B. W. (1968). J. Mol. Biol. 33, 491-497.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "angstroms_cubed_per_dalton", "rcsb_description" : [ { "text" : "The density of the crystal, expressed as the ratio of the\n volume of the asymmetric unit to the molecular mass of a\n monomer of the structure, in units of angstroms^3^ per dalton.\n\n Ref: Matthews, B. W. (1968). J. Mol. Biol. 33, 491-497.", "context" : "dictionary" }, { "text" : "Vm/M : Vm= unit cell volume and M= total molecular weight of molecules/cell", "context" : "deposition" }, { "text" : "Density (Matthews)", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Crystal Properties", "priority_order" : 5 } ], "rcsb_current_maximum_value" : 45.14, "rcsb_current_minimum_value" : 0.0 }, "density_meas" : { "type" : "number", "description" : "Density values measured using standard chemical and physical\n methods. The units are megagrams per cubic metre (grams per\n cubic centimetre).", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "megagrams_per_cubic_metre", "rcsb_description" : [ { "text" : "Density values measured using standard chemical and physical\n methods. The units are megagrams per cubic metre (grams per\n cubic centimetre).", "context" : "dictionary" }, { "text" : "Density Meas (Exptl Crystal)", "context" : "brief" } ], "rcsb_current_maximum_value" : 2572802.25, "rcsb_current_minimum_value" : 3.158E-4 }, "density_percent_sol" : { "type" : "number", "description" : "Density value P calculated from the crystal cell and contents,\n expressed as per cent solvent.\n\n P = 1 - (1.23 N MMass) / V\n\n N = the number of molecules in the unit cell\n MMass = the molecular mass of each molecule (gm/mole)\n V = the volume of the unit cell (A^3^)\n 1.23 = a conversion factor evaluated as:\n\n (0.74 cm^3^/g) (10^24^ A^3^/cm^3^)\n --------------------------------------\n (6.02*10^23^) molecules/mole\n\n where 0.74 is an assumed value for the partial specific\n volume of the molecule", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Density value P calculated from the crystal cell and contents,\n expressed as per cent solvent.\n\n P = 1 - (1.23 N MMass) / V\n\n N = the number of molecules in the unit cell\n MMass = the molecular mass of each molecule (gm/mole)\n V = the volume of the unit cell (A^3^)\n 1.23 = a conversion factor evaluated as:\n\n (0.74 cm^3^/g) (10^24^ A^3^/cm^3^)\n --------------------------------------\n (6.02*10^23^) molecules/mole\n\n where 0.74 is an assumed value for the partial specific\n volume of the molecule", "context" : "dictionary" }, { "text" : "Percent solvent content of cell", "context" : "deposition" }, { "text" : "Density (% solvent)", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Crystal Properties", "priority_order" : 10 } ], "rcsb_current_maximum_value" : 96.06, "rcsb_current_minimum_value" : 0.0 }, "description" : { "type" : "string", "description" : "A description of the quality and habit of the crystal.\n The crystal dimensions should not normally be reported here;\n use instead the specific items in the EXPTL_CRYSTAL category\n relating to size for the gross dimensions of the crystal and\n data items in the EXPTL_CRYSTAL_FACE category to describe the\n relationship between individual faces.", "rcsb_description" : [ { "text" : "A description of the quality and habit of the crystal.\n The crystal dimensions should not normally be reported here;\n use instead the specific items in the EXPTL_CRYSTAL category\n relating to size for the gross dimensions of the crystal and\n data items in the EXPTL_CRYSTAL_FACE category to describe the\n relationship between individual faces.", "context" : "dictionary" } ] }, "id" : { "type" : "string", "description" : "The value of _exptl_crystal.id must uniquely identify a record in\n the EXPTL_CRYSTAL list.\n\n Note that this item need not be a number; it can be any unique\n identifier.", "rcsb_description" : [ { "text" : "The value of _exptl_crystal.id must uniquely identify a record in\n the EXPTL_CRYSTAL list.\n\n Note that this item need not be a number; it can be any unique\n identifier.", "context" : "dictionary" } ] }, "pdbx_mosaicity" : { "type" : "number", "description" : "Isotropic approximation of the distribution of mis-orientation angles\nspecified in degrees of all the mosaic domain blocks in the crystal,\nrepresented as a standard deviation. Here, a mosaic block is a set of\ncontiguous unit cells assumed to be perfectly aligned. Lower mosaicity\nindicates better ordered crystals. See for example:\n\nNave, C. (1998). Acta Cryst. D54, 848-853.\n\nNote that many software packages estimate the mosaic rotation distribution\ndifferently and may combine several physical properties of the experiment\ninto a single mosaic term. This term will help fit the modeled spots\nto the observed spots without necessarily being directly related to the\nphysics of the crystal itself.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "degrees", "rcsb_description" : [ { "text" : "Isotropic approximation of the distribution of mis-orientation angles\nspecified in degrees of all the mosaic domain blocks in the crystal,\nrepresented as a standard deviation. Here, a mosaic block is a set of\ncontiguous unit cells assumed to be perfectly aligned. Lower mosaicity\nindicates better ordered crystals. See for example:\n\nNave, C. (1998). Acta Cryst. D54, 848-853.\n\nNote that many software packages estimate the mosaic rotation distribution\ndifferently and may combine several physical properties of the experiment\ninto a single mosaic term. This term will help fit the modeled spots\nto the observed spots without necessarily being directly related to the\nphysics of the crystal itself.", "context" : "dictionary" }, { "text" : "Mosaicity (Exptl Crystal)", "context" : "brief" } ], "rcsb_current_maximum_value" : 20.715, "rcsb_current_minimum_value" : 0.0 }, "pdbx_mosaicity_esd" : { "type" : "number", "description" : "The uncertainty in the mosaicity estimate for the crystal.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "degrees", "rcsb_description" : [ { "text" : "The uncertainty in the mosaicity estimate for the crystal.", "context" : "dictionary" }, { "text" : "Mosaicity Esd (Exptl Crystal)", "context" : "brief" } ], "rcsb_current_maximum_value" : 15.975, "rcsb_current_minimum_value" : 0.002 }, "preparation" : { "type" : "string", "examples" : [ "mounted in an argon-filled quartz capillary" ], "description" : "Details of crystal growth and preparation of the crystal (e.g.\n mounting) prior to the intensity measurements.", "rcsb_description" : [ { "text" : "Details of crystal growth and preparation of the crystal (e.g.\n mounting) prior to the intensity measurements.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "id" ] }, "minItems" : 1, "uniqueItems" : true }, "exptl_crystal_grow" : { "type" : "array", "items" : { "type" : "object", "properties" : { "crystal_id" : { "type" : "string", "description" : "This data item is a pointer to _exptl_crystal.id in the\n EXPTL_CRYSTAL category.", "rcsb_description" : [ { "text" : "This data item is a pointer to _exptl_crystal.id in the\n EXPTL_CRYSTAL category.", "context" : "dictionary" } ] }, "details" : { "type" : "string", "examples" : [ "Solution 2 was prepared as a well solution and\n mixed. A droplet containing 2 \\ml of solution\n 1 was delivered onto a cover slip; 2 \\ml of\n solution 2 was added to the droplet without\n mixing.", "Crystal plates were originally stored at room\n temperature for 1 week but no nucleation\n occurred. They were then transferred to 4\n degrees C, at which temperature well formed\n single crystals grew in 2 days.", "The dependence on pH for successful crystal\n growth is very sharp. At pH 7.4 only showers\n of tiny crystals grew, at pH 7.5 well formed\n single crystals grew, at pH 7.6 no\n crystallization occurred at all." ], "description" : "A description of special aspects of the crystal growth.", "rcsb_description" : [ { "text" : "A description of special aspects of the crystal growth.", "context" : "dictionary" } ] }, "method" : { "type" : "string", "examples" : [ "MICROBATCH", "VAPOR DIFFUSION, HANGING DROP" ], "description" : "The method used to grow the crystals.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The method used to grow the crystals.", "context" : "dictionary" }, { "text" : "Crystallization Method", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Crystal Properties", "priority_order" : 25 } ] }, "pH" : { "type" : "number", "examples" : [ 7.4, 7.6, 4.3 ], "description" : "The pH at which the crystal was grown. If more than one pH was\n employed during the crystallization process, the final pH should\n be noted here and the protocol involving multiple pH values\n should be described in _exptl_crystal_grow.details.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The pH at which the crystal was grown. If more than one pH was\n employed during the crystallization process, the final pH should\n be noted here and the protocol involving multiple pH values\n should be described in _exptl_crystal_grow.details.", "context" : "dictionary" }, { "text" : "Provide the pH of the buffer used in crystallization", "context" : "deposition" }, { "text" : "pH", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Crystal Properties", "priority_order" : 20 } ], "rcsb_current_maximum_value" : 12.0, "rcsb_current_minimum_value" : 0.0 }, "pdbx_details" : { "type" : "string", "examples" : [ "PEG 4000, potassium phosphate, magnesium chloride, cacodylate" ], "description" : "Text description of crystal growth procedure.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Text description of crystal growth procedure.", "context" : "dictionary" }, { "text" : "Crystallization Details", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Crystal Properties", "priority_order" : 30 } ] }, "pdbx_pH_range" : { "type" : "string", "examples" : [ "5.6 - 6.4" ], "description" : "The range of pH values at which the crystal was grown. Used when\n a point estimate of pH is not appropriate.", "rcsb_description" : [ { "text" : "The range of pH values at which the crystal was grown. Used when\n a point estimate of pH is not appropriate.", "context" : "dictionary" } ] }, "temp" : { "type" : "number", "description" : "The temperature in kelvins at which the crystal was grown.\n If more than one temperature was employed during the\n crystallization process, the final temperature should be noted\n here and the protocol involving multiple temperatures should be\n described in _exptl_crystal_grow.details.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "kelvins", "rcsb_description" : [ { "text" : "The temperature in kelvins at which the crystal was grown.\n If more than one temperature was employed during the\n crystallization process, the final temperature should be noted\n here and the protocol involving multiple temperatures should be\n described in _exptl_crystal_grow.details.", "context" : "dictionary" }, { "text" : "Temperature", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Crystal Properties", "priority_order" : 15 } ], "rcsb_current_maximum_value" : 349.0, "rcsb_current_minimum_value" : 100.0 }, "temp_details" : { "type" : "string", "description" : "A description of special aspects of temperature control during\n crystal growth.", "rcsb_description" : [ { "text" : "A description of special aspects of temperature control during\n crystal growth.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "crystal_id" ] }, "minItems" : 1, "uniqueItems" : true }, "ihm_entry_collection_mapping" : { "type" : "array", "items" : { "type" : "object", "properties" : { "collection_id" : { "type" : "string", "description" : "Identifier for the entry collection. \n This data item is a pointer to _ihm_entry_collection.id in the \n IHM_ENTRY_COLLECTION category.", "rcsb_search_context" : [ "exact-match", "suggest" ], "rcsb_full_text_priority" : 20, "rcsb_description" : [ { "text" : "Identifier for the entry collection. \n This data item is a pointer to _ihm_entry_collection.id in the \n IHM_ENTRY_COLLECTION category.", "context" : "dictionary" }, { "text" : "IHM Entry Collection ID(s)", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "ID(s) and Keywords", "priority_order" : 30 } ] } }, "additionalProperties" : false, "required" : [ "collection_id" ] }, "minItems" : 1, "uniqueItems" : true }, "ihm_external_reference_info" : { "type" : "array", "items" : { "type" : "object", "properties" : { "associated_url" : { "type" : "string", "description" : "The Uniform Resource Locator (URL) corresponding to the external reference (DOI). \n This URL should link to the corresponding downloadable file or archive and is provided \n to enable automated software to download the referenced file or archive.", "rcsb_description" : [ { "text" : "The Uniform Resource Locator (URL) corresponding to the external reference (DOI). \n This URL should link to the corresponding downloadable file or archive and is provided \n to enable automated software to download the referenced file or archive.", "context" : "dictionary" } ] }, "reference" : { "type" : "string", "examples" : [ "10.5281/zenodo.46266" ], "description" : "The external reference or the Digital Object Identifier (DOI).\n This field is not relevant for local files.", "rcsb_description" : [ { "text" : "The external reference or the Digital Object Identifier (DOI).\n This field is not relevant for local files.", "context" : "dictionary" } ] }, "reference_provider" : { "type" : "string", "examples" : [ "Zenodo", "Figshare", "Crossref" ], "description" : "The name of the reference provider.", "rcsb_description" : [ { "text" : "The name of the reference provider.", "context" : "dictionary" } ] } }, "additionalProperties" : false }, "minItems" : 1, "uniqueItems" : true }, "ma_data" : { "type" : "array", "items" : { "type" : "object", "properties" : { "content_type" : { "type" : "string", "enum" : [ "coevolution MSA", "input structure", "model coordinates", "other", "polymeric template library", "reference database", "spatial restraints", "target", "target-template alignment", "template structure" ], "description" : "The type of data held in the dataset.", "rcsb_enum_annotated" : [ { "value" : "coevolution MSA", "detail" : "coevolution MSA" }, { "value" : "input structure", "detail" : "input structure used in deep learning methods" }, { "value" : "model coordinates", "detail" : "model coordinates" }, { "value" : "other", "detail" : "other" }, { "value" : "polymeric template library", "detail" : "polymeric template library" }, { "value" : "reference database", "detail" : "reference database used" }, { "value" : "spatial restraints", "detail" : "spatial restraints" }, { "value" : "target", "detail" : "target" }, { "value" : "target-template alignment", "detail" : "target-template alignment" }, { "value" : "template structure", "detail" : "template structure" } ], "rcsb_description" : [ { "text" : "The type of data held in the dataset.", "context" : "dictionary" } ] }, "content_type_other_details" : { "type" : "string", "description" : "Details for other content types.", "rcsb_description" : [ { "text" : "Details for other content types.", "context" : "dictionary" } ] }, "id" : { "type" : "integer", "description" : "A unique identifier for the data.", "rcsb_description" : [ { "text" : "A unique identifier for the data.", "context" : "dictionary" } ] }, "name" : { "type" : "string", "examples" : [ "NMR NOE Distances", "Target Template Alignment", "Coevolution Data" ], "description" : "An author-given name for the content held in the dataset.", "rcsb_description" : [ { "text" : "An author-given name for the content held in the dataset.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "id" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_SG_project" : { "type" : "array", "items" : { "type" : "object", "properties" : { "full_name_of_center" : { "type" : "string", "enum" : [ "Accelerated Technologies Center for Gene to 3D Structure", "Assembly, Dynamics and Evolution of Cell-Cell and Cell-Matrix Adhesions", "Atoms-to-Animals: The Immune Function Network", "Bacterial targets at IGS-CNRS, France", "Berkeley Structural Genomics Center", "Center for Eukaryotic Structural Genomics", "Center for High-Throughput Structural Biology", "Center for Membrane Proteins of Infectious Diseases", "Center for Structural Biology of Infectious Diseases", "Center for Structural Genomics of Infectious Diseases", "Center for Structures of Membrane Proteins", "Center for the X-ray Structure Determination of Human Transporters", "Chaperone-Enabled Studies of Epigenetic Regulation Enzymes", "Enzyme Discovery for Natural Product Biosynthesis", "GPCR Network", "Integrated Center for Structure and Function Innovation", "Israel Structural Proteomics Center", "Joint Center for Structural Genomics", "Marseilles Structural Genomics Program @ AFMB", "Medical Structural Genomics of Pathogenic Protozoa", "Membrane Protein Structural Biology Consortium", "Membrane Protein Structures by Solution NMR", "Midwest Center for Macromolecular Research", "Midwest Center for Structural Genomics", "Mitochondrial Protein Partnership", "Montreal-Kingston Bacterial Structural Genomics Initiative", "Mycobacterium Tuberculosis Structural Proteomics Project", "New York Consortium on Membrane Protein Structure", "New York SGX Research Center for Structural Genomics", "New York Structural GenomiX Research Consortium", "New York Structural Genomics Research Consortium", "Northeast Structural Genomics Consortium", "Nucleocytoplasmic Transport: a Target for Cellular Control", "Ontario Centre for Structural Proteomics", "Oxford Protein Production Facility", "Paris-Sud Yeast Structural Genomics", "Partnership for Nuclear Receptor Signaling Code Biology", "Partnership for Stem Cell Biology", "Partnership for T-Cell Biology", "Program for the Characterization of Secreted Effector Proteins", "Protein Structure Factory", "RIKEN Structural Genomics/Proteomics Initiative", "Scottish Structural Proteomics Facility", "Seattle Structural Genomics Center for Infectious Disease", "South Africa Structural Targets Annotation Database", "Southeast Collaboratory for Structural Genomics", "Structural Genomics Consortium", "Structural Genomics Consortium for Research on Gene Expression", "Structural Genomics of Pathogenic Protozoa Consortium", "Structural Proteomics in Europe", "Structural Proteomics in Europe 2", "Structure 2 Function Project", "Structure, Dynamics and Activation Mechanisms of Chemokine Receptors", "Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes", "Structure-Function Studies of Tight Junction Membrane Proteins", "Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors", "TB Structural Genomics Consortium", "Transcontinental EM Initiative for Membrane Protein Structure", "Transmembrane Protein Center" ], "examples" : [ "Midwest Center for Structural Genomics" ], "description" : "The value identifies the full name of center.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "Accelerated Technologies Center for Gene to 3D Structure", "detail" : "ATCG3D" }, { "value" : "Assembly, Dynamics and Evolution of Cell-Cell and Cell-Matrix Adhesions", "detail" : "CELLMAT" }, { "value" : "Atoms-to-Animals: The Immune Function Network", "detail" : "IFN" }, { "value" : "Bacterial targets at IGS-CNRS, France", "detail" : "BIGS" }, { "value" : "Berkeley Structural Genomics Center", "detail" : "BSGC" }, { "value" : "Center for Eukaryotic Structural Genomics", "detail" : "CESG" }, { "value" : "Center for High-Throughput Structural Biology", "detail" : "CHTSB" }, { "value" : "Center for Membrane Proteins of Infectious Diseases", "detail" : "MPID" }, { "value" : "Center for Structural Biology of Infectious Diseases", "detail" : "CSBID" }, { "value" : "Center for Structural Genomics of Infectious Diseases", "detail" : "CSGID" }, { "value" : "Center for Structures of Membrane Proteins", "detail" : "CSMP" }, { "value" : "Center for the X-ray Structure Determination of Human Transporters", "detail" : "TransportPDB" }, { "value" : "Chaperone-Enabled Studies of Epigenetic Regulation Enzymes", "detail" : "CEBS" }, { "value" : "Enzyme Discovery for Natural Product Biosynthesis", "detail" : "NatPro" }, { "value" : "GPCR Network", "detail" : "GPCR" }, { "value" : "Integrated Center for Structure and Function Innovation", "detail" : "ISFI" }, { "value" : "Israel Structural Proteomics Center", "detail" : "ISPC" }, { "value" : "Joint Center for Structural Genomics", "detail" : "JCSG" }, { "value" : "Marseilles Structural Genomics Program @ AFMB", "detail" : "MSGP" }, { "value" : "Medical Structural Genomics of Pathogenic Protozoa", "detail" : "MSGPP" }, { "value" : "Membrane Protein Structural Biology Consortium", "detail" : "MPSBC" }, { "value" : "Membrane Protein Structures by Solution NMR", "detail" : "MPSbyNMR" }, { "value" : "Midwest Center for Macromolecular Research", "detail" : "MCMR" }, { "value" : "Midwest Center for Structural Genomics", "detail" : "MCSG" }, { "value" : "Mitochondrial Protein Partnership", "detail" : "MPP" }, { "value" : "Montreal-Kingston Bacterial Structural Genomics Initiative", "detail" : "BSGI" }, { "value" : "Mycobacterium Tuberculosis Structural Proteomics Project", "detail" : "XMTB" }, { "value" : "New York Consortium on Membrane Protein Structure", "detail" : "NYCOMPS" }, { "value" : "New York SGX Research Center for Structural Genomics", "detail" : "NYSGXRC" }, { "value" : "New York Structural GenomiX Research Consortium", "detail" : "NYSGXRC" }, { "value" : "New York Structural Genomics Research Consortium", "detail" : "NYSGRC" }, { "value" : "Northeast Structural Genomics Consortium", "detail" : "NESG" }, { "value" : "Nucleocytoplasmic Transport: a Target for Cellular Control", "detail" : "NPCXstals" }, { "value" : "Ontario Centre for Structural Proteomics", "detail" : "OCSP" }, { "value" : "Oxford Protein Production Facility", "detail" : "OPPF" }, { "value" : "Paris-Sud Yeast Structural Genomics", "detail" : "YSG" }, { "value" : "Partnership for Nuclear Receptor Signaling Code Biology", "detail" : "NHRs" }, { "value" : "Partnership for Stem Cell Biology", "detail" : "STEMCELL" }, { "value" : "Partnership for T-Cell Biology", "detail" : "TCELL" }, { "value" : "Program for the Characterization of Secreted Effector Proteins", "detail" : "PCSEP" }, { "value" : "Protein Structure Factory", "detail" : "PSF" }, { "value" : "RIKEN Structural Genomics/Proteomics Initiative", "detail" : "RSGI" }, { "value" : "Scottish Structural Proteomics Facility", "detail" : "SSPF" }, { "value" : "Seattle Structural Genomics Center for Infectious Disease", "detail" : "SSGCID" }, { "value" : "South Africa Structural Targets Annotation Database", "detail" : "SASTAD" }, { "value" : "Southeast Collaboratory for Structural Genomics", "detail" : "SECSG" }, { "value" : "Structural Genomics Consortium", "detail" : "SGC" }, { "value" : "Structural Genomics Consortium for Research on Gene Expression", "detail" : "SGCGES" }, { "value" : "Structural Genomics of Pathogenic Protozoa Consortium", "detail" : "SGPP" }, { "value" : "Structural Proteomics in Europe", "detail" : "SPINE" }, { "value" : "Structural Proteomics in Europe 2", "detail" : "SPINE-2" }, { "value" : "Structure 2 Function Project", "detail" : "S2F" }, { "value" : "Structure, Dynamics and Activation Mechanisms of Chemokine Receptors", "detail" : "CHSAM" }, { "value" : "Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes", "detail" : "UC4CDI" }, { "value" : "Structure-Function Studies of Tight Junction Membrane Proteins", "detail" : "TJMP" }, { "value" : "Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors", "detail" : "MTBI" }, { "value" : "TB Structural Genomics Consortium", "detail" : "TBSGC" }, { "value" : "Transcontinental EM Initiative for Membrane Protein Structure", "detail" : "TEMIMPS" }, { "value" : "Transmembrane Protein Center", "detail" : "TMPC" } ], "rcsb_description" : [ { "text" : "The value identifies the full name of center.", "context" : "dictionary" }, { "text" : "The full name of Structural Genomics center", "context" : "deposition" }, { "text" : "Structural Genomics Project Center Name", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Structure Details", "priority_order" : 45 } ] }, "id" : { "type" : "integer", "enum" : [ 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 ], "description" : "A unique integer identifier for this center", "rcsb_description" : [ { "text" : "A unique integer identifier for this center", "context" : "dictionary" } ] }, "initial_of_center" : { "type" : "string", "enum" : [ "ATCG3D", "BIGS", "BSGC", "BSGI", "CEBS", "CELLMAT", "CESG", "CHSAM", "CHTSB", "CSBID", "CSGID", "CSMP", "GPCR", "IFN", "ISFI", "ISPC", "JCSG", "MCMR", "MCSG", "MPID", "MPP", "MPSBC", "MPSbyNMR", "MSGP", "MSGPP", "MTBI", "NESG", "NHRs", "NPCXstals", "NYCOMPS", "NYSGRC", "NYSGXRC", "NatPro", "OCSP", "OPPF", "PCSEP", "PSF", "RSGI", "S2F", "SASTAD", "SECSG", "SGC", "SGCGES", "SGPP", "SPINE", "SPINE-2", "SSGCID", "SSPF", "STEMCELL", "TBSGC", "TCELL", "TEMIMPS", "TJMP", "TMPC", "TransportPDB", "UC4CDI", "XMTB", "YSG" ], "examples" : [ "JCSG" ], "description" : "The value identifies the full name of center.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "ATCG3D", "detail" : "Accelerated Technologies Center for Gene to 3D Structure" }, { "value" : "BIGS", "detail" : "Bacterial targets at IGS-CNRS, France" }, { "value" : "BSGC", "detail" : "Berkeley Structural Genomics Center" }, { "value" : "BSGI", "detail" : "Montreal-Kingston Bacterial Structural Genomics Initiative" }, { "value" : "CEBS", "detail" : "Chaperone-Enabled Studies of Epigenetic Regulation Enzymes" }, { "value" : "CELLMAT", "detail" : "Assembly, Dynamics and Evolution of Cell-Cell and Cell-Matrix Adhesions" }, { "value" : "CESG", "detail" : "Center for Eukaryotic Structural Genomics" }, { "value" : "CHSAM", "detail" : "Structure, Dynamics and Activation Mechanisms of Chemokine Receptors" }, { "value" : "CHTSB", "detail" : "Center for High-Throughput Structural Biology" }, { "value" : "CSBID", "detail" : "Center for Structural Biology of Infectious Diseases" }, { "value" : "CSGID", "detail" : "Center for Structural Genomics of Infectious Diseases" }, { "value" : "CSMP", "detail" : "Center for Structures of Membrane Proteins" }, { "value" : "GPCR", "detail" : "GPCR Network" }, { "value" : "IFN", "detail" : "Atoms-to-Animals: The Immune Function Network" }, { "value" : "ISFI", "detail" : "Integrated Center for Structure and Function Innovation" }, { "value" : "ISPC", "detail" : "Israel Structural Proteomics Center" }, { "value" : "JCSG", "detail" : "Joint Center for Structural Genomics" }, { "value" : "MCMR", "detail" : "Midwest Center for Macromolecular Research" }, { "value" : "MCSG", "detail" : "Midwest Center for Structural Genomics" }, { "value" : "MPID", "detail" : "Center for Membrane Proteins of Infectious Diseases" }, { "value" : "MPP", "detail" : "Mitochondrial Protein Partnership" }, { "value" : "MPSBC", "detail" : "Membrane Protein Structural Biology Consortium" }, { "value" : "MPSbyNMR", "detail" : "Membrane Protein Structures by Solution NMR" }, { "value" : "MSGP", "detail" : "Marseilles Structural Genomics Program @ AFMB" }, { "value" : "MSGPP", "detail" : "Medical Structural Genomics of Pathogenic Protozoa" }, { "value" : "MTBI", "detail" : "Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors" }, { "value" : "NESG", "detail" : "Northeast Structural Genomics Consortium" }, { "value" : "NHRs", "detail" : "Partnership for Nuclear Receptor Signaling Code Biology" }, { "value" : "NPCXstals", "detail" : "Nucleocytoplasmic Transport: a Target for Cellular Control" }, { "value" : "NYCOMPS", "detail" : "New York Consortium on Membrane Protein Structure" }, { "value" : "NYSGRC", "detail" : "New York Structural Genomics Research Consortium" }, { "value" : "NYSGXRC", "detail" : "New York Structural GenomiX Research Consortium" }, { "value" : "NatPro", "detail" : "Enzyme Discovery for Natural Product Biosynthesis" }, { "value" : "OCSP", "detail" : "Ontario Centre for Structural Proteomics" }, { "value" : "OPPF", "detail" : "Oxford Protein Production Facility" }, { "value" : "PCSEP", "detail" : "Program for the Characterization of Secreted Effector Proteins" }, { "value" : "PSF", "detail" : "Protein Structure Factory" }, { "value" : "RSGI", "detail" : "RIKEN Structural Genomics/Proteomics Initiative" }, { "value" : "S2F", "detail" : "Structure 2 Function Project" }, { "value" : "SASTAD", "detail" : "South Africa Structural Targets Annotation Database" }, { "value" : "SECSG", "detail" : "Southeast Collaboratory for Structural Genomics" }, { "value" : "SGC", "detail" : "Structural Genomics Consortium" }, { "value" : "SGCGES", "detail" : "Structural Genomics Consortium for Research on Gene Expression" }, { "value" : "SGPP", "detail" : "Structural Genomics of Pathogenic Protozoa Consortium" }, { "value" : "SPINE", "detail" : "Structural Proteomics in Europe" }, { "value" : "SPINE-2", "detail" : "Structural Proteomics in Europe 2" }, { "value" : "SSGCID", "detail" : "Seattle Structural Genomics Center for Infectious Disease" }, { "value" : "SSPF", "detail" : "Scottish Structural Proteomics Facility" }, { "value" : "STEMCELL", "detail" : "Partnership for Stem Cell Biology" }, { "value" : "TBSGC", "detail" : "TB Structural Genomics Consortium" }, { "value" : "TCELL", "detail" : "Partnership for T-Cell Biology" }, { "value" : "TEMIMPS", "detail" : "Transcontinental EM Initiative for Membrane Protein Structure" }, { "value" : "TJMP", "detail" : "Structure-Function Studies of Tight Junction Membrane Proteins" }, { "value" : "TMPC", "detail" : "Transmembrane Protein Center" }, { "value" : "TransportPDB", "detail" : "Center for the X-ray Structure Determination of Human Transporters" }, { "value" : "UC4CDI", "detail" : "Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes" }, { "value" : "XMTB", "detail" : "Mycobacterium Tuberculosis Structural Proteomics Project" }, { "value" : "YSG", "detail" : "Paris-Sud Yeast Structural Genomics" } ], "rcsb_description" : [ { "text" : "The value identifies the full name of center.", "context" : "dictionary" }, { "text" : "Structural Genomics Project Center Initials", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Structure Details", "priority_order" : 40 } ] }, "project_name" : { "type" : "string", "enum" : [ "Enzyme Function Initiative", "NIAID, National Institute of Allergy and Infectious Diseases", "NPPSFA, National Project on Protein Structural and Functional Analyses", "PSI, Protein Structure Initiative", "PSI:Biology" ], "examples" : [ "PSI, Protein Structure Initiative" ], "description" : "The value identifies the Structural Genomics project.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The value identifies the Structural Genomics project.", "context" : "dictionary" }, { "text" : "This specific Structural Genomics project name", "context" : "deposition" }, { "text" : "Structural Genomics Project Name", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Structure Details", "priority_order" : 35 } ] } }, "additionalProperties" : false, "required" : [ "id" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_audit_revision_category" : { "type" : "array", "items" : { "type" : "object", "properties" : { "category" : { "type" : "string", "examples" : [ "audit_author", "citation" ], "description" : "The category updated in the pdbx_audit_revision_category record.", "rcsb_description" : [ { "text" : "The category updated in the pdbx_audit_revision_category record.", "context" : "dictionary" } ] }, "data_content_type" : { "type" : "string", "enum" : [ "Additional map", "Chemical component", "EM metadata", "FSC", "Half map", "Image", "Mask", "NMR restraints", "NMR shifts", "Primary map", "Structure factors", "Structure model" ], "examples" : [ "Structure model" ], "description" : "The type of file that the pdbx_audit_revision_history record refers to.", "rcsb_enum_annotated" : [ { "value" : "Additional map", "detail" : "EM map" }, { "value" : "Chemical component", "detail" : "Chemical component definition file" }, { "value" : "EM metadata", "detail" : "Data describing EM experimental data" }, { "value" : "FSC", "detail" : "EM Fourier Shell Correlation data" }, { "value" : "Half map", "detail" : "EM half map" }, { "value" : "Image", "detail" : "Image that represents primary map" }, { "value" : "Mask", "detail" : "EM mask map" }, { "value" : "NMR restraints", "detail" : "NMR restraints file" }, { "value" : "NMR shifts", "detail" : "NMR chemical shifts file" }, { "value" : "Primary map", "detail" : "EM primary map" }, { "value" : "Structure factors", "detail" : "Diffraction structure factors file" }, { "value" : "Structure model", "detail" : "Coordinate model file" } ], "rcsb_description" : [ { "text" : "The type of file that the pdbx_audit_revision_history record refers to.", "context" : "dictionary" } ] }, "ordinal" : { "type" : "integer", "description" : "A unique identifier for the pdbx_audit_revision_category record.", "rcsb_description" : [ { "text" : "A unique identifier for the pdbx_audit_revision_category record.", "context" : "dictionary" } ] }, "revision_ordinal" : { "type" : "integer", "description" : "A pointer to _pdbx_audit_revision_history.ordinal", "rcsb_description" : [ { "text" : "A pointer to _pdbx_audit_revision_history.ordinal", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "data_content_type", "ordinal", "revision_ordinal" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_audit_revision_details" : { "type" : "array", "items" : { "type" : "object", "properties" : { "data_content_type" : { "type" : "string", "enum" : [ "Additional map", "Chemical component", "EM metadata", "FSC", "Half map", "Image", "Mask", "NMR restraints", "NMR shifts", "Primary map", "Structure factors", "Structure model" ], "examples" : [ "Structure model" ], "description" : "The type of file that the pdbx_audit_revision_history record refers to.", "rcsb_enum_annotated" : [ { "value" : "Additional map", "detail" : "EM map" }, { "value" : "Chemical component", "detail" : "Chemical component definition file" }, { "value" : "EM metadata", "detail" : "Data describing EM experimental data" }, { "value" : "FSC", "detail" : "EM Fourier Shell Correlation data" }, { "value" : "Half map", "detail" : "EM half map" }, { "value" : "Image", "detail" : "Image that represents primary map" }, { "value" : "Mask", "detail" : "EM mask map" }, { "value" : "NMR restraints", "detail" : "NMR restraints file" }, { "value" : "NMR shifts", "detail" : "NMR chemical shifts file" }, { "value" : "Primary map", "detail" : "EM primary map" }, { "value" : "Structure factors", "detail" : "Diffraction structure factors file" }, { "value" : "Structure model", "detail" : "Coordinate model file" } ], "rcsb_description" : [ { "text" : "The type of file that the pdbx_audit_revision_history record refers to.", "context" : "dictionary" } ] }, "description" : { "type" : "string", "description" : "Additional details describing the revision.", "rcsb_description" : [ { "text" : "Additional details describing the revision.", "context" : "dictionary" } ] }, "details" : { "type" : "string", "description" : "Further details describing the revision.", "rcsb_description" : [ { "text" : "Further details describing the revision.", "context" : "dictionary" } ] }, "ordinal" : { "type" : "integer", "description" : "A unique identifier for the pdbx_audit_revision_details record.", "rcsb_description" : [ { "text" : "A unique identifier for the pdbx_audit_revision_details record.", "context" : "dictionary" } ] }, "provider" : { "type" : "string", "enum" : [ "author", "repository" ], "examples" : [ "repository" ], "description" : "The provider of the revision.", "rcsb_description" : [ { "text" : "The provider of the revision.", "context" : "dictionary" } ] }, "revision_ordinal" : { "type" : "integer", "description" : "A pointer to _pdbx_audit_revision_history.ordinal", "rcsb_description" : [ { "text" : "A pointer to _pdbx_audit_revision_history.ordinal", "context" : "dictionary" } ] }, "type" : { "type" : "string", "enum" : [ "Coordinate replacement", "Data added", "Data removed", "Data updated", "Initial release", "Obsolete", "Remediation" ], "examples" : [ "Initial release" ], "description" : "A type classification of the revision", "rcsb_description" : [ { "text" : "A type classification of the revision", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "data_content_type", "ordinal", "revision_ordinal" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_audit_revision_group" : { "type" : "array", "items" : { "type" : "object", "properties" : { "data_content_type" : { "type" : "string", "enum" : [ "Additional map", "Chemical component", "EM metadata", "FSC", "Half map", "Image", "Mask", "NMR restraints", "NMR shifts", "Primary map", "Structure factors", "Structure model" ], "examples" : [ "Structure model" ], "description" : "The type of file that the pdbx_audit_revision_history record refers to.", "rcsb_enum_annotated" : [ { "value" : "Additional map", "detail" : "EM map" }, { "value" : "Chemical component", "detail" : "Chemical component definition file" }, { "value" : "EM metadata", "detail" : "Data describing EM experimental data" }, { "value" : "FSC", "detail" : "EM Fourier Shell Correlation data" }, { "value" : "Half map", "detail" : "EM half map" }, { "value" : "Image", "detail" : "Image that represents primary map" }, { "value" : "Mask", "detail" : "EM mask map" }, { "value" : "NMR restraints", "detail" : "NMR restraints file" }, { "value" : "NMR shifts", "detail" : "NMR chemical shifts file" }, { "value" : "Primary map", "detail" : "EM primary map" }, { "value" : "Structure factors", "detail" : "Diffraction structure factors file" }, { "value" : "Structure model", "detail" : "Coordinate model file" } ], "rcsb_description" : [ { "text" : "The type of file that the pdbx_audit_revision_history record refers to.", "context" : "dictionary" } ] }, "group" : { "type" : "string", "enum" : [ "Advisory", "Atomic model", "Author supporting evidence", "Data collection", "Data processing", "Database references", "Derived calculations", "Experimental data", "Experimental preparation", "Experimental summary", "Non-polymer description", "Other", "Polymer sequence", "Refinement description", "Source and taxonomy", "Structure summary", "Version format compliance" ], "examples" : [ "citation" ], "description" : "The collection of categories updated with this revision.", "rcsb_enum_annotated" : [ { "value" : "Advisory", "detail" : "Categories describing caveats and other validation outliers" }, { "value" : "Atomic model", "detail" : "Categories describing the model coordinates" }, { "value" : "Author supporting evidence", "detail" : "Categories supporting author provided experimental evidence" }, { "value" : "Data collection", "detail" : "Categories describing the data collection experiment and summary statistics" }, { "value" : "Data processing", "detail" : "Categories describing data processing" }, { "value" : "Database references", "detail" : "Categories describing citation and correspondences with related archives" }, { "value" : "Derived calculations", "detail" : "Categories describing secondary structurem linkages, binding sites and quaternary structure" }, { "value" : "Experimental data", "detail" : "Method-specific experimental data" }, { "value" : "Experimental preparation", "detail" : "Categories describing the experimental sample preparation" }, { "value" : "Experimental summary", "detail" : "Categories that describe the title, authorship and molecular description" }, { "value" : "Non-polymer description", "detail" : "Categories describing non-polymer chemical description" }, { "value" : "Other", "detail" : "Unclassified categories (legacy)" }, { "value" : "Polymer sequence", "detail" : "Categories describing the polymer sample sequences" }, { "value" : "Refinement description", "detail" : "Categories pertaining to the refinement of the model" }, { "value" : "Source and taxonomy", "detail" : "Categories describing the sample source" }, { "value" : "Structure summary", "detail" : "Categories that describe the title, authorship and molecular description" }, { "value" : "Version format compliance", "detail" : "Categories to conform to the version of the mmCIF dictionary" } ], "rcsb_description" : [ { "text" : "The collection of categories updated with this revision.", "context" : "dictionary" } ] }, "ordinal" : { "type" : "integer", "description" : "A unique identifier for the pdbx_audit_revision_group record.", "rcsb_description" : [ { "text" : "A unique identifier for the pdbx_audit_revision_group record.", "context" : "dictionary" } ] }, "revision_ordinal" : { "type" : "integer", "description" : "A pointer to _pdbx_audit_revision_history.ordinal", "rcsb_description" : [ { "text" : "A pointer to _pdbx_audit_revision_history.ordinal", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "data_content_type", "ordinal", "revision_ordinal" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_audit_revision_history" : { "type" : "array", "items" : { "type" : "object", "properties" : { "data_content_type" : { "type" : "string", "enum" : [ "Additional map", "Chemical component", "EM metadata", "FSC", "Half map", "Image", "Mask", "NMR restraints", "NMR shifts", "Primary map", "Structure factors", "Structure model" ], "examples" : [ "Structure model" ], "description" : "The type of file that the pdbx_audit_revision_history record refers to.", "rcsb_enum_annotated" : [ { "value" : "Additional map", "detail" : "EM map" }, { "value" : "Chemical component", "detail" : "Chemical component definition file" }, { "value" : "EM metadata", "detail" : "Data describing EM experimental data" }, { "value" : "FSC", "detail" : "EM Fourier Shell Correlation data" }, { "value" : "Half map", "detail" : "EM half map" }, { "value" : "Image", "detail" : "Image that represents primary map" }, { "value" : "Mask", "detail" : "EM mask map" }, { "value" : "NMR restraints", "detail" : "NMR restraints file" }, { "value" : "NMR shifts", "detail" : "NMR chemical shifts file" }, { "value" : "Primary map", "detail" : "EM primary map" }, { "value" : "Structure factors", "detail" : "Diffraction structure factors file" }, { "value" : "Structure model", "detail" : "Coordinate model file" } ], "rcsb_description" : [ { "text" : "The type of file that the pdbx_audit_revision_history record refers to.", "context" : "dictionary" } ] }, "major_revision" : { "type" : "integer", "description" : "The major version number of deposition release.", "rcsb_description" : [ { "text" : "The major version number of deposition release.", "context" : "dictionary" } ] }, "minor_revision" : { "type" : "integer", "description" : "The minor version number of deposition release.", "rcsb_description" : [ { "text" : "The minor version number of deposition release.", "context" : "dictionary" } ] }, "ordinal" : { "type" : "integer", "description" : "A unique identifier for the pdbx_audit_revision_history record.", "rcsb_description" : [ { "text" : "A unique identifier for the pdbx_audit_revision_history record.", "context" : "dictionary" } ] }, "revision_date" : { "type" : "string", "format" : "date", "examples" : [ "2017-03-08" ], "description" : "The release date of the revision", "rcsb_description" : [ { "text" : "The release date of the revision", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "data_content_type", "ordinal" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_audit_revision_item" : { "type" : "array", "items" : { "type" : "object", "properties" : { "data_content_type" : { "type" : "string", "enum" : [ "Additional map", "Chemical component", "EM metadata", "FSC", "Half map", "Image", "Mask", "NMR restraints", "NMR shifts", "Primary map", "Structure factors", "Structure model" ], "examples" : [ "Structure model" ], "description" : "The type of file that the pdbx_audit_revision_history record refers to.", "rcsb_enum_annotated" : [ { "value" : "Additional map", "detail" : "EM map" }, { "value" : "Chemical component", "detail" : "Chemical component definition file" }, { "value" : "EM metadata", "detail" : "Data describing EM experimental data" }, { "value" : "FSC", "detail" : "EM Fourier Shell Correlation data" }, { "value" : "Half map", "detail" : "EM half map" }, { "value" : "Image", "detail" : "Image that represents primary map" }, { "value" : "Mask", "detail" : "EM mask map" }, { "value" : "NMR restraints", "detail" : "NMR restraints file" }, { "value" : "NMR shifts", "detail" : "NMR chemical shifts file" }, { "value" : "Primary map", "detail" : "EM primary map" }, { "value" : "Structure factors", "detail" : "Diffraction structure factors file" }, { "value" : "Structure model", "detail" : "Coordinate model file" } ], "rcsb_description" : [ { "text" : "The type of file that the pdbx_audit_revision_history record refers to.", "context" : "dictionary" } ] }, "item" : { "type" : "string", "examples" : [ "_atom_site.type_symbol" ], "description" : "A high level explanation the author has provided for submitting a revision.", "rcsb_description" : [ { "text" : "A high level explanation the author has provided for submitting a revision.", "context" : "dictionary" } ] }, "ordinal" : { "type" : "integer", "description" : "A unique identifier for the pdbx_audit_revision_item record.", "rcsb_description" : [ { "text" : "A unique identifier for the pdbx_audit_revision_item record.", "context" : "dictionary" } ] }, "revision_ordinal" : { "type" : "integer", "description" : "A pointer to _pdbx_audit_revision_history.ordinal", "rcsb_description" : [ { "text" : "A pointer to _pdbx_audit_revision_history.ordinal", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "data_content_type", "ordinal", "revision_ordinal" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_audit_support" : { "type" : "array", "items" : { "type" : "object", "properties" : { "country" : { "type" : "string", "description" : "The country/region providing the funding support for the entry.\n Funding information is optionally provided for entries after June 2016.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The country/region providing the funding support for the entry.\n Funding information is optionally provided for entries after June 2016.", "context" : "dictionary" }, { "text" : "Funding Country", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Structure Details", "priority_order" : 70 } ] }, "funding_organization" : { "type" : "string", "examples" : [ "National Institutes of Health", "Wellcome Trust", "National Institutes of Health/National Institute of General Medical Sciences" ], "description" : "The name of the organization providing funding support for the\n entry. Funding information is optionally provided for entries\n after June 2016.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The name of the organization providing funding support for the\n entry. Funding information is optionally provided for entries\n after June 2016.", "context" : "dictionary" }, { "text" : "Funding Organization", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Structure Details", "priority_order" : 60 } ] }, "grant_number" : { "type" : "string", "description" : "The grant number associated with this source of support.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The grant number associated with this source of support.", "context" : "dictionary" }, { "text" : "Funding Grant Number", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Structure Details", "priority_order" : 65 } ] }, "ordinal" : { "type" : "integer", "description" : "A unique sequential integer identifier for each source of support for this entry.", "rcsb_description" : [ { "text" : "A unique sequential integer identifier for each source of support for this entry.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "ordinal" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_database_PDB_obs_spr" : { "type" : "array", "items" : { "type" : "object", "properties" : { "date" : { "type" : "string", "format" : "date-time", "examples" : [ "1997-03-30" ], "description" : "The date of replacement.", "rcsb_description" : [ { "text" : "The date of replacement.", "context" : "dictionary" } ] }, "details" : { "type" : "string", "description" : "Details related to the replaced or replacing entry.", "rcsb_description" : [ { "text" : "Details related to the replaced or replacing entry.", "context" : "dictionary" } ] }, "id" : { "type" : "string", "enum" : [ "OBSLTE", "SPRSDE" ], "examples" : [ "OBSLTE" ], "description" : "Identifier for the type of obsolete entry to be added to this entry.", "rcsb_description" : [ { "text" : "Identifier for the type of obsolete entry to be added to this entry.", "context" : "dictionary" } ] }, "pdb_id" : { "type" : "string", "examples" : [ "2ABC" ], "description" : "The new PDB identifier for the replaced entry.", "rcsb_description" : [ { "text" : "The new PDB identifier for the replaced entry.", "context" : "dictionary" } ] }, "replace_pdb_id" : { "type" : "string", "examples" : [ "3ABC" ], "description" : "The PDB identifier for the replaced (OLD) entry/entries.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The PDB identifier for the replaced (OLD) entry/entries.", "context" : "dictionary" }, { "text" : "The PDB identifier(s) for the entry/entries to be replaced by this on-going deposition", "context" : "deposition" }, { "text" : "Replace Pdb Id (Database Pdb Obs Spr)", "context" : "brief" } ] } }, "additionalProperties" : false, "required" : [ "pdb_id", "replace_pdb_id" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_database_related" : { "type" : "array", "items" : { "type" : "object", "properties" : { "content_type" : { "type" : "string", "enum" : [ "associated EM volume", "associated NMR restraints", "associated SAS data", "associated structure factors", "complete structure", "consensus EM volume", "derivative structure", "ensemble", "focused EM volume", "minimized average structure", "native structure", "other", "other EM volume", "protein target sequence and/or protocol data", "re-refinement", "representative structure", "split", "unspecified" ], "examples" : [ "minimized average structure", "representative structure", "ensemble", "derivative structure", "native structure", "associated EM volume", "other EM volume", "associated NMR restraints", "associated structure factors", "associated SAS data", "protein target sequence and/or protocol data", "split", "re-refinement", "complete structure", "unspecified", "other" ], "description" : "The identifying content type of the related entry.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The identifying content type of the related entry.", "context" : "dictionary" }, { "text" : "Content Types Available in a Related Resource", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Structure Details", "priority_order" : 80 } ] }, "db_id" : { "type" : "string", "examples" : [ "1ABC", "BDL001" ], "description" : "The identifying code in the related database.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The identifying code in the related database.", "context" : "dictionary" }, { "text" : "The identifying code in the related database", "context" : "deposition" }, { "text" : "Db Id (Database Related)", "context" : "brief" } ] }, "db_name" : { "type" : "string", "enum" : [ "BIOISIS", "BMCD", "BMRB", "EMDB", "NDB", "PDB", "PDB-Dev", "SASBDB", "TargetDB", "TargetTrack" ], "examples" : [ "PDB - Protein Databank\nNDB - Nucleic Acid Database\nBMRB - BioMagResBank\nEMDB - Electron Microscopy Database\nBMCD - Biological Macromolecule Crystallization Database\nTargetTrack - Target Registration and Protocol Database\nSASBDB - Small Angle Scattering Biological Data Bank" ], "description" : "The name of the database containing the related entry.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The name of the database containing the related entry.", "context" : "dictionary" }, { "text" : "The name of the database containing the related entry", "context" : "deposition" }, { "text" : "Related Resource Name Containing Additional Content", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Structure Details", "priority_order" : 85 } ] }, "details" : { "type" : "string", "examples" : [ "1ABC contains the same protein complexed with Netropsin." ], "description" : "A description of the related entry.", "rcsb_description" : [ { "text" : "A description of the related entry.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "content_type", "db_id", "db_name" ] }, "minItems" : 1, "uniqueItems" : true, "rcsb_nested_indexing" : true }, "pdbx_database_status" : { "type" : "object", "properties" : { "SG_entry" : { "type" : "string", "enum" : [ "N", "Y" ], "examples" : [ "Y" ], "description" : "This code indicates whether the entry belongs to\n Structural Genomics Project.", "rcsb_enum_annotated" : [ { "value" : "N", "detail" : "No" }, { "value" : "Y", "detail" : "Yes" } ], "rcsb_description" : [ { "text" : "This code indicates whether the entry belongs to\n Structural Genomics Project.", "context" : "dictionary" } ] }, "deposit_site" : { "type" : "string", "enum" : [ "BMRB", "BNL", "NDB", "PDBC", "PDBE", "PDBJ", "RCSB" ], "examples" : [ "NDB", "RCSB", "PDBE", "PDBJ", "BMRB", "BNL", "PDBC" ], "description" : "The site where the file was deposited.", "rcsb_description" : [ { "text" : "The site where the file was deposited.", "context" : "dictionary" } ] }, "methods_development_category" : { "type" : "string", "enum" : [ "CAPRI", "CASD-NMR", "CASP", "D3R", "FoldIt", "GPCR Dock", "RNA-Puzzles" ], "examples" : [ "CASP", "CASD-NMR" ], "description" : "The methods development category in which this\n entry has been placed.", "rcsb_description" : [ { "text" : "The methods development category in which this\n entry has been placed.", "context" : "dictionary" }, { "text" : "For more information about CASP, depositors should consult http://predictioncenter.org. For more information about CASD-NMR, depositors should consult http://www.wenmr.eu/wenmr/casd-nmr. For more information about Foldit, depositors should consult http://fold.it/portal/", "context" : "deposition" } ] }, "pdb_format_compatible" : { "type" : "string", "enum" : [ "N", "Y" ], "examples" : [ "Y" ], "description" : "A flag indicating that the entry is compatible with the PDB format.\n\n A value of 'N' indicates that the no PDB format data file is\n corresponding to this entry is available in the PDB archive.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "N", "detail" : "No" }, { "value" : "Y", "detail" : "Yes" } ], "rcsb_description" : [ { "text" : "A flag indicating that the entry is compatible with the PDB format.\n\n A value of 'N' indicates that the no PDB format data file is\n corresponding to this entry is available in the PDB archive.", "context" : "dictionary" }, { "text" : "Compatible with PDB Format", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Structure Details", "priority_order" : 55 } ] }, "process_site" : { "type" : "string", "enum" : [ "BNL", "NDB", "PDBC", "PDBE", "PDBJ", "RCSB" ], "examples" : [ "NDB", "RCSB", "PDBE", "PDBJ", "BNL", "PDBC" ], "description" : "The site where the file was deposited.", "rcsb_description" : [ { "text" : "The site where the file was deposited.", "context" : "dictionary" } ] }, "recvd_initial_deposition_date" : { "type" : "string", "format" : "date", "examples" : [ "1983-02-21" ], "description" : "The date of initial deposition. (The first message for\n deposition has been received.)", "rcsb_description" : [ { "text" : "The date of initial deposition. (The first message for\n deposition has been received.)", "context" : "dictionary" } ] }, "status_code" : { "type" : "string", "enum" : [ "AUCO", "AUTH", "BIB", "DEL", "HOLD", "HPUB", "OBS", "POLC", "PROC", "REFI", "REL", "REPL", "REV", "RMVD", "TRSF", "UPD", "WAIT", "WDRN" ], "examples" : [ "REL", "HPUB" ], "description" : "Code for status of file.", "rcsb_enum_annotated" : [ { "value" : "AUCO", "detail" : "Author corrections pending review" }, { "value" : "AUTH", "detail" : "Processed, waiting for author review and approval" }, { "value" : "BIB", "detail" : "Deprecated code" }, { "value" : "DEL", "detail" : "Deprecated code" }, { "value" : "HOLD", "detail" : "On hold until yyyy-mm-dd" }, { "value" : "HPUB", "detail" : "On hold until publication" }, { "value" : "OBS", "detail" : "Entry has been obsoleted" }, { "value" : "POLC", "detail" : "Processing, waiting for a policy decision" }, { "value" : "PROC", "detail" : "To be processed" }, { "value" : "REFI", "detail" : "Re-refined entry" }, { "value" : "REL", "detail" : "Released" }, { "value" : "REPL", "detail" : "Author sent new coordinates to be incorporated" }, { "value" : "REV", "detail" : "Deprecated code" }, { "value" : "RMVD", "detail" : "Entry has been removed" }, { "value" : "TRSF", "detail" : "Entry transferred to another data repository" }, { "value" : "UPD", "detail" : "Deprecated code" }, { "value" : "WAIT", "detail" : "Processing started, waiting for author input to continue processing" }, { "value" : "WDRN", "detail" : "Deposition has been withdrawn" } ], "rcsb_description" : [ { "text" : "Code for status of file.", "context" : "dictionary" } ] }, "status_code_cs" : { "type" : "string", "enum" : [ "AUCO", "AUTH", "HOLD", "HPUB", "OBS", "POLC", "PROC", "REL", "REPL", "RMVD", "WAIT", "WDRN" ], "examples" : [ "PROC = Processing in progress\n WAIT = Awaiting author approval\n REL = Release\n HOLD = On hold until yyyy-mm-dd\n HPUB = On hold until publication\n OBS = Entry has been obsoleted\n WDRN = Entry has been withdrawn by depositor" ], "description" : "Code for status of chemical shift data file.", "rcsb_enum_annotated" : [ { "value" : "AUCO", "detail" : "Author corrections pending review" }, { "value" : "AUTH", "detail" : "Processed, waiting for author review and approval" }, { "value" : "HOLD", "detail" : "On hold until yyyy-mm-dd" }, { "value" : "HPUB", "detail" : "On hold until publication" }, { "value" : "OBS", "detail" : "Entry has been obsoleted" }, { "value" : "POLC", "detail" : "Waiting for a policy decision" }, { "value" : "PROC", "detail" : "Processing in progress" }, { "value" : "REL", "detail" : "Released" }, { "value" : "REPL", "detail" : "Author sent new coordinates" }, { "value" : "RMVD", "detail" : "Entry has been removed" }, { "value" : "WAIT", "detail" : "Processing started, waiting for author input to continue processing" }, { "value" : "WDRN", "detail" : "Entry has been withdrawn" } ], "rcsb_description" : [ { "text" : "Code for status of chemical shift data file.", "context" : "dictionary" } ] }, "status_code_mr" : { "type" : "string", "enum" : [ "AUCO", "AUTH", "HOLD", "HPUB", "OBS", "POLC", "PROC", "REL", "REPL", "RMVD", "WAIT", "WDRN" ], "examples" : [ "PROC = To be processed\n REL = Release\n HOLD = On hold until yyyy-mm-dd\n HPUB = On hold until publication\n OBS = Entry has been obsoleted\n WDRN = Entry has been withdrawn by depositor\n WAIT = Awaiting author approval" ], "description" : "Code for status of NMR constraints file.", "rcsb_enum_annotated" : [ { "value" : "AUCO", "detail" : "Author corrections pending review" }, { "value" : "AUTH", "detail" : "Processed, waiting for author review and approval" }, { "value" : "HOLD", "detail" : "On hold until yyyy-mm-dd" }, { "value" : "HPUB", "detail" : "On hold until publication" }, { "value" : "OBS", "detail" : "Entry has been obsoleted" }, { "value" : "POLC", "detail" : "Processing, waiting for a policy decision" }, { "value" : "PROC", "detail" : "To be processed" }, { "value" : "REL", "detail" : "Released" }, { "value" : "REPL", "detail" : "Author sent new data to be incorporated" }, { "value" : "RMVD", "detail" : "Entry has been removed" }, { "value" : "WAIT", "detail" : "Processing started, waiting for author input to continue processing" }, { "value" : "WDRN", "detail" : "Deposition has been withdrawn" } ], "rcsb_description" : [ { "text" : "Code for status of NMR constraints file.", "context" : "dictionary" } ] }, "status_code_sf" : { "type" : "string", "enum" : [ "AUTH", "HOLD", "HPUB", "OBS", "POLC", "PROC", "REL", "REPL", "RMVD", "WAIT", "WDRN" ], "examples" : [ "PROC = To be processed\n REL = Released\n HOLD = On hold until yyyy-mm-dd\n HPUB = On hold until publication\n OBS = Entry has been obsoleted\n WDRN = Entry has been withdrawn by depositor\n WAIT = Awaiting author approval" ], "description" : "Code for status of structure factor file.", "rcsb_enum_annotated" : [ { "value" : "AUTH", "detail" : "Processed, waiting for author review and approval" }, { "value" : "HOLD", "detail" : "On hold until yyyy-mm-dd" }, { "value" : "HPUB", "detail" : "On hold until publication" }, { "value" : "OBS", "detail" : "Entry has been obsoleted" }, { "value" : "POLC", "detail" : "Processing, waiting for a policy decision" }, { "value" : "PROC", "detail" : "To be processed" }, { "value" : "REL", "detail" : "Released" }, { "value" : "REPL", "detail" : "Author sent new data to be incorporated" }, { "value" : "RMVD", "detail" : "Entry has been removed" }, { "value" : "WAIT", "detail" : "Processing started, waiting for author input to continue processing" }, { "value" : "WDRN", "detail" : "Deposition has been withdrawn" } ], "rcsb_description" : [ { "text" : "Code for status of structure factor file.", "context" : "dictionary" } ] } }, "additionalProperties" : false }, "pdbx_deposit_group" : { "type" : "array", "items" : { "type" : "object", "properties" : { "group_description" : { "type" : "string", "description" : "A description of the contents of entries in the collection.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "A description of the contents of entries in the collection.", "context" : "dictionary" }, { "text" : "Group Description (Deposit Group)", "context" : "brief" } ] }, "group_id" : { "type" : "string", "examples" : [ "G_1002119", "G_1002043" ], "description" : "A unique identifier for a group of entries deposited as a collection.", "rcsb_search_context" : [ "exact-match", "suggest" ], "rcsb_full_text_priority" : 20, "rcsb_description" : [ { "text" : "A unique identifier for a group of entries deposited as a collection.", "context" : "dictionary" }, { "text" : "PDB Deposit Group ID(s)", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "ID(s) and Keywords", "priority_order" : 20 } ] }, "group_title" : { "type" : "string", "description" : "A title to describe the group of entries deposited in the collection.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "A title to describe the group of entries deposited in the collection.", "context" : "dictionary" }, { "text" : "Group Title (Deposit Group)", "context" : "brief" } ] }, "group_type" : { "type" : "string", "enum" : [ "changed state", "ground state", "undefined" ], "description" : "Text to describe a grouping of entries in multiple collections", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Text to describe a grouping of entries in multiple collections", "context" : "dictionary" }, { "text" : "Group Type (Deposit Group)", "context" : "brief" } ] } }, "additionalProperties" : false, "required" : [ "group_id" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_initial_refinement_model" : { "type" : "array", "items" : { "type" : "object", "properties" : { "accession_code" : { "type" : "string", "description" : "This item identifies an accession code of the resource where the initial model\n is used", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "This item identifies an accession code of the resource where the initial model\n is used", "context" : "dictionary" }, { "text" : "Starting Model Accession", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Methods", "priority_order" : 40 } ] }, "details" : { "type" : "string", "description" : "A description of special aspects of the initial model", "rcsb_description" : [ { "text" : "A description of special aspects of the initial model", "context" : "dictionary" } ] }, "entity_id_list" : { "type" : "array", "items" : { "type" : "string", "description" : "A comma separated list of entities reflecting the initial model used for refinement", "rcsb_description" : [ { "text" : "A comma separated list of entities reflecting the initial model used for refinement", "context" : "dictionary" }, { "text" : "A comma separated list of macromolecule entities in the current entry for which the specified initial refinement model was used.", "context" : "deposition" } ] }, "uniqueItems" : false }, "id" : { "type" : "integer", "description" : "A unique identifier for the starting model record.", "rcsb_description" : [ { "text" : "A unique identifier for the starting model record.", "context" : "dictionary" } ] }, "source_name" : { "type" : "string", "enum" : [ "AlphaFold", "ITasser", "InsightII", "ModelArchive", "Modeller", "Other", "PDB", "PDB-Dev", "PHYRE", "Robetta", "RoseTTAFold", "SwissModel" ], "description" : "This item identifies the resource of initial model used for refinement", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "This item identifies the resource of initial model used for refinement", "context" : "dictionary" }, { "text" : "Starting Model Source", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Methods", "priority_order" : 35 } ] }, "type" : { "type" : "string", "enum" : [ "experimental model", "in silico model", "integrative model", "other" ], "description" : "This item describes the type of the initial model was generated", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "This item describes the type of the initial model was generated", "context" : "dictionary" }, { "text" : "Starting Model Type", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Methods", "priority_order" : 30 } ] } }, "additionalProperties" : false, "required" : [ "id" ] }, "minItems" : 1, "uniqueItems" : true, "rcsb_nested_indexing" : true }, "pdbx_molecule_features" : { "type" : "array", "items" : { "type" : "object", "properties" : { "class" : { "type" : "string", "enum" : [ "Antagonist", "Anthelmintic", "Antibiotic", "Antibiotic, Anthelmintic", "Antibiotic, Antimicrobial", "Antibiotic, Antineoplastic", "Anticancer", "Anticoagulant", "Anticoagulant, Antithrombotic", "Antifungal", "Antigen", "Antiinflammatory", "Antimicrobial", "Antimicrobial, Antiparasitic, Antibiotic", "Antimicrobial, Antiretroviral", "Antimicrobial, Antitumor", "Antineoplastic", "Antiparasitic", "Antiretroviral", "Antithrombotic", "Antitumor", "Antiviral", "CASPASE inhibitor", "Chaperone binding", "Drug delivery", "Enzyme inhibitor", "Glycan component", "Growth factor", "Immunosuppressant", "Inducer", "Inhibitor", "Lantibiotic", "Metabolism", "Metal transport", "Nutrient", "Oxidation-reduction", "Protein binding", "Receptor", "Substrate analog", "Synthetic opioid", "Thrombin inhibitor", "Thrombin inhibitor, Trypsin inhibitor", "Toxin", "Transition state mimetic", "Transport activator", "Trypsin inhibitor", "Unknown", "Water retention" ], "description" : "Broadly defines the function of the molecule.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Broadly defines the function of the molecule.", "context" : "dictionary" }, { "text" : "Class (Molecule Features)", "context" : "brief" } ] }, "details" : { "type" : "string", "description" : "Additional details describing the molecule.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Additional details describing the molecule.", "context" : "dictionary" }, { "text" : "Details (Molecule Features)", "context" : "brief" } ] }, "name" : { "type" : "string", "examples" : [ "thiostrepton" ], "description" : "A name of the molecule.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "A name of the molecule.", "context" : "dictionary" }, { "text" : "Name (Molecule Features)", "context" : "brief" } ] }, "prd_id" : { "type" : "string", "description" : "The value of _pdbx_molecule_features.prd_id is the accession code for this\n reference molecule.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The value of _pdbx_molecule_features.prd_id is the accession code for this\n reference molecule.", "context" : "dictionary" }, { "text" : "Prd Id (Molecule Features)", "context" : "brief" } ] }, "type" : { "type" : "string", "enum" : [ "Amino acid", "Aminoglycoside", "Ansamycin", "Anthracycline", "Anthraquinone", "Chalkophore", "Chalkophore, Polypeptide", "Chromophore", "Cyclic depsipeptide", "Cyclic lipopeptide", "Cyclic peptide", "Glycopeptide", "Heterocyclic", "Imino sugar", "Keto acid", "Lipoglycopeptide", "Lipopeptide", "Macrolide", "Non-polymer", "Nucleoside", "Oligopeptide", "Oligosaccharide", "Peptaibol", "Peptide-like", "Polycyclic", "Polypeptide", "Polysaccharide", "Quinolone", "Siderophore", "Thiolactone", "Thiopeptide", "Unknown" ], "examples" : [ "Peptide-like", "Macrolide" ], "description" : "Defines the structural classification of the molecule.", "rcsb_description" : [ { "text" : "Defines the structural classification of the molecule.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "prd_id" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_nmr_details" : { "type" : "object", "properties" : { "text" : { "type" : "string", "examples" : [ "This structure was determined using standard 2D homonuclear techniques.", "The structure was determined using triple-resonance NMR spectroscopy." ], "description" : "Additional details describing the NMR experiment.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Additional details describing the NMR experiment.", "context" : "dictionary" }, { "text" : "Text (Nmr Details)", "context" : "brief" } ] } }, "additionalProperties" : false }, "pdbx_nmr_ensemble" : { "type" : "object", "properties" : { "average_constraint_violations_per_residue" : { "type" : "integer", "examples" : [ 0.25 ], "description" : "The average number of constraint violations on a per residue basis for\n the ensemble.", "rcsb_description" : [ { "text" : "The average number of constraint violations on a per residue basis for\n the ensemble.", "context" : "dictionary" } ] }, "average_constraints_per_residue" : { "type" : "integer", "examples" : [ 30.2 ], "description" : "The average number of constraints per residue for the ensemble", "rcsb_description" : [ { "text" : "The average number of constraints per residue for the ensemble", "context" : "dictionary" } ] }, "average_distance_constraint_violation" : { "type" : "number", "examples" : [ 0.11 ], "description" : "The average distance restraint violation for the ensemble.", "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "The average distance restraint violation for the ensemble.", "context" : "dictionary" } ] }, "average_torsion_angle_constraint_violation" : { "type" : "number", "examples" : [ 2.4 ], "description" : "The average torsion angle constraint violation for the ensemble.", "rcsb_units" : "degrees", "rcsb_description" : [ { "text" : "The average torsion angle constraint violation for the ensemble.", "context" : "dictionary" } ] }, "conformer_selection_criteria" : { "type" : "string", "examples" : [ "structures with the lowest energy", "structures with the least restraint violations", "structures with acceptable covalent geometry", "structures with favorable non-bond energy", "target function", "back calculated data agree with experimental NOESY spectrum", "all calculated structures submitted", "The submitted conformer models are the 25 structures with the lowest\n energy.", "The submitted conformer models are those with the fewest number of\n constraint violations." ], "description" : "By highlighting the appropriate choice(s), describe how the submitted\nconformer (models) were selected.", "rcsb_description" : [ { "text" : "By highlighting the appropriate choice(s), describe how the submitted\nconformer (models) were selected.", "context" : "dictionary" }, { "text" : "Select the appropriate phrase to describe how the submitted conformer (models) were selected.", "context" : "deposition" } ] }, "conformers_calculated_total_number" : { "type" : "integer", "description" : "The total number of conformer (models) that were calculated in the final round.", "rcsb_description" : [ { "text" : "The total number of conformer (models) that were calculated in the final round.", "context" : "dictionary" } ] }, "conformers_submitted_total_number" : { "type" : "integer", "description" : "The number of conformer (models) that are submitted for the ensemble.", "rcsb_description" : [ { "text" : "The number of conformer (models) that are submitted for the ensemble.", "context" : "dictionary" } ] }, "distance_constraint_violation_method" : { "type" : "string", "examples" : [ "Statistics were calculated over all of the distance constraints.", "Statistics were calculated for violations only" ], "description" : "Describe the method used to calculate the distance constraint violation statistics,\n i.e. are they calculated over all the distance constraints or calculated for\n violations only?", "rcsb_description" : [ { "text" : "Describe the method used to calculate the distance constraint violation statistics,\n i.e. are they calculated over all the distance constraints or calculated for\n violations only?", "context" : "dictionary" } ] }, "maximum_distance_constraint_violation" : { "type" : "number", "examples" : [ 0.4 ], "description" : "The maximum distance constraint violation for the ensemble.", "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "The maximum distance constraint violation for the ensemble.", "context" : "dictionary" } ] }, "maximum_lower_distance_constraint_violation" : { "type" : "number", "examples" : [ 0.3 ], "description" : "The maximum lower distance constraint violation for the ensemble.", "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "The maximum lower distance constraint violation for the ensemble.", "context" : "dictionary" } ] }, "maximum_torsion_angle_constraint_violation" : { "type" : "number", "description" : "The maximum torsion angle constraint violation for the ensemble.", "rcsb_units" : "degrees", "rcsb_description" : [ { "text" : "The maximum torsion angle constraint violation for the ensemble.", "context" : "dictionary" } ] }, "maximum_upper_distance_constraint_violation" : { "type" : "number", "examples" : [ 0.4 ], "description" : "The maximum upper distance constraint violation for the ensemble.", "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "The maximum upper distance constraint violation for the ensemble.", "context" : "dictionary" } ] }, "representative_conformer" : { "type" : "integer", "description" : "The number of the conformer identified as most representative.", "rcsb_description" : [ { "text" : "The number of the conformer identified as most representative.", "context" : "dictionary" } ] }, "torsion_angle_constraint_violation_method" : { "type" : "string", "examples" : [ "Statistics were calculated over all the torsion angle constraints.", "Statistics were calculated for torsion angle constraints violations only." ], "description" : "This item describes the method used to calculate the torsion angle constraint violation statistics.\ni.e. are the entered values based on all torsion angle or calculated for violations only?", "rcsb_description" : [ { "text" : "This item describes the method used to calculate the torsion angle constraint violation statistics.\ni.e. are the entered values based on all torsion angle or calculated for violations only?", "context" : "dictionary" } ] } }, "additionalProperties" : false }, "pdbx_nmr_exptl" : { "type" : "array", "items" : { "type" : "object", "properties" : { "conditions_id" : { "type" : "string", "examples" : [ "1", "2", "3" ], "description" : "The number to identify the set of sample conditions.", "rcsb_description" : [ { "text" : "The number to identify the set of sample conditions.", "context" : "dictionary" }, { "text" : "The previously specified sample conditions ID and label, identifying the conditions in each of these experiments.", "context" : "deposition" } ] }, "experiment_id" : { "type" : "string", "examples" : [ "1", "2", "3" ], "description" : "A numerical ID for each experiment.", "rcsb_description" : [ { "text" : "A numerical ID for each experiment.", "context" : "dictionary" } ] }, "sample_state" : { "type" : "string", "enum" : [ "anisotropic", "isotropic" ], "examples" : [ "isotropic" ], "description" : "Physical state of the sample either anisotropic or isotropic.", "rcsb_description" : [ { "text" : "Physical state of the sample either anisotropic or isotropic.", "context" : "dictionary" }, { "text" : "Physical state of the sample, either anisotropic or isotropic.", "context" : "deposition" } ] }, "solution_id" : { "type" : "string", "examples" : [ "1", "2", "3" ], "description" : "The solution_id from the Experimental Sample to identify the sample\n that these conditions refer to.\n\n [Remember to save the entries here before returning to the\n Experimental Sample form]", "rcsb_description" : [ { "text" : "The solution_id from the Experimental Sample to identify the sample\n that these conditions refer to.\n\n [Remember to save the entries here before returning to the\n Experimental Sample form]", "context" : "dictionary" }, { "text" : "The previously specified sample ID and label, identifying which sample was used in each of these experiments.", "context" : "deposition" } ] }, "spectrometer_id" : { "type" : "integer", "description" : "Pointer to '_pdbx_nmr_spectrometer.spectrometer_id'", "rcsb_description" : [ { "text" : "Pointer to '_pdbx_nmr_spectrometer.spectrometer_id'", "context" : "dictionary" }, { "text" : "The previously specified NMR spectrometer ID and information identifying the spectrometer used for each of these experiments.", "context" : "deposition" } ] }, "type" : { "type" : "string", "examples" : [ "2D NOESY", "3D_15N-separated_NOESY", "3D_13C-separated_NOESY", "4D_13C-separated_NOESY", "4D_13C/15N-separated_NOESY", "3D_15N-separated_ROESY", "3D_13C-separated_ROESY", "HNCA-J", "HNHA", "DQF-COSY", "P-COSY", "PE-COSY", "E-COSY" ], "description" : "The type of NMR experiment.", "rcsb_description" : [ { "text" : "The type of NMR experiment.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "conditions_id", "experiment_id", "solution_id" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_nmr_exptl_sample_conditions" : { "type" : "array", "items" : { "type" : "object", "properties" : { "conditions_id" : { "type" : "string", "examples" : [ "1", "2", "3" ], "description" : "The condition number as defined above.", "rcsb_description" : [ { "text" : "The condition number as defined above.", "context" : "dictionary" } ] }, "details" : { "type" : "string", "examples" : [ "The high salinity of the sample may have contributed to overheating of the sample during experiments with long saturation periods like the TOCSY experiments." ], "description" : "General details describing conditions of both the sample and the environment\nduring measurements.", "rcsb_description" : [ { "text" : "General details describing conditions of both the sample and the environment\nduring measurements.", "context" : "dictionary" } ] }, "ionic_strength" : { "type" : "string", "description" : "The ionic strength at which the NMR data were collected -in lieu of\n this enter the concentration and identity of the salt in the sample.", "rcsb_description" : [ { "text" : "The ionic strength at which the NMR data were collected -in lieu of\n this enter the concentration and identity of the salt in the sample.", "context" : "dictionary" }, { "text" : "The ionic strength at which NMR data were collected. Alternatively, give the concentration and identity of the salt in the sample.", "context" : "deposition" } ] }, "ionic_strength_err" : { "type" : "number", "examples" : [ 0.2 ], "description" : "Estimate of the standard error for the value for the sample ionic strength.", "rcsb_description" : [ { "text" : "Estimate of the standard error for the value for the sample ionic strength.", "context" : "dictionary" }, { "text" : "Estimate of the standard error for the sample ionic strength.", "context" : "deposition" } ] }, "ionic_strength_units" : { "type" : "string", "enum" : [ "M", "Not defined", "mM" ], "examples" : [ "M" ], "description" : "Units for the value of the sample condition ionic strength..", "rcsb_description" : [ { "text" : "Units for the value of the sample condition ionic strength..", "context" : "dictionary" }, { "text" : "Units of the sample condition ionic strength.", "context" : "deposition" } ] }, "label" : { "type" : "string", "examples" : [ "conditions_1" ], "description" : "A descriptive label that uniquely identifies this set of sample conditions.", "rcsb_description" : [ { "text" : "A descriptive label that uniquely identifies this set of sample conditions.", "context" : "dictionary" }, { "text" : "A name that uniquely identifies this set of sample conditions from the others listed in the entry.", "context" : "deposition" } ] }, "pH" : { "type" : "string", "examples" : [ 3.1, 7.0 ], "description" : "The pH at which the NMR data were collected.", "rcsb_description" : [ { "text" : "The pH at which the NMR data were collected.", "context" : "dictionary" } ] }, "pH_err" : { "type" : "number", "examples" : [ 0.05 ], "description" : "Estimate of the standard error for the value for the sample pH.", "rcsb_description" : [ { "text" : "Estimate of the standard error for the value for the sample pH.", "context" : "dictionary" }, { "text" : "Estimate of the standard error for the sample pH.", "context" : "deposition" } ] }, "pH_units" : { "type" : "string", "enum" : [ "Not defined", "pD", "pH", "pH*" ], "examples" : [ "pH" ], "description" : "Units for the value of the sample condition pH.", "rcsb_description" : [ { "text" : "Units for the value of the sample condition pH.", "context" : "dictionary" }, { "text" : "Units of the sample condition pH.", "context" : "deposition" } ] }, "pressure" : { "type" : "string", "examples" : [ "1", "ambient", "1atm" ], "description" : "The pressure at which NMR data were collected.", "rcsb_description" : [ { "text" : "The pressure at which NMR data were collected.", "context" : "dictionary" } ] }, "pressure_err" : { "type" : "number", "examples" : [ 0.01 ], "description" : "Estimate of the standard error for the value for the sample pressure.", "rcsb_description" : [ { "text" : "Estimate of the standard error for the value for the sample pressure.", "context" : "dictionary" }, { "text" : "Estimate of the standard error for the sample pressure.", "context" : "deposition" } ] }, "pressure_units" : { "type" : "string", "examples" : [ "Pa", "atm", "Torr" ], "description" : "The units of pressure at which NMR data were collected.", "rcsb_description" : [ { "text" : "The units of pressure at which NMR data were collected.", "context" : "dictionary" }, { "text" : "Units of the sample condition pressure.", "context" : "deposition" } ] }, "temperature" : { "type" : "string", "description" : "The temperature (in kelvin) at which NMR data were\n collected.", "rcsb_description" : [ { "text" : "The temperature (in kelvin) at which NMR data were\n collected.", "context" : "dictionary" } ] }, "temperature_err" : { "type" : "number", "examples" : [ 0.2 ], "description" : "Estimate of the standard error for the value for the sample temperature.", "rcsb_description" : [ { "text" : "Estimate of the standard error for the value for the sample temperature.", "context" : "dictionary" }, { "text" : "Estimate of the standard error for the sample temperature.", "context" : "deposition" } ] }, "temperature_units" : { "type" : "string", "enum" : [ "C", "K", "Not defined" ], "examples" : [ "K" ], "description" : "Units for the value of the sample condition temperature.", "rcsb_enum_annotated" : [ { "value" : "C", "detail" : "Centigrade" }, { "value" : "K", "detail" : "Kelvin" }, { "value" : "Not defined" } ], "rcsb_description" : [ { "text" : "Units for the value of the sample condition temperature.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "conditions_id" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_nmr_refine" : { "type" : "array", "items" : { "type" : "object", "properties" : { "details" : { "type" : "string", "examples" : [ "Additional comments about the NMR refinement can be placed here, e.g.\nthe structures are based on a total of 3344 restraints, 3167 are NOE-derived\ndistance constraints, 68 dihedral angle restraints,109 distance restraints\nfrom hydrogen bonds." ], "description" : "Additional details about the NMR refinement.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Additional details about the NMR refinement.", "context" : "dictionary" }, { "text" : "Details (Nmr Refine)", "context" : "brief" } ] }, "method" : { "type" : "string", "examples" : [ "simulated annealing", "distance geometry\n simulated annealing\n molecular dynamics\n matrix relaxation\n torsion angle dynamics" ], "description" : "The method used to determine the structure.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The method used to determine the structure.", "context" : "dictionary" }, { "text" : "NMR Method to Determination Structure", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "NMR Method Details", "priority_order" : 20 } ] }, "software_ordinal" : { "type" : "integer", "description" : "Pointer to _software.ordinal", "rcsb_description" : [ { "text" : "Pointer to _software.ordinal", "context" : "dictionary" }, { "text" : "Previously specified software type used for refinement of the structure.", "context" : "deposition" } ] } }, "additionalProperties" : false, "required" : [ "software_ordinal" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_nmr_representative" : { "type" : "object", "properties" : { "conformer_id" : { "type" : "string", "examples" : [ "15" ], "description" : "If a member of the ensemble has been selected as a representative\n structure, identify it by its model number.", "rcsb_description" : [ { "text" : "If a member of the ensemble has been selected as a representative\n structure, identify it by its model number.", "context" : "dictionary" }, { "text" : "Please give the model number of the conformer selected as a representative structure", "context" : "deposition" } ] }, "selection_criteria" : { "type" : "string", "examples" : [ "The structure closest to the average.\nThe structure with the lowest energy was selected.\nThe structure with the fewest number of violations was selected.\nA minimized average structure was calculated." ], "description" : "By highlighting the appropriate choice(s), describe the criteria used to\nselect this structure as a representative structure, or if an average\nstructure has been calculated describe how this was done.", "rcsb_description" : [ { "text" : "By highlighting the appropriate choice(s), describe the criteria used to\nselect this structure as a representative structure, or if an average\nstructure has been calculated describe how this was done.", "context" : "dictionary" }, { "text" : "Select the appropriate phrase to describe the criteria used to select this as the representative structure. Or, if an average structure has been calculated, describe the method used to do this.", "context" : "deposition" } ] } }, "additionalProperties" : false }, "pdbx_nmr_sample_details" : { "type" : "array", "items" : { "type" : "object", "properties" : { "contents" : { "type" : "string", "examples" : [ "2mM Ribonuclease U-15N,13C; 50mM phosphate buffer NA; 90% H2O, 10% D2O" ], "description" : "A complete description of each NMR sample. Include the concentration\nand concentration units for each component (include buffers, etc.). For each\ncomponent describe the isotopic composition, including the % labeling level,\nif known.\n\nFor example:\n1. Uniform (random) labeling with 15N: U-15N\n2. Uniform (random) labeling with 13C, 15N at known labeling\n levels: U-95% 13C;U-98% 15N\n3. Residue selective labeling: U-95% 15N-Thymine\n4. Site specific labeling: 95% 13C-Ala18,\n5. Natural abundance labeling in an otherwise uniformly labeled\n biomolecule is designated by NA: U-13C; NA-K,H", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "A complete description of each NMR sample. Include the concentration\nand concentration units for each component (include buffers, etc.). For each\ncomponent describe the isotopic composition, including the % labeling level,\nif known.\n\nFor example:\n1. Uniform (random) labeling with 15N: U-15N\n2. Uniform (random) labeling with 13C, 15N at known labeling\n levels: U-95% 13C;U-98% 15N\n3. Residue selective labeling: U-95% 15N-Thymine\n4. Site specific labeling: 95% 13C-Ala18,\n5. Natural abundance labeling in an otherwise uniformly labeled\n biomolecule is designated by NA: U-13C; NA-K,H", "context" : "dictionary" }, { "text" : "Contents (Nmr Sample Details)", "context" : "brief" } ] }, "details" : { "type" : "string", "examples" : [ "The added glycerol was used to raise the viscosity of the solution to 1.05 poisson." ], "description" : "Brief description of the sample providing additional information not captured by other items in the category.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Brief description of the sample providing additional information not captured by other items in the category.", "context" : "dictionary" }, { "text" : "Brief description of the sample, providing additional information not captured by other items in the category.", "context" : "deposition" }, { "text" : "Details (Nmr Sample Details)", "context" : "brief" } ] }, "label" : { "type" : "string", "examples" : [ "15N_sample" ], "description" : "A value that uniquely identifies this sample from the other samples listed\nin the entry.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "A value that uniquely identifies this sample from the other samples listed\nin the entry.", "context" : "dictionary" }, { "text" : "A name that uniquely identifies this sample from the others listed in the entry.", "context" : "deposition" }, { "text" : "Label (Nmr Sample Details)", "context" : "brief" } ] }, "solution_id" : { "type" : "string", "examples" : [ "1", "2", "3" ], "description" : "The name (number) of the sample.", "rcsb_description" : [ { "text" : "The name (number) of the sample.", "context" : "dictionary" }, { "text" : "The number that uniquely identifies this sample from the others listed in the entry.", "context" : "deposition" } ] }, "solvent_system" : { "type" : "string", "examples" : [ "90% H2O, 10% D2O" ], "description" : "The solvent system used for this sample.", "rcsb_description" : [ { "text" : "The solvent system used for this sample.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "enum" : [ "bicelle", "emulsion", "fiber", "fibrous protein", "filamentous virus", "gel solid", "gel solution", "liposome", "lyophilized powder", "membrane", "micelle", "oriented membrane film", "polycrystalline powder", "reverse micelle", "single crystal", "solid", "solution" ], "examples" : [ "bicelle" ], "description" : "A descriptive term for the sample that defines the general physical properties\nof the sample.", "rcsb_enum_annotated" : [ { "value" : "bicelle" }, { "value" : "emulsion" }, { "value" : "fiber", "detail" : "solid-state fiber sample" }, { "value" : "fibrous protein" }, { "value" : "filamentous virus" }, { "value" : "gel solid", "detail" : "gel samples used for solid-state NMR" }, { "value" : "gel solution", "detail" : "gel samples used for solution NMR" }, { "value" : "liposome" }, { "value" : "lyophilized powder" }, { "value" : "membrane" }, { "value" : "micelle" }, { "value" : "oriented membrane film" }, { "value" : "polycrystalline powder" }, { "value" : "reverse micelle" }, { "value" : "single crystal" }, { "value" : "solid" }, { "value" : "solution" } ], "rcsb_description" : [ { "text" : "A descriptive term for the sample that defines the general physical properties\nof the sample.", "context" : "dictionary" }, { "text" : "The term that best describes the general physical properties of the sample.", "context" : "deposition" } ] } }, "additionalProperties" : false, "required" : [ "solution_id" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_nmr_software" : { "type" : "array", "items" : { "type" : "object", "properties" : { "authors" : { "type" : "string", "examples" : [ "Brunger", "Guentert" ], "description" : "The name of the authors of the software used in this\n procedure.", "rcsb_description" : [ { "text" : "The name of the authors of the software used in this\n procedure.", "context" : "dictionary" } ] }, "classification" : { "type" : "string", "examples" : [ "collection", "processing", "data analysis", "structure solution", "refinement", "iterative matrix relaxation" ], "description" : "The purpose of the software.", "rcsb_description" : [ { "text" : "The purpose of the software.", "context" : "dictionary" }, { "text" : "The term that best describes the purpose of the software.", "context" : "deposition" } ] }, "name" : { "type" : "string", "examples" : [ "ANSIG", "AURELIA", "AZARA", "CHARMM", "CoMAND", "CORMA", "DIANA", "DYANA", "DSPACE", "DISGEO", "DGII", "DISMAN", "DINOSAUR", "DISCOVER", "FELIX", "FT_NMR", "GROMOS", "IRMA", "MARDIGRAS", "NMRPipe", "SA", "UXNMR", "VNMR", "X-PLOR", "XWINNMR" ], "description" : "The name of the software used for the task.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The name of the software used for the task.", "context" : "dictionary" }, { "text" : "The name of the software used for this procedure.", "context" : "deposition" }, { "text" : "Name (Nmr Software)", "context" : "brief" } ] }, "ordinal" : { "type" : "integer", "description" : "An ordinal index for this category", "rcsb_description" : [ { "text" : "An ordinal index for this category", "context" : "dictionary" }, { "text" : "The number that uniquely identifies this software from the others listed in the entry.", "context" : "deposition" } ] }, "version" : { "type" : "string", "examples" : [ "940501.3", "2.1" ], "description" : "The version of the software.", "rcsb_description" : [ { "text" : "The version of the software.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "ordinal" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_nmr_spectrometer" : { "type" : "array", "items" : { "type" : "object", "properties" : { "details" : { "type" : "string", "description" : "A text description of the NMR spectrometer.", "rcsb_description" : [ { "text" : "A text description of the NMR spectrometer.", "context" : "dictionary" }, { "text" : "Further details about the NMR spectrometer.", "context" : "deposition" } ] }, "field_strength" : { "type" : "number", "description" : "The field strength in MHz of the spectrometer", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "megahertz", "rcsb_description" : [ { "text" : "The field strength in MHz of the spectrometer", "context" : "dictionary" }, { "text" : "Select the field strength in MHz", "context" : "deposition" }, { "text" : "NMR Spectrometer Field Strength", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "NMR Method Details", "priority_order" : 15 } ], "rcsb_current_maximum_value" : 3400.0, "rcsb_current_minimum_value" : 0.0 }, "manufacturer" : { "type" : "string", "examples" : [ "Varian", "Bruker", "JEOL", "GE" ], "description" : "The name of the manufacturer of the spectrometer.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The name of the manufacturer of the spectrometer.", "context" : "dictionary" }, { "text" : "NMR Spectrometer Manufacturer", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "NMR Method Details", "priority_order" : 5 } ] }, "model" : { "type" : "string", "examples" : [ "AVANCE", "AVANCE II", "AVANCE III", "AVANCE III HD", "WH", "WM", "AC+", "Alpha", "AM", "AMX", "AMX II", "DMX", "DRX", "DSX", "MSL", "OMEGA", "OMEGA PSG", "GX", "GSX", "A", "AL", "EC", "EX", "LA", "ECP", "Infinityplus", "Mercury", "VNMRS", "VXR", "UNITY", "UNITY INOVA", "UNITYPLUS", "INOVA", "home-built" ], "description" : "The model of the NMR spectrometer.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The model of the NMR spectrometer.", "context" : "dictionary" }, { "text" : "NMR Spectrometer Model", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "NMR Method Details", "priority_order" : 10 } ] }, "spectrometer_id" : { "type" : "string", "examples" : [ "1", "2", "3" ], "description" : "Assign a numerical ID to each instrument.", "rcsb_description" : [ { "text" : "Assign a numerical ID to each instrument.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "examples" : [ "Bruker WH", "Bruker WM", "Bruker AM", "Bruker AMX", "Bruker DMX", "Bruker DRX", "Bruker MSL", "Bruker AVANCE", "GE Omega", "GE Omega PSG", "JEOL GX", "JEOL GSX", "JEOL A", "JEOL AL", "JEOL EC", "JEOL EX", "JEOL LA", "JEOL ECP", "Varian VXRS", "Varian UNITY", "Varian UNITYplus", "Varian INOVA", "other" ], "description" : "Select the instrument manufacturer(s) and the model(s) of the NMR(s)\nused for this work.", "rcsb_description" : [ { "text" : "Select the instrument manufacturer(s) and the model(s) of the NMR(s)\nused for this work.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "spectrometer_id" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_reflns_twin" : { "type" : "array", "items" : { "type" : "object", "properties" : { "crystal_id" : { "type" : "string", "description" : "The crystal identifier. A reference to\n _exptl_crystal.id in category EXPTL_CRYSTAL.", "rcsb_description" : [ { "text" : "The crystal identifier. A reference to\n _exptl_crystal.id in category EXPTL_CRYSTAL.", "context" : "dictionary" } ] }, "diffrn_id" : { "type" : "string", "description" : "The diffraction data set identifier. A reference to\n _diffrn.id in category DIFFRN.", "rcsb_description" : [ { "text" : "The diffraction data set identifier. A reference to\n _diffrn.id in category DIFFRN.", "context" : "dictionary" } ] }, "domain_id" : { "type" : "string", "description" : "An identifier for the twin domain.", "rcsb_description" : [ { "text" : "An identifier for the twin domain.", "context" : "dictionary" } ] }, "fraction" : { "type" : "number", "description" : "The twin fraction or twin factor represents a quantitative parameter for the\ncrystal twinning. The value 0 represents no twinning, < 0.5 partial twinning,\n = 0.5 for perfect twinning.", "rcsb_description" : [ { "text" : "The twin fraction or twin factor represents a quantitative parameter for the\ncrystal twinning. The value 0 represents no twinning, < 0.5 partial twinning,\n = 0.5 for perfect twinning.", "context" : "dictionary" } ] }, "operator" : { "type" : "string", "examples" : [ "h,-h-k,-l", "h+k,-k,-l", "-h,-k,l", "h,-k,-l", "h,-h-k,-l", "-h,-k,l", "k,-h,l" ], "description" : "The possible merohedral or hemihedral twinning operators for different\npoint groups are:\n\nTrue point group \tTwin operation \thkl related to\n3 \t2 along a,b h,-h-k,-l\n \t2 along a*,b* h+k,-k,-l\n 2 along c -h,-k,l\n4 2 along a,b,a*,b* h,-k,-l\n6 2 along a,b,a*,b* h,-h-k,-l\n321 2 along a*,b*,c -h,-k,l\n312 2 along a,b,c -h,-k,l\n23 4 along a,b,c k,-h,l\n\nReferences:\n Yeates, T.O. (1997) Methods in Enzymology 276, 344-358. Detecting and\n Overcoming Crystal Twinning.\n\n and information from the following on-line sites:\n\n CNS site http://cns.csb.yale.edu/v1.1/\n CCP4 site http://www.ccp4.ac.uk/dist/html/detwin.html\n SHELX site http://shelx.uni-ac.gwdg.de/~rherbst/twin.html", "rcsb_description" : [ { "text" : "The possible merohedral or hemihedral twinning operators for different\npoint groups are:\n\nTrue point group \tTwin operation \thkl related to\n3 \t2 along a,b h,-h-k,-l\n \t2 along a*,b* h+k,-k,-l\n 2 along c -h,-k,l\n4 2 along a,b,a*,b* h,-k,-l\n6 2 along a,b,a*,b* h,-h-k,-l\n321 2 along a*,b*,c -h,-k,l\n312 2 along a,b,c -h,-k,l\n23 4 along a,b,c k,-h,l\n\nReferences:\n Yeates, T.O. (1997) Methods in Enzymology 276, 344-358. Detecting and\n Overcoming Crystal Twinning.\n\n and information from the following on-line sites:\n\n CNS site http://cns.csb.yale.edu/v1.1/\n CCP4 site http://www.ccp4.ac.uk/dist/html/detwin.html\n SHELX site http://shelx.uni-ac.gwdg.de/~rherbst/twin.html", "context" : "dictionary" } ] }, "type" : { "type" : "string", "enum" : [ "epitaxial", "hemihedral", "merohedral", "non-merohedral", "pseudo-merohedral", "tetartohedral" ], "description" : "There are two types of twinning: merohedral or hemihedral\n non-merohedral or epitaxial\n\nFor merohedral twinning the diffraction patterns from the different domains are\ncompletely superimposable. Hemihedral twinning is a special case of merohedral\ntwinning. It only involves two distinct domains. Pseudo-merohedral twinning is\na subclass merohedral twinning in which lattice is coincidentally superimposable.\n\nIn the case of non-merohedral or epitaxial twinning the reciprocal\nlattices do not superimpose exactly. In this case the diffraction pattern\nconsists of two (or more) interpenetrating lattices, which can in principle\nbe separated.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "There are two types of twinning: merohedral or hemihedral\n non-merohedral or epitaxial\n\nFor merohedral twinning the diffraction patterns from the different domains are\ncompletely superimposable. Hemihedral twinning is a special case of merohedral\ntwinning. It only involves two distinct domains. Pseudo-merohedral twinning is\na subclass merohedral twinning in which lattice is coincidentally superimposable.\n\nIn the case of non-merohedral or epitaxial twinning the reciprocal\nlattices do not superimpose exactly. In this case the diffraction pattern\nconsists of two (or more) interpenetrating lattices, which can in principle\nbe separated.", "context" : "dictionary" }, { "text" : "Type of Twinning", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Crystal Properties", "priority_order" : 35 } ] } }, "additionalProperties" : false, "required" : [ "crystal_id", "diffrn_id", "operator" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_related_exp_data_set" : { "type" : "array", "items" : { "type" : "object", "properties" : { "data_reference" : { "type" : "string", "examples" : [ "10.000/10002/image_data/cif" ], "description" : "A DOI reference to the related data set.", "rcsb_description" : [ { "text" : "A DOI reference to the related data set.", "context" : "dictionary" } ] }, "data_set_type" : { "type" : "string", "examples" : [ "diffraction image data", "NMR free induction decay data" ], "description" : "The type of the experimenatal data set.", "rcsb_description" : [ { "text" : "The type of the experimenatal data set.", "context" : "dictionary" } ] }, "db_source" : { "type" : "string", "enum" : [ "Apollo - University of Cambridge Repository", "CXIDB", "DRYAD Database", "EMPIAR", "ESRF Data Portal", "ETH Zurich Research Collection", "Etsin", "Integrated Resource for Reproducibility in Macromolecular Crystallography", "International Union of Crystallography", "KAUST Repository", "Keele Data Repository", "MAXIV Public Data Repository", "MX-RDR (Macromolecular Xtallography Raw Data Repository)", "Manchester eScholar Services", "Mendeley Data", "PSI Public Data Repository", "ProteinDiffraction", "RMIT University Figshare", "SBGrid Data Bank", "Xtal Raw Data Archive", "Zenodo" ], "description" : "For external sources, the name of the resource.", "rcsb_description" : [ { "text" : "For external sources, the name of the resource.", "context" : "dictionary" } ] }, "details" : { "type" : "string", "description" : "Additional details describing the content of the related data set and its application to\n the current investigation.", "rcsb_description" : [ { "text" : "Additional details describing the content of the related data set and its application to\n the current investigation.", "context" : "dictionary" } ] }, "metadata_reference" : { "type" : "string", "examples" : [ "10.000/10002/image_data/txt" ], "description" : "A DOI reference to the metadata decribing the related data set.", "rcsb_description" : [ { "text" : "A DOI reference to the metadata decribing the related data set.", "context" : "dictionary" } ] } }, "additionalProperties" : false }, "minItems" : 1, "uniqueItems" : true }, "pdbx_serial_crystallography_data_reduction" : { "type" : "array", "items" : { "type" : "object", "properties" : { "crystal_hits" : { "type" : "integer", "description" : "For experiments in which samples are provided in a\n continuous stream, the total number of frames collected\n in which the crystal was hit.", "rcsb_description" : [ { "text" : "For experiments in which samples are provided in a\n continuous stream, the total number of frames collected\n in which the crystal was hit.", "context" : "dictionary" } ] }, "diffrn_id" : { "type" : "string", "examples" : [ "1" ], "description" : "The data item is a pointer to _diffrn.id in the DIFFRN\n category.", "rcsb_description" : [ { "text" : "The data item is a pointer to _diffrn.id in the DIFFRN\n category.", "context" : "dictionary" } ] }, "droplet_hits" : { "type" : "integer", "description" : "For experiments in which samples are provided in a\n continuous stream, the total number of frames collected\n in which a droplet was hit.", "rcsb_description" : [ { "text" : "For experiments in which samples are provided in a\n continuous stream, the total number of frames collected\n in which a droplet was hit.", "context" : "dictionary" } ] }, "frame_hits" : { "type" : "integer", "description" : "For experiments in which samples are provided in a\n continuous stream, the total number of data frames collected\n in which the sample was hit.", "rcsb_description" : [ { "text" : "For experiments in which samples are provided in a\n continuous stream, the total number of data frames collected\n in which the sample was hit.", "context" : "dictionary" } ] }, "frames_failed_index" : { "type" : "integer", "description" : "For experiments in which samples are provided in a\n continuous stream, the total number of data frames collected\n that contained a \"hit\" but failed to index.", "rcsb_description" : [ { "text" : "For experiments in which samples are provided in a\n continuous stream, the total number of data frames collected\n that contained a \"hit\" but failed to index.", "context" : "dictionary" } ] }, "frames_indexed" : { "type" : "integer", "description" : "For experiments in which samples are provided in a\n continuous stream, the total number of data frames collected\n that were indexed.", "rcsb_description" : [ { "text" : "For experiments in which samples are provided in a\n continuous stream, the total number of data frames collected\n that were indexed.", "context" : "dictionary" } ] }, "frames_total" : { "type" : "integer", "description" : "The total number of data frames collected for this\n data set.", "rcsb_description" : [ { "text" : "The total number of data frames collected for this\n data set.", "context" : "dictionary" } ] }, "lattices_indexed" : { "type" : "integer", "description" : "For experiments in which samples are provided in a\n continuous stream, the total number of lattices indexed.", "rcsb_description" : [ { "text" : "For experiments in which samples are provided in a\n continuous stream, the total number of lattices indexed.", "context" : "dictionary" } ] }, "lattices_merged" : { "type" : "integer", "description" : "For experiments in which samples are provided in a\n continuous stream, the total number of crystal lattices\n that were merged in the final dataset. Can be\n less than frames_indexed depending on filtering during merging or\n\t can be more than frames_indexed if there are multiple lattices.\n\t per frame.", "rcsb_description" : [ { "text" : "For experiments in which samples are provided in a\n continuous stream, the total number of crystal lattices\n that were merged in the final dataset. Can be\n less than frames_indexed depending on filtering during merging or\n\t can be more than frames_indexed if there are multiple lattices.\n\t per frame.", "context" : "dictionary" } ] }, "xfel_pulse_events" : { "type" : "integer", "description" : "For FEL experiments, the number of pulse events in the dataset.", "rcsb_description" : [ { "text" : "For FEL experiments, the number of pulse events in the dataset.", "context" : "dictionary" } ] }, "xfel_run_numbers" : { "type" : "string", "description" : "For FEL experiments, in which data collection was performed\n\t in batches, indicates which subset of the data collected\n were used in producing this dataset.", "rcsb_description" : [ { "text" : "For FEL experiments, in which data collection was performed\n\t in batches, indicates which subset of the data collected\n were used in producing this dataset.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "diffrn_id" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_serial_crystallography_measurement" : { "type" : "array", "items" : { "type" : "object", "properties" : { "collection_time_total" : { "type" : "number", "examples" : [ 120.0 ], "description" : "The total number of hours required to measure this data set.", "rcsb_units" : "hours", "rcsb_description" : [ { "text" : "The total number of hours required to measure this data set.", "context" : "dictionary" } ] }, "collimation" : { "type" : "string", "examples" : [ "Kirkpatrick-Baez mirrors", "Beryllium compound refractive lenses", "Fresnel zone plates" ], "description" : "The collimation or type of focusing optics applied to the radiation.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The collimation or type of focusing optics applied to the radiation.", "context" : "dictionary" }, { "text" : "Collimation (Serial Crystallography Measurement)", "context" : "brief" } ] }, "diffrn_id" : { "type" : "string", "examples" : [ "1" ], "description" : "The data item is a pointer to _diffrn.id in the DIFFRN\n category.", "rcsb_description" : [ { "text" : "The data item is a pointer to _diffrn.id in the DIFFRN\n category.", "context" : "dictionary" } ] }, "focal_spot_size" : { "type" : "number", "description" : "The focal spot size of the beam\n impinging on the sample (micrometres squared).", "rcsb_units" : "micrometres_squared", "rcsb_description" : [ { "text" : "The focal spot size of the beam\n impinging on the sample (micrometres squared).", "context" : "dictionary" } ] }, "photons_per_pulse" : { "type" : "number", "description" : "The photons per pulse measured in (tera photons (10^(12)^)/pulse units).", "rcsb_units" : "teraphotons_per_pulse", "rcsb_description" : [ { "text" : "The photons per pulse measured in (tera photons (10^(12)^)/pulse units).", "context" : "dictionary" } ] }, "pulse_duration" : { "type" : "number", "description" : "The average duration (femtoseconds)\n\t of the pulse energy measured at the sample.", "rcsb_units" : "femtoseconds", "rcsb_description" : [ { "text" : "The average duration (femtoseconds)\n\t of the pulse energy measured at the sample.", "context" : "dictionary" } ] }, "pulse_energy" : { "type" : "number", "description" : "The energy/pulse of the X-ray pulse impacting the sample measured in microjoules.", "rcsb_units" : "microjoules", "rcsb_description" : [ { "text" : "The energy/pulse of the X-ray pulse impacting the sample measured in microjoules.", "context" : "dictionary" } ] }, "pulse_photon_energy" : { "type" : "number", "description" : "The photon energy of the X-ray pulse measured in KeV.", "rcsb_units" : "kiloelectron_volts", "rcsb_description" : [ { "text" : "The photon energy of the X-ray pulse measured in KeV.", "context" : "dictionary" } ] }, "source_distance" : { "type" : "number", "description" : "The distance from source to the sample along the optical axis (metres).", "rcsb_units" : "metres", "rcsb_description" : [ { "text" : "The distance from source to the sample along the optical axis (metres).", "context" : "dictionary" } ] }, "source_size" : { "type" : "number", "description" : "The dimension of the source beam measured at the source (micrometres squared).", "rcsb_units" : "micrometres_squared", "rcsb_description" : [ { "text" : "The dimension of the source beam measured at the source (micrometres squared).", "context" : "dictionary" } ] }, "xfel_pulse_repetition_rate" : { "type" : "number", "description" : "For FEL experiments, the pulse repetition rate measured in cycles per seconds.", "rcsb_units" : "hertz", "rcsb_description" : [ { "text" : "For FEL experiments, the pulse repetition rate measured in cycles per seconds.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "diffrn_id" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_serial_crystallography_sample_delivery" : { "type" : "array", "items" : { "type" : "object", "properties" : { "description" : { "type" : "string", "examples" : [ "fixed target", "electrospin", "MESH", "CoMESH", "gas dynamic virtual nozzle", "LCP injector", "addressable microarray" ], "description" : "The description of the mechanism by which the specimen in placed in the path\n of the source.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The description of the mechanism by which the specimen in placed in the path\n of the source.", "context" : "dictionary" }, { "text" : "Description (Serial Crystallography Sample Delivery)", "context" : "brief" } ] }, "diffrn_id" : { "type" : "string", "examples" : [ "1" ], "description" : "The data item is a pointer to _diffrn.id in the DIFFRN\n category.", "rcsb_description" : [ { "text" : "The data item is a pointer to _diffrn.id in the DIFFRN\n category.", "context" : "dictionary" } ] }, "method" : { "type" : "string", "enum" : [ "fixed target", "injection" ], "description" : "The description of the mechanism by which the specimen in placed in the path\n of the source.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The description of the mechanism by which the specimen in placed in the path\n of the source.", "context" : "dictionary" }, { "text" : "Method (Serial Crystallography Sample Delivery)", "context" : "brief" } ] } }, "additionalProperties" : false, "required" : [ "diffrn_id" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_serial_crystallography_sample_delivery_fixed_target" : { "type" : "array", "items" : { "type" : "object", "properties" : { "crystals_per_unit" : { "type" : "integer", "description" : "The number of crystals per dropplet or pore in fixed target", "rcsb_description" : [ { "text" : "The number of crystals per dropplet or pore in fixed target", "context" : "dictionary" } ] }, "description" : { "type" : "string", "description" : "For a fixed target sample, a description of sample preparation", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "For a fixed target sample, a description of sample preparation", "context" : "dictionary" }, { "text" : "Description (Serial Crystallography Sample Delivery Fixed Target)", "context" : "brief" } ] }, "details" : { "type" : "string", "description" : "Any details pertinent to the fixed sample target", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Any details pertinent to the fixed sample target", "context" : "dictionary" }, { "text" : "Details (Serial Crystallography Sample Delivery Fixed Target)", "context" : "brief" } ] }, "diffrn_id" : { "type" : "string", "examples" : [ "1" ], "description" : "The data item is a pointer to _diffrn.id in the DIFFRN\n category.", "rcsb_description" : [ { "text" : "The data item is a pointer to _diffrn.id in the DIFFRN\n category.", "context" : "dictionary" } ] }, "motion_control" : { "type" : "string", "examples" : [ "DMC-4080" ], "description" : "Device used to control movement of the fixed sample", "rcsb_description" : [ { "text" : "Device used to control movement of the fixed sample", "context" : "dictionary" } ] }, "sample_dehydration_prevention" : { "type" : "string", "examples" : [ "seal", "humidifed gas", "flash freezing" ], "description" : "Method to prevent dehydration of sample", "rcsb_description" : [ { "text" : "Method to prevent dehydration of sample", "context" : "dictionary" } ] }, "sample_holding" : { "type" : "string", "examples" : [ "mesh", "loop", "grid" ], "description" : "For a fixed target sample, mechanism to hold sample in the beam", "rcsb_description" : [ { "text" : "For a fixed target sample, mechanism to hold sample in the beam", "context" : "dictionary" } ] }, "sample_solvent" : { "type" : "string", "description" : "The sample solution content and concentration", "rcsb_description" : [ { "text" : "The sample solution content and concentration", "context" : "dictionary" } ] }, "sample_unit_size" : { "type" : "number", "description" : "Size of pore in grid supporting sample. Diameter or length in micrometres,\n e.g. pore diameter", "rcsb_units" : "micrometres", "rcsb_description" : [ { "text" : "Size of pore in grid supporting sample. Diameter or length in micrometres,\n e.g. pore diameter", "context" : "dictionary" } ] }, "support_base" : { "type" : "string", "examples" : [ "goniometer" ], "description" : "Type of base holding the support", "rcsb_description" : [ { "text" : "Type of base holding the support", "context" : "dictionary" } ] }, "velocity_horizontal" : { "type" : "number", "description" : "Velocity of sample horizontally relative to a perpendicular beam in millimetres/second", "rcsb_description" : [ { "text" : "Velocity of sample horizontally relative to a perpendicular beam in millimetres/second", "context" : "dictionary" } ] }, "velocity_vertical" : { "type" : "number", "description" : "Velocity of sample vertically relative to a perpendicular beam in millimetres/second", "rcsb_description" : [ { "text" : "Velocity of sample vertically relative to a perpendicular beam in millimetres/second", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "diffrn_id" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_serial_crystallography_sample_delivery_injection" : { "type" : "array", "items" : { "type" : "object", "properties" : { "carrier_solvent" : { "type" : "string", "examples" : [ "LCP", "grease", "liquid" ], "description" : "For continuous sample flow experiments, the carrier buffer used\n to move the sample into the beam. Should include protein\n concentration.", "rcsb_description" : [ { "text" : "For continuous sample flow experiments, the carrier buffer used\n to move the sample into the beam. Should include protein\n concentration.", "context" : "dictionary" } ] }, "crystal_concentration" : { "type" : "number", "description" : "For continuous sample flow experiments, the concentration of\n crystals in the solution being injected.\n\n The concentration is measured in million crystals/ml.", "rcsb_description" : [ { "text" : "For continuous sample flow experiments, the concentration of\n crystals in the solution being injected.\n\n The concentration is measured in million crystals/ml.", "context" : "dictionary" } ] }, "description" : { "type" : "string", "examples" : [ "microextrusion injector" ], "description" : "For continuous sample flow experiments, a description of the injector used\n to move the sample into the beam.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "For continuous sample flow experiments, a description of the injector used\n to move the sample into the beam.", "context" : "dictionary" }, { "text" : "Description (Serial Crystallography Sample Delivery Injection)", "context" : "brief" } ] }, "diffrn_id" : { "type" : "string", "examples" : [ "1" ], "description" : "The data item is a pointer to _diffrn.id in the DIFFRN\n category.", "rcsb_description" : [ { "text" : "The data item is a pointer to _diffrn.id in the DIFFRN\n category.", "context" : "dictionary" } ] }, "filter_size" : { "type" : "number", "description" : "The size of filter in micrometres in filtering crystals", "rcsb_units" : "micrometres", "rcsb_description" : [ { "text" : "The size of filter in micrometres in filtering crystals", "context" : "dictionary" } ] }, "flow_rate" : { "type" : "number", "description" : "For continuous sample flow experiments, the flow rate of\n solution being injected measured in ul/min.", "rcsb_units" : "microliters_per_min", "rcsb_description" : [ { "text" : "For continuous sample flow experiments, the flow rate of\n solution being injected measured in ul/min.", "context" : "dictionary" } ] }, "injector_diameter" : { "type" : "number", "description" : "For continuous sample flow experiments, the diameter of the\n injector in micrometres.", "rcsb_units" : "micrometres", "rcsb_description" : [ { "text" : "For continuous sample flow experiments, the diameter of the\n injector in micrometres.", "context" : "dictionary" } ] }, "injector_nozzle" : { "type" : "string", "examples" : [ "gas", "GDVN" ], "description" : "The type of nozzle to deliver and focus sample jet", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The type of nozzle to deliver and focus sample jet", "context" : "dictionary" }, { "text" : "Injector Nozzle (Serial Crystallography Sample Delivery Injection)", "context" : "brief" } ] }, "injector_pressure" : { "type" : "number", "description" : "For continuous sample flow experiments, the mean pressure\n in kilopascals at which the sample is injected into the beam.", "rcsb_units" : "kilopascals", "rcsb_description" : [ { "text" : "For continuous sample flow experiments, the mean pressure\n in kilopascals at which the sample is injected into the beam.", "context" : "dictionary" } ] }, "injector_temperature" : { "type" : "number", "description" : "For continuous sample flow experiments, the temperature in\n Kelvins of the speciman injected. This may be different from\n the temperature of the sample.", "rcsb_units" : "kelvins", "rcsb_description" : [ { "text" : "For continuous sample flow experiments, the temperature in\n Kelvins of the speciman injected. This may be different from\n the temperature of the sample.", "context" : "dictionary" } ] }, "jet_diameter" : { "type" : "number", "description" : "Diameter in micrometres of jet stream of sample delivery", "rcsb_units" : "micrometres", "rcsb_description" : [ { "text" : "Diameter in micrometres of jet stream of sample delivery", "context" : "dictionary" } ] }, "power_by" : { "type" : "string", "examples" : [ "syringe", "gas", "electronic potential" ], "description" : "Sample deliver driving force, e.g. Gas, Electronic Potential", "rcsb_description" : [ { "text" : "Sample deliver driving force, e.g. Gas, Electronic Potential", "context" : "dictionary" } ] }, "preparation" : { "type" : "string", "examples" : [ "Crystals transfered to carrier solvent at room temperature" ], "description" : "Details of crystal growth and preparation of the crystals", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Details of crystal growth and preparation of the crystals", "context" : "dictionary" }, { "text" : "Preparation (Serial Crystallography Sample Delivery Injection)", "context" : "brief" } ] } }, "additionalProperties" : false, "required" : [ "diffrn_id" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_soln_scatter" : { "type" : "array", "items" : { "type" : "object", "properties" : { "buffer_name" : { "type" : "string", "examples" : [ "acetic acid" ], "description" : "The name of the buffer used for the sample in the solution scattering\n experiment.", "rcsb_description" : [ { "text" : "The name of the buffer used for the sample in the solution scattering\n experiment.", "context" : "dictionary" } ] }, "concentration_range" : { "type" : "string", "examples" : [ "0.7 - 14" ], "description" : "The concentration range (mg/mL) of the complex in the\n sample used in the solution scattering experiment to\n determine the mean radius of structural elongation.", "rcsb_units" : "mg_per_ml", "rcsb_description" : [ { "text" : "The concentration range (mg/mL) of the complex in the\n sample used in the solution scattering experiment to\n determine the mean radius of structural elongation.", "context" : "dictionary" } ] }, "data_analysis_software_list" : { "type" : "string", "examples" : [ "SCTPL5 GNOM" ], "description" : "A list of the software used in the data analysis", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "A list of the software used in the data analysis", "context" : "dictionary" }, { "text" : "Data Analysis Software List (Soln Scatter)", "context" : "brief" } ] }, "data_reduction_software_list" : { "type" : "string", "examples" : [ "OTOKO" ], "description" : "A list of the software used in the data reduction", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "A list of the software used in the data reduction", "context" : "dictionary" }, { "text" : "Data Reduction Software List (Soln Scatter)", "context" : "brief" } ] }, "detector_specific" : { "type" : "string", "description" : "The particular radiation detector. In general this will be a\n manufacturer, description, model number or some combination of\n these.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The particular radiation detector. In general this will be a\n manufacturer, description, model number or some combination of\n these.", "context" : "dictionary" }, { "text" : "Detector Specific (Soln Scatter)", "context" : "brief" } ] }, "detector_type" : { "type" : "string", "description" : "The general class of the radiation detector.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The general class of the radiation detector.", "context" : "dictionary" }, { "text" : "Detector Type (Soln Scatter)", "context" : "brief" } ] }, "id" : { "type" : "string", "description" : "The value of _pdbx_soln_scatter.id must\n uniquely identify the sample in the category PDBX_SOLN_SCATTER", "rcsb_description" : [ { "text" : "The value of _pdbx_soln_scatter.id must\n uniquely identify the sample in the category PDBX_SOLN_SCATTER", "context" : "dictionary" } ] }, "max_mean_cross_sectional_radii_gyration" : { "type" : "number", "description" : "The maximum mean radius of structural elongation of the sample.\n In a given solute-solvent contrast, the radius of gyration\n R_G is a measure of structural elongation if the internal\n inhomogeneity of scattering densities has no effect. Guiner\n analysis at low Q give the R_G and the forward scattering at\n zero angle I(0).\n\n lnl(Q) = lnl(0) - R_G^2Q^2/3\n\n where\n Q = 4(pi)sin(theta/lamda)\n 2theta = scattering angle\n lamda = wavelength\n\n The above expression is valid in a QR_G range for extended\n rod-like particles. The relative I(0)/c values ( where\n c = sample concentration) for sample measurements in a\n constant buffer for a single sample data session, gives the\n relative masses of the protein(s) studied when referenced\n against a standard.\n\n see:\n O.Glatter & O.Kratky, (1982). Editors of \"Small angle\n X-ray Scattering, Academic Press, New York.\n O.Kratky. (1963). X-ray small angle scattering with\n substances of biological interest in diluted solutions.\n Prog. Biophys. Chem., 13, 105-173.\n G.D.Wignall & F.S.Bates, (1987). The small-angle approximation\n of X-ray and neutron scatter from rigid rods of non-uniform\n cross section and finite length. J.Appl. Crystallog., 18, 452-460.\n\n If the structure is elongated, the mean radius of gyration\n of the cross-sectional structure R_XS and the mean cross sectional\n intensity at zero angle [I(Q).Q]_Q->0 is obtained from\n ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2", "rcsb_units" : "nanometres", "rcsb_description" : [ { "text" : "The maximum mean radius of structural elongation of the sample.\n In a given solute-solvent contrast, the radius of gyration\n R_G is a measure of structural elongation if the internal\n inhomogeneity of scattering densities has no effect. Guiner\n analysis at low Q give the R_G and the forward scattering at\n zero angle I(0).\n\n lnl(Q) = lnl(0) - R_G^2Q^2/3\n\n where\n Q = 4(pi)sin(theta/lamda)\n 2theta = scattering angle\n lamda = wavelength\n\n The above expression is valid in a QR_G range for extended\n rod-like particles. The relative I(0)/c values ( where\n c = sample concentration) for sample measurements in a\n constant buffer for a single sample data session, gives the\n relative masses of the protein(s) studied when referenced\n against a standard.\n\n see:\n O.Glatter & O.Kratky, (1982). Editors of \"Small angle\n X-ray Scattering, Academic Press, New York.\n O.Kratky. (1963). X-ray small angle scattering with\n substances of biological interest in diluted solutions.\n Prog. Biophys. Chem., 13, 105-173.\n G.D.Wignall & F.S.Bates, (1987). The small-angle approximation\n of X-ray and neutron scatter from rigid rods of non-uniform\n cross section and finite length. J.Appl. Crystallog., 18, 452-460.\n\n If the structure is elongated, the mean radius of gyration\n of the cross-sectional structure R_XS and the mean cross sectional\n intensity at zero angle [I(Q).Q]_Q->0 is obtained from\n ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2", "context" : "dictionary" } ] }, "max_mean_cross_sectional_radii_gyration_esd" : { "type" : "number", "description" : "The estimated standard deviation for the\nminimum mean radius of structural elongation of the sample.\nIn a given solute-solvent contrast, the radius of gyration\nR_G is a measure of structural elongation if the internal\ninhomogeneity of scattering densities has no effect. Guiner\nanalysis at low Q give the R_G and the forward scattering at\nzero angle I(0).\n\n lnl(Q) = lnl(0) - R_G^2Q^2/3\n\nwhere\n Q = 4(pi)sin(theta/lamda)\n 2theta = scattering angle\n lamda = wavelength\n\nThe above expression is valid in a QR_G range for extended\nrod-like particles. The relative I(0)/c values ( where\n c = sample concentration) for sample measurements in a\nconstant buffer for a single sample data session, gives the\nrelative masses of the protein(s) studied when referenced\nagainst a standard.\n\nsee:\n O.Glatter & O.Kratky, (1982). Editors of \"Small angle\n X-ray Scattering, Academic Press, New York.\n O.Kratky. (1963). X-ray small angle scattering with\n substances of biological interest in diluted solutions.\n Prog. Biophys. Chem., 13, 105-173.\n G.D.Wignall & F.S.Bates, (1987). The small-angle approximation\n of X-ray and neutron scatter from rigid rods of non-uniform\n cross section and finite length. J.Appl. Crystallog., 18, 452-460.\n\nIf the structure is elongated, the mean radius of gyration\nof the cross-sectional structure R_XS and the mean cross sectional\nintensity at zero angle [I(Q).Q]_Q->0 is obtained from\n ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2", "rcsb_units" : "nanometres", "rcsb_description" : [ { "text" : "The estimated standard deviation for the\nminimum mean radius of structural elongation of the sample.\nIn a given solute-solvent contrast, the radius of gyration\nR_G is a measure of structural elongation if the internal\ninhomogeneity of scattering densities has no effect. Guiner\nanalysis at low Q give the R_G and the forward scattering at\nzero angle I(0).\n\n lnl(Q) = lnl(0) - R_G^2Q^2/3\n\nwhere\n Q = 4(pi)sin(theta/lamda)\n 2theta = scattering angle\n lamda = wavelength\n\nThe above expression is valid in a QR_G range for extended\nrod-like particles. The relative I(0)/c values ( where\n c = sample concentration) for sample measurements in a\nconstant buffer for a single sample data session, gives the\nrelative masses of the protein(s) studied when referenced\nagainst a standard.\n\nsee:\n O.Glatter & O.Kratky, (1982). Editors of \"Small angle\n X-ray Scattering, Academic Press, New York.\n O.Kratky. (1963). X-ray small angle scattering with\n substances of biological interest in diluted solutions.\n Prog. Biophys. Chem., 13, 105-173.\n G.D.Wignall & F.S.Bates, (1987). The small-angle approximation\n of X-ray and neutron scatter from rigid rods of non-uniform\n cross section and finite length. J.Appl. Crystallog., 18, 452-460.\n\nIf the structure is elongated, the mean radius of gyration\nof the cross-sectional structure R_XS and the mean cross sectional\nintensity at zero angle [I(Q).Q]_Q->0 is obtained from\n ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2", "context" : "dictionary" } ] }, "mean_guiner_radius" : { "type" : "number", "description" : "The mean radius of structural elongation of the sample.\n In a given solute-solvent contrast, the radius of gyration\n R_G is a measure of structural elongation if the internal\n inhomogeneity of scattering densities has no effect. Guiner\n analysis at low Q gives the R_G and the forward scattering at\n zero angle I(0).\n\n lnl(Q) = lnl(0) - R_G^2Q^2/3\n\n where\n Q = 4(pi)sin(theta/lamda)\n 2theta = scattering angle\n lamda = wavelength\n\n The above expression is valid in a QR_G range for extended\n rod-like particles. The relative I(0)/c values ( where\n c = sample concentration) for sample measurements in a\n constant buffer for a single sample data session, gives the\n relative masses of the protein(s) studied when referenced\n against a standard.\n\n see: O.Glatter & O.Kratky, (1982). Editors of \"Small angle\n X-ray Scattering, Academic Press, New York.\n O.Kratky. (1963). X-ray small angle scattering with\n substances of biological interest in diluted solutions.\n Prog. Biophys. Chem., 13, 105-173.\n\n G.D.Wignall & F.S.Bates, (1987). The small-angle approximation\n of X-ray and neutron scatter from rigid rods of non-uniform\n cross section and finite length. J.Appl. Crystallog., 18, 452-460.\n\n If the structure is elongated, the mean radius of gyration\n of the cross-sectional structure R_XS and the mean cross sectional\n intensity at zero angle [I(Q).Q]_Q->0 is obtained from\n\n ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2", "rcsb_units" : "nanometres", "rcsb_description" : [ { "text" : "The mean radius of structural elongation of the sample.\n In a given solute-solvent contrast, the radius of gyration\n R_G is a measure of structural elongation if the internal\n inhomogeneity of scattering densities has no effect. Guiner\n analysis at low Q gives the R_G and the forward scattering at\n zero angle I(0).\n\n lnl(Q) = lnl(0) - R_G^2Q^2/3\n\n where\n Q = 4(pi)sin(theta/lamda)\n 2theta = scattering angle\n lamda = wavelength\n\n The above expression is valid in a QR_G range for extended\n rod-like particles. The relative I(0)/c values ( where\n c = sample concentration) for sample measurements in a\n constant buffer for a single sample data session, gives the\n relative masses of the protein(s) studied when referenced\n against a standard.\n\n see: O.Glatter & O.Kratky, (1982). Editors of \"Small angle\n X-ray Scattering, Academic Press, New York.\n O.Kratky. (1963). X-ray small angle scattering with\n substances of biological interest in diluted solutions.\n Prog. Biophys. Chem., 13, 105-173.\n\n G.D.Wignall & F.S.Bates, (1987). The small-angle approximation\n of X-ray and neutron scatter from rigid rods of non-uniform\n cross section and finite length. J.Appl. Crystallog., 18, 452-460.\n\n If the structure is elongated, the mean radius of gyration\n of the cross-sectional structure R_XS and the mean cross sectional\n intensity at zero angle [I(Q).Q]_Q->0 is obtained from\n\n ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2", "context" : "dictionary" } ] }, "mean_guiner_radius_esd" : { "type" : "number", "description" : "The estimated standard deviation for the\n mean radius of structural elongation of the sample.\n In a given solute-solvent contrast, the radius of gyration\n R_G is a measure of structural elongation if the internal\n inhomogeneity of scattering densities has no effect. Guiner\n analysis at low Q give the R_G and the forward scattering at\n zero angle I(0).\n\n lnl(Q) = lnl(0) - R_G^2Q^2/3\n\n where\n Q = 4(pi)sin(theta/lamda)\n 2theta = scattering angle\n lamda = wavelength\n\n The above expression is valid in a QR_G range for extended\n rod-like particles. The relative I(0)/c values ( where\n c = sample concentration) for sample measurements in a\n constant buffer for a single sample data session, gives the\n relative masses of the protein(s) studied when referenced\n against a standard.\n\n see:\n O.Glatter & O.Kratky, (1982). Editors of \"Small angle\n X-ray Scattering, Academic Press, New York.\n O.Kratky. (1963). X-ray small angle scattering with\n substances of biological interest in diluted solutions.\n Prog. Biophys. Chem., 13, 105-173.\n G.D.Wignall & F.S.Bates, (1987). The small-angle approximation\n of X-ray and neutron scatter from rigid rods of non-uniform\n cross section and finite length. J.Appl. Crystallog., 18, 452-460.\n\n If the structure is elongated, the mean radius of gyration\n of the cross-sectional structure R_XS and the mean cross sectional\n intensity at zero angle [I(Q).Q]_Q->0 is obtained from\n ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2", "rcsb_units" : "nanometres", "rcsb_description" : [ { "text" : "The estimated standard deviation for the\n mean radius of structural elongation of the sample.\n In a given solute-solvent contrast, the radius of gyration\n R_G is a measure of structural elongation if the internal\n inhomogeneity of scattering densities has no effect. Guiner\n analysis at low Q give the R_G and the forward scattering at\n zero angle I(0).\n\n lnl(Q) = lnl(0) - R_G^2Q^2/3\n\n where\n Q = 4(pi)sin(theta/lamda)\n 2theta = scattering angle\n lamda = wavelength\n\n The above expression is valid in a QR_G range for extended\n rod-like particles. The relative I(0)/c values ( where\n c = sample concentration) for sample measurements in a\n constant buffer for a single sample data session, gives the\n relative masses of the protein(s) studied when referenced\n against a standard.\n\n see:\n O.Glatter & O.Kratky, (1982). Editors of \"Small angle\n X-ray Scattering, Academic Press, New York.\n O.Kratky. (1963). X-ray small angle scattering with\n substances of biological interest in diluted solutions.\n Prog. Biophys. Chem., 13, 105-173.\n G.D.Wignall & F.S.Bates, (1987). The small-angle approximation\n of X-ray and neutron scatter from rigid rods of non-uniform\n cross section and finite length. J.Appl. Crystallog., 18, 452-460.\n\n If the structure is elongated, the mean radius of gyration\n of the cross-sectional structure R_XS and the mean cross sectional\n intensity at zero angle [I(Q).Q]_Q->0 is obtained from\n ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2", "context" : "dictionary" } ] }, "min_mean_cross_sectional_radii_gyration" : { "type" : "number", "description" : "The minimum mean radius of structural elongation of the sample.\nIn a given solute-solvent contrast, the radius of gyration\nR_G is a measure of structural elongation if the internal\ninhomogeneity of scattering densities has no effect. Guiner\nanalysis at low Q give the R_G and the forward scattering at\nzero angle I(0).\n\n lnl(Q) = lnl(0) - R_G^2Q^2/3\n\nwhere\n Q = 4(pi)sin(theta/lamda)\n 2theta = scattering angle\n lamda = wavelength\n\nThe above expression is valid in a QR_G range for extended\nrod-like particles. The relative I(0)/c values ( where\n c = sample concentration) for sample measurements in a\nconstant buffer for a single sample data session, gives the\nrelative masses of the protein(s) studied when referenced\nagainst a standard.\n\nsee:\n O.Glatter & O.Kratky, (1982). Editors of \"Small angle\n X-ray Scattering, Academic Press, New York.\n O.Kratky. (1963). X-ray small angle scattering with\n substances of biological interest in diluted solutions.\n Prog. Biophys. Chem., 13, 105-173.\n G.D.Wignall & F.S.Bates, (1987). The small-angle approximation\n of X-ray and neutron scatter from rigid rods of non-uniform\n cross section and finite length. J.Appl. Crystallog., 18, 452-460.\n\nIf the structure is elongated, the mean radius of gyration\nof the cross-sectional structure R_XS and the mean cross sectional\nintensity at zero angle [I(Q).Q]_Q->0 is obtained from\n ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2", "rcsb_units" : "nanometres", "rcsb_description" : [ { "text" : "The minimum mean radius of structural elongation of the sample.\nIn a given solute-solvent contrast, the radius of gyration\nR_G is a measure of structural elongation if the internal\ninhomogeneity of scattering densities has no effect. Guiner\nanalysis at low Q give the R_G and the forward scattering at\nzero angle I(0).\n\n lnl(Q) = lnl(0) - R_G^2Q^2/3\n\nwhere\n Q = 4(pi)sin(theta/lamda)\n 2theta = scattering angle\n lamda = wavelength\n\nThe above expression is valid in a QR_G range for extended\nrod-like particles. The relative I(0)/c values ( where\n c = sample concentration) for sample measurements in a\nconstant buffer for a single sample data session, gives the\nrelative masses of the protein(s) studied when referenced\nagainst a standard.\n\nsee:\n O.Glatter & O.Kratky, (1982). Editors of \"Small angle\n X-ray Scattering, Academic Press, New York.\n O.Kratky. (1963). X-ray small angle scattering with\n substances of biological interest in diluted solutions.\n Prog. Biophys. Chem., 13, 105-173.\n G.D.Wignall & F.S.Bates, (1987). The small-angle approximation\n of X-ray and neutron scatter from rigid rods of non-uniform\n cross section and finite length. J.Appl. Crystallog., 18, 452-460.\n\nIf the structure is elongated, the mean radius of gyration\nof the cross-sectional structure R_XS and the mean cross sectional\nintensity at zero angle [I(Q).Q]_Q->0 is obtained from\n ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2", "context" : "dictionary" } ] }, "min_mean_cross_sectional_radii_gyration_esd" : { "type" : "number", "description" : "The estimated standard deviation for the\nminimum mean radius of structural elongation of the sample.\nIn a given solute-solvent contrast, the radius of gyration\nR_G is a measure of structural elongation if the internal\ninhomogeneity of scattering densities has no effect. Guiner\nanalysis at low Q give the R_G and the forward scattering at\nzero angle I(0).\n\n lnl(Q) = lnl(0) - R_G^2Q^2/3\n\nwhere\n Q = 4(pi)sin(theta/lamda)\n 2theta = scattering angle\n lamda = wavelength\n\nThe above expression is valid in a QR_G range for extended\nrod-like particles. The relative I(0)/c values ( where\n c = sample concentration) for sample measurements in a\nconstant buffer for a single sample data session, gives the\nrelative masses of the protein(s) studied when referenced\nagainst a standard.\n\nsee:\n O.Glatter & O.Kratky, (1982). Editors of \"Small angle\n X-ray Scattering, Academic Press, New York.\n O.Kratky. (1963). X-ray small angle scattering with\n substances of biological interest in diluted solutions.\n Prog. Biophys. Chem., 13, 105-173.\n G.D.Wignall & F.S.Bates, (1987). The small-angle approximation\n of X-ray and neutron scatter from rigid rods of non-uniform\n cross section and finite length. J.Appl. Crystallog., 18, 452-460.\n\nIf the structure is elongated, the mean radius of gyration\nof the cross-sectional structure R_XS and the mean cross sectional\nintensity at zero angle [I(Q).Q]_Q->0 is obtained from\n\n ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2", "rcsb_units" : "nanometres", "rcsb_description" : [ { "text" : "The estimated standard deviation for the\nminimum mean radius of structural elongation of the sample.\nIn a given solute-solvent contrast, the radius of gyration\nR_G is a measure of structural elongation if the internal\ninhomogeneity of scattering densities has no effect. Guiner\nanalysis at low Q give the R_G and the forward scattering at\nzero angle I(0).\n\n lnl(Q) = lnl(0) - R_G^2Q^2/3\n\nwhere\n Q = 4(pi)sin(theta/lamda)\n 2theta = scattering angle\n lamda = wavelength\n\nThe above expression is valid in a QR_G range for extended\nrod-like particles. The relative I(0)/c values ( where\n c = sample concentration) for sample measurements in a\nconstant buffer for a single sample data session, gives the\nrelative masses of the protein(s) studied when referenced\nagainst a standard.\n\nsee:\n O.Glatter & O.Kratky, (1982). Editors of \"Small angle\n X-ray Scattering, Academic Press, New York.\n O.Kratky. (1963). X-ray small angle scattering with\n substances of biological interest in diluted solutions.\n Prog. Biophys. Chem., 13, 105-173.\n G.D.Wignall & F.S.Bates, (1987). The small-angle approximation\n of X-ray and neutron scatter from rigid rods of non-uniform\n cross section and finite length. J.Appl. Crystallog., 18, 452-460.\n\nIf the structure is elongated, the mean radius of gyration\nof the cross-sectional structure R_XS and the mean cross sectional\nintensity at zero angle [I(Q).Q]_Q->0 is obtained from\n\n ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2", "context" : "dictionary" } ] }, "num_time_frames" : { "type" : "integer", "description" : "The number of time frame solution scattering images used.", "rcsb_description" : [ { "text" : "The number of time frame solution scattering images used.", "context" : "dictionary" } ] }, "protein_length" : { "type" : "string", "description" : "The length (or range) of the protein sample under study.\nIf the solution structure is approximated as an elongated elliptical\ncyclinder the length L is determined from,\n\n L = sqrt [12( (R_G)^2 - (R_XS)^2 ) ]\n\nThe length should also be given by\n\n L = pi I(0) / [ I(Q).Q]_Q->0", "rcsb_description" : [ { "text" : "The length (or range) of the protein sample under study.\nIf the solution structure is approximated as an elongated elliptical\ncyclinder the length L is determined from,\n\n L = sqrt [12( (R_G)^2 - (R_XS)^2 ) ]\n\nThe length should also be given by\n\n L = pi I(0) / [ I(Q).Q]_Q->0", "context" : "dictionary" } ] }, "sample_pH" : { "type" : "number", "description" : "The pH value of the buffered sample.", "rcsb_description" : [ { "text" : "The pH value of the buffered sample.", "context" : "dictionary" } ] }, "source_beamline" : { "type" : "string", "description" : "The beamline name used for the experiment", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The beamline name used for the experiment", "context" : "dictionary" }, { "text" : "Source Beamline (Soln Scatter)", "context" : "brief" } ] }, "source_beamline_instrument" : { "type" : "string", "description" : "The instrumentation used on the beamline", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The instrumentation used on the beamline", "context" : "dictionary" }, { "text" : "Source Beamline Instrument (Soln Scatter)", "context" : "brief" } ] }, "source_class" : { "type" : "string", "examples" : [ "neutron source", "synchrotron" ], "description" : "The general class of the radiation source.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The general class of the radiation source.", "context" : "dictionary" }, { "text" : "Source Class (Soln Scatter)", "context" : "brief" } ] }, "source_type" : { "type" : "string", "description" : "The make, model, name or beamline of the source of radiation.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The make, model, name or beamline of the source of radiation.", "context" : "dictionary" }, { "text" : "Source Type (Soln Scatter)", "context" : "brief" } ] }, "temperature" : { "type" : "number", "description" : "The temperature in kelvins at which the experiment\n was conducted", "rcsb_units" : "kelvins", "rcsb_description" : [ { "text" : "The temperature in kelvins at which the experiment\n was conducted", "context" : "dictionary" } ] }, "type" : { "type" : "string", "enum" : [ "modelling", "neutron", "x-ray" ], "description" : "The type of solution scattering experiment carried out", "rcsb_description" : [ { "text" : "The type of solution scattering experiment carried out", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "id" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_soln_scatter_model" : { "type" : "array", "items" : { "type" : "object", "properties" : { "conformer_selection_criteria" : { "type" : "string", "examples" : [ "The modelled scattering curves were assessed by calculation of the\n RG, RSX-1 and RXS-2 values in the same Q ranges\n used in the experimental Guinier fits. models were\n then ranked using a goodness-of-fit R-factor\n defined by analogy with protein crystallography\n and based on the experimental curves in the Q range\n extending to 1.4 nm-1." ], "description" : "A description of the conformer selection criteria\n used.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "A description of the conformer selection criteria\n used.", "context" : "dictionary" }, { "text" : "Conformer Selection Criteria (Soln Scatter Model)", "context" : "brief" } ] }, "details" : { "type" : "string", "examples" : [ "Homology models were built for\n the 17 SCR domains and energy minimisations were\n performed to improve the connectivity in the fh model.\n triantennary complex-type carbohydrate structures\n (MAN3GLCNAC6GAL3FUC3NEUNAC1) were added to each of the\n N-linked glycosylation sites. a library of linker peptide\n conformations was used in domain modelling constrained\n by the solution scattering fits. modelling with the\n scattering data was also carried out by rotational\n search methods. the x-ray and neutron scattering curve\n I(Q) was calculated assuming a uniform scattering density\n for the spheres using the debye equation as adapted to\n spheres. x-ray curves were calculated from the hydrated\n sphere models without corrections for wavelength spread or\n beam divergence, while these corrections were applied for\n the neutron curves but now using unhydrated models." ], "description" : "A description of any additional details concerning the experiment.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "A description of any additional details concerning the experiment.", "context" : "dictionary" }, { "text" : "Details (Soln Scatter Model)", "context" : "brief" } ] }, "entry_fitting_list" : { "type" : "string", "examples" : [ "PDB CODE 1HFI, 1HCC, 1HFH, 1VCC" ], "description" : "A list of the entries used to fit the model\n to the scattering data", "rcsb_description" : [ { "text" : "A list of the entries used to fit the model\n to the scattering data", "context" : "dictionary" } ] }, "id" : { "type" : "string", "description" : "The value of _pdbx_soln_scatter_model.id must\n uniquely identify the sample in the category PDBX_SOLN_SCATTER_MODEL", "rcsb_description" : [ { "text" : "The value of _pdbx_soln_scatter_model.id must\n uniquely identify the sample in the category PDBX_SOLN_SCATTER_MODEL", "context" : "dictionary" } ] }, "method" : { "type" : "string", "examples" : [ "Constrained scattering fitting of homology models" ], "description" : "A description of the methods used in the modelling", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "A description of the methods used in the modelling", "context" : "dictionary" }, { "text" : "Method (Soln Scatter Model)", "context" : "brief" } ] }, "num_conformers_calculated" : { "type" : "integer", "description" : "The number of model conformers calculated.", "rcsb_description" : [ { "text" : "The number of model conformers calculated.", "context" : "dictionary" } ] }, "num_conformers_submitted" : { "type" : "integer", "description" : "The number of model conformers submitted in the entry", "rcsb_description" : [ { "text" : "The number of model conformers submitted in the entry", "context" : "dictionary" } ] }, "representative_conformer" : { "type" : "integer", "description" : "The index of the representative conformer among the submitted conformers for the entry", "rcsb_description" : [ { "text" : "The index of the representative conformer among the submitted conformers for the entry", "context" : "dictionary" } ] }, "scatter_id" : { "type" : "string", "description" : "This data item is a pointer to _pdbx_soln_scatter.id in the PDBX_SOLN_SCATTER category.", "rcsb_description" : [ { "text" : "This data item is a pointer to _pdbx_soln_scatter.id in the PDBX_SOLN_SCATTER category.", "context" : "dictionary" } ] }, "software_author_list" : { "type" : "string", "examples" : [ "MSI" ], "description" : "A list of the software authors", "rcsb_description" : [ { "text" : "A list of the software authors", "context" : "dictionary" } ] }, "software_list" : { "type" : "string", "examples" : [ "INSIGHT II, HOMOLOGY, DISCOVERY, BIOPOLYMER, DELPHI" ], "description" : "A list of the software used in the modeeling", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "A list of the software used in the modeeling", "context" : "dictionary" }, { "text" : "Software List (Soln Scatter Model)", "context" : "brief" } ] } }, "additionalProperties" : false, "required" : [ "id", "scatter_id" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_vrpt_summary" : { "type" : "object", "properties" : { "RNA_suiteness" : { "type" : "number", "examples" : [ 0.89 ], "description" : "The MolProbity conformer-match quality parameter for RNA structures.\nLow values are worse. Specific to structures that contain RNA polymers.", "rcsb_description" : [ { "text" : "The MolProbity conformer-match quality parameter for RNA structures.\nLow values are worse. Specific to structures that contain RNA polymers.", "context" : "dictionary" } ] }, "attempted_validation_steps" : { "type" : "string", "description" : "The steps that were attempted by the validation pipeline software. \nA step typically involves running a 3rd party validation tool, for instance \"mogul\"\nEach step will be enumerated in _pdbx_vrpt_software category.", "rcsb_description" : [ { "text" : "The steps that were attempted by the validation pipeline software. \nA step typically involves running a 3rd party validation tool, for instance \"mogul\"\nEach step will be enumerated in _pdbx_vrpt_software category.", "context" : "dictionary" } ] }, "ligands_for_buster_report" : { "type" : "string", "enum" : [ "N", "Y" ], "description" : "A flag indicating if there are ligands in the model used for detailed Buster analysis.", "rcsb_description" : [ { "text" : "A flag indicating if there are ligands in the model used for detailed Buster analysis.", "context" : "dictionary" } ] }, "report_creation_date" : { "type" : "string", "format" : "date-time", "description" : "The date, time and time-zone that the validation report was created. \nThe string will be formatted like yyyy-mm-dd:hh:mm in GMT time.", "rcsb_description" : [ { "text" : "The date, time and time-zone that the validation report was created. \nThe string will be formatted like yyyy-mm-dd:hh:mm in GMT time.", "context" : "dictionary" } ] }, "restypes_notchecked_for_bond_angle_geometry" : { "type" : "array", "items" : { "type" : "string", "description" : "This is a comma separated list of the residue types whose bond lengths and bond angles have \nnot been checked against \"standard geometry\" using the MolProbity dangle program.\nStandard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996)", "rcsb_description" : [ { "text" : "This is a comma separated list of the residue types whose bond lengths and bond angles have \nnot been checked against \"standard geometry\" using the MolProbity dangle program.\nStandard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996)", "context" : "dictionary" } ] }, "uniqueItems" : false } }, "additionalProperties" : false }, "pdbx_vrpt_summary_diffraction" : { "type" : "array", "items" : { "type" : "object", "properties" : { "B_factor_type" : { "type" : "string", "enum" : [ "FULL", "PARTIAL" ], "description" : "An indicator if isotropic B factors are partial or full values.", "rcsb_description" : [ { "text" : "An indicator if isotropic B factors are partial or full values.", "context" : "dictionary" } ] }, "Babinet_b" : { "type" : "number", "description" : "REFMAC scaling parameter as reported in log output line starting 'bulk solvent: scale'.\nX-ray entry specific, obtained in the EDS step from REFMAC calculation.", "rcsb_description" : [ { "text" : "REFMAC scaling parameter as reported in log output line starting 'bulk solvent: scale'.\nX-ray entry specific, obtained in the EDS step from REFMAC calculation.", "context" : "dictionary" } ] }, "Babinet_k" : { "type" : "number", "description" : "REFMAC scaling parameter as reported in log output line starting 'bulk solvent: scale'.\nX-ray entry specific, obtained in the EDS step from REFMAC calculation.", "rcsb_description" : [ { "text" : "REFMAC scaling parameter as reported in log output line starting 'bulk solvent: scale'.\nX-ray entry specific, obtained in the EDS step from REFMAC calculation.", "context" : "dictionary" } ] }, "CCP4_version" : { "type" : "string", "description" : "The version of CCP4 suite used in the analysis.", "rcsb_description" : [ { "text" : "The version of CCP4 suite used in the analysis.", "context" : "dictionary" } ] }, "DCC_R" : { "type" : "number", "description" : "The overall R-factor from a DCC recalculation of an electron density map.\nCurrently value is rounded to 2 decimal places.\nX-ray entry specific, obtained from the DCC program.", "rcsb_description" : [ { "text" : "The overall R-factor from a DCC recalculation of an electron density map.\nCurrently value is rounded to 2 decimal places.\nX-ray entry specific, obtained from the DCC program.", "context" : "dictionary" } ] }, "DCC_Rfree" : { "type" : "number", "description" : "Rfree as calculated by DCC.", "rcsb_description" : [ { "text" : "Rfree as calculated by DCC.", "context" : "dictionary" } ] }, "EDS_R" : { "type" : "number", "description" : "The overall R factor from the EDS REFMAC calculation (no free set is used in this).\nCurrently value is rounded to 2 decimal places.\nX-ray entry specific, obtained in the eds step from REFMAC calculation.", "rcsb_description" : [ { "text" : "The overall R factor from the EDS REFMAC calculation (no free set is used in this).\nCurrently value is rounded to 2 decimal places.\nX-ray entry specific, obtained in the eds step from REFMAC calculation.", "context" : "dictionary" } ] }, "EDS_R_warning" : { "type" : "string", "description" : "Warning message when EDS calculated R vs reported R is higher than a threshold", "rcsb_description" : [ { "text" : "Warning message when EDS calculated R vs reported R is higher than a threshold", "context" : "dictionary" } ] }, "EDS_res_high" : { "type" : "number", "description" : "The data high resolution diffraction limit, in Angstroms, found in the input structure factor file.\nX-ray entry specific, obtained in the EDS step.", "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "The data high resolution diffraction limit, in Angstroms, found in the input structure factor file.\nX-ray entry specific, obtained in the EDS step.", "context" : "dictionary" } ] }, "EDS_res_low" : { "type" : "number", "description" : "The data low resolution diffraction limit, in Angstroms, found in the input structure factor file.\nX-ray entry specific, obtained in the EDS step.", "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "The data low resolution diffraction limit, in Angstroms, found in the input structure factor file.\nX-ray entry specific, obtained in the EDS step.", "context" : "dictionary" } ] }, "Fo_Fc_correlation" : { "type" : "number", "description" : "Fo,Fc correlation: The difference between the observed structure factors (Fo) and the \ncalculated structure factors (Fc) measures the correlation between the model and the\nexperimental data. \nX-ray entry specific, obtained in the eds step from REFMAC calculation.", "rcsb_description" : [ { "text" : "Fo,Fc correlation: The difference between the observed structure factors (Fo) and the \ncalculated structure factors (Fc) measures the correlation between the model and the\nexperimental data. \nX-ray entry specific, obtained in the eds step from REFMAC calculation.", "context" : "dictionary" } ] }, "I_over_sigma" : { "type" : "string", "description" : "Each reflection has an intensity (I) and an uncertainty in measurement \n(sigma(I)), so I/sigma(I) is the signal-to-noise ratio. This\nratio decreases at higher resolution. is the mean of individual I/sigma(I)\nvalues. Value for outer resolution shell is given in parentheses. In case\nstructure factor amplitudes are deposited, Xtriage estimates the intensities\nfirst and then calculates this metric. When intensities are available in the\ndeposited file, these are converted to amplitudes and then back to intensity\nestimate before calculating the metric. \nX-ray entry specific, calculated by Phenix Xtriage program.", "rcsb_description" : [ { "text" : "Each reflection has an intensity (I) and an uncertainty in measurement \n(sigma(I)), so I/sigma(I) is the signal-to-noise ratio. This\nratio decreases at higher resolution. is the mean of individual I/sigma(I)\nvalues. Value for outer resolution shell is given in parentheses. In case\nstructure factor amplitudes are deposited, Xtriage estimates the intensities\nfirst and then calculates this metric. When intensities are available in the\ndeposited file, these are converted to amplitudes and then back to intensity\nestimate before calculating the metric. \nX-ray entry specific, calculated by Phenix Xtriage program.", "context" : "dictionary" } ] }, "Padilla_Yeates_L2_mean" : { "type" : "number", "description" : "Padilla and Yeates twinning parameter <|L**2|>.\nTheoretical values is 0.333 in the untwinned case, and 0.2 in the perfectly twinned case.\nX-ray entry specific, obtained from the Xtriage program.", "rcsb_description" : [ { "text" : "Padilla and Yeates twinning parameter <|L**2|>.\nTheoretical values is 0.333 in the untwinned case, and 0.2 in the perfectly twinned case.\nX-ray entry specific, obtained from the Xtriage program.", "context" : "dictionary" } ] }, "Padilla_Yeates_L_mean" : { "type" : "number", "description" : "Padilla and Yeates twinning parameter <|L|>.\nTheoretical values is 0.5 in the untwinned case, and 0.375 in the perfectly twinned case.\nX-ray entry specific, obtained from the Xtriage program.", "rcsb_description" : [ { "text" : "Padilla and Yeates twinning parameter <|L|>.\nTheoretical values is 0.5 in the untwinned case, and 0.375 in the perfectly twinned case.\nX-ray entry specific, obtained from the Xtriage program.", "context" : "dictionary" } ] }, "Q_score" : { "type" : "number", "description" : "The overall Q-score of the fit of coordinates to the electron map.\nThe Q-score is defined in Pintilie, GH. et al., Nature Methods, 17, 328-334 (2020)", "rcsb_description" : [ { "text" : "The overall Q-score of the fit of coordinates to the electron map.\nThe Q-score is defined in Pintilie, GH. et al., Nature Methods, 17, 328-334 (2020)", "context" : "dictionary" } ] }, "Wilson_B_aniso" : { "type" : "string", "description" : "Result of absolute likelihood based Wilson scaling, \nThe anisotropic B value of the data is determined using a likelihood based approach. \nThe resulting B tensor is reported, the 3 diagonal values are given first, followed\nby the 3 off diagonal values.\nA large spread in (especially the diagonal) values indicates anisotropy. \nX-ray entry specific, calculated by Phenix Xtriage program.", "rcsb_description" : [ { "text" : "Result of absolute likelihood based Wilson scaling, \nThe anisotropic B value of the data is determined using a likelihood based approach. \nThe resulting B tensor is reported, the 3 diagonal values are given first, followed\nby the 3 off diagonal values.\nA large spread in (especially the diagonal) values indicates anisotropy. \nX-ray entry specific, calculated by Phenix Xtriage program.", "context" : "dictionary" } ] }, "Wilson_B_estimate" : { "type" : "number", "description" : "An estimate of the overall B-value of the structure, calculated from the diffraction data. \nUnits Angstroms squared.\nIt serves as an indicator of the degree of order in the crystal and the value is usually \nnot hugely different from the average B-value calculated from the model.\nX-ray entry specific, calculated by Phenix Xtriage program.", "rcsb_units" : "angstroms_squared", "rcsb_description" : [ { "text" : "An estimate of the overall B-value of the structure, calculated from the diffraction data. \nUnits Angstroms squared.\nIt serves as an indicator of the degree of order in the crystal and the value is usually \nnot hugely different from the average B-value calculated from the model.\nX-ray entry specific, calculated by Phenix Xtriage program.", "context" : "dictionary" } ] }, "acentric_outliers" : { "type" : "integer", "description" : "The number of acentric reflections that Xtriage identifies as outliers on the basis \nof Wilson statistics. Note that if pseudo translational symmetry is present, \na large number of 'outliers' will be present.\nX-ray entry specific, calculated by Phenix Xtriage program.", "rcsb_description" : [ { "text" : "The number of acentric reflections that Xtriage identifies as outliers on the basis \nof Wilson statistics. Note that if pseudo translational symmetry is present, \na large number of 'outliers' will be present.\nX-ray entry specific, calculated by Phenix Xtriage program.", "context" : "dictionary" } ] }, "bulk_solvent_b" : { "type" : "number", "description" : "REFMAC scaling parameter as reported in log output file.\nX-ray entry specific, obtained in the EDS step from REFMAC calculation.", "rcsb_description" : [ { "text" : "REFMAC scaling parameter as reported in log output file.\nX-ray entry specific, obtained in the EDS step from REFMAC calculation.", "context" : "dictionary" } ] }, "bulk_solvent_k" : { "type" : "number", "description" : "REFMAC reported scaling parameter.\nX-ray entry specific, obtained in the EDS step from REFMAC calculation.", "rcsb_description" : [ { "text" : "REFMAC reported scaling parameter.\nX-ray entry specific, obtained in the EDS step from REFMAC calculation.", "context" : "dictionary" } ] }, "centric_outliers" : { "type" : "integer", "description" : "The number of centric reflections that Xtriage identifies as outliers.\nX-ray entry specific, calculated by Phenix Xtriage program.", "rcsb_description" : [ { "text" : "The number of centric reflections that Xtriage identifies as outliers.\nX-ray entry specific, calculated by Phenix Xtriage program.", "context" : "dictionary" } ] }, "data_anisotropy" : { "type" : "number", "description" : "The ratio (Bmax - Bmin) / Bmean where Bmax, Bmin and Bmean are computed from the B-values \nassociated with the principal axes of the anisotropic thermal ellipsoid. \nThis ratio is usually less than 0.5; for only 1% of PDB entries it is more than 1.0 (Read et al., 2011).\nX-ray entry specific, obtained from the Xtriage program.", "rcsb_description" : [ { "text" : "The ratio (Bmax - Bmin) / Bmean where Bmax, Bmin and Bmean are computed from the B-values \nassociated with the principal axes of the anisotropic thermal ellipsoid. \nThis ratio is usually less than 0.5; for only 1% of PDB entries it is more than 1.0 (Read et al., 2011).\nX-ray entry specific, obtained from the Xtriage program.", "context" : "dictionary" } ] }, "data_completeness" : { "type" : "number", "description" : "The percent completeness of diffraction data.", "rcsb_description" : [ { "text" : "The percent completeness of diffraction data.", "context" : "dictionary" } ] }, "density_fitness_version" : { "type" : "string", "description" : "The version of density-fitness suite programs used in the analysis.", "rcsb_description" : [ { "text" : "The version of density-fitness suite programs used in the analysis.", "context" : "dictionary" } ] }, "exp_method" : { "type" : "string", "description" : "Experimental method for statistics", "rcsb_description" : [ { "text" : "Experimental method for statistics", "context" : "dictionary" } ] }, "num_miller_indices" : { "type" : "integer", "description" : "The number of Miller Indices reported by the Xtriage program. This should be the same as the\nnumber of _refln in the input structure factor file.\nX-ray entry specific, calculated by Phenix Xtriage program.", "rcsb_description" : [ { "text" : "The number of Miller Indices reported by the Xtriage program. This should be the same as the\nnumber of _refln in the input structure factor file.\nX-ray entry specific, calculated by Phenix Xtriage program.", "context" : "dictionary" } ] }, "number_reflns_R_free" : { "type" : "integer", "description" : "The number of reflections in the free set as defined in the input structure factor file supplied to the validation pipeline. \nX-ray entry specific, obtained from the DCC program.", "rcsb_description" : [ { "text" : "The number of reflections in the free set as defined in the input structure factor file supplied to the validation pipeline. \nX-ray entry specific, obtained from the DCC program.", "context" : "dictionary" } ] }, "percent_RSRZ_outliers" : { "type" : "number", "description" : "The percent of RSRZ outliers.", "rcsb_description" : [ { "text" : "The percent of RSRZ outliers.", "context" : "dictionary" } ] }, "percent_free_reflections" : { "type" : "number", "description" : "A percentage, Normally percent proportion of the total number. Between 0% and 100%.", "rcsb_description" : [ { "text" : "A percentage, Normally percent proportion of the total number. Between 0% and 100%.", "context" : "dictionary" } ] }, "servalcat_version" : { "type" : "string", "description" : "The version of Servalcat program used in the analysis.", "rcsb_description" : [ { "text" : "The version of Servalcat program used in the analysis.", "context" : "dictionary" } ] }, "trans_NCS_details" : { "type" : "string", "examples" : [ "The largest off-origin peak in the Patterson function is 8.82% of the height of the origin peak. No significant pseudotranslation is detected." ], "description" : "A sentence giving the result of Xtriage's analysis on translational NCS.\nX-ray entry specific, obtained from the Xtriage program.", "rcsb_description" : [ { "text" : "A sentence giving the result of Xtriage's analysis on translational NCS.\nX-ray entry specific, obtained from the Xtriage program.", "context" : "dictionary" } ] }, "twin_fraction" : { "type" : "string", "examples" : [ "h,h-k,h-l:0.477;-h,-h+k,-l:0.020;-h,-k,-h+l:0.017" ], "description" : "Estimated twinning fraction for operators as identified by Xtriage. A semicolon separated\nlist of operators with fractions is givens \nX-ray entry specific, obtained from the Xtriage program.", "rcsb_description" : [ { "text" : "Estimated twinning fraction for operators as identified by Xtriage. A semicolon separated\nlist of operators with fractions is givens \nX-ray entry specific, obtained from the Xtriage program.", "context" : "dictionary" } ] } }, "additionalProperties" : false }, "minItems" : 1, "uniqueItems" : true }, "pdbx_vrpt_summary_em" : { "type" : "array", "items" : { "type" : "object", "properties" : { "Q_score" : { "type" : "number", "description" : "The overall Q-score of the fit of coordinates to the electron map.\nThe Q-score is defined in Pintilie, GH. et al., Nature Methods, 17, 328-334 (2020)", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The overall Q-score of the fit of coordinates to the electron map.\nThe Q-score is defined in Pintilie, GH. et al., Nature Methods, 17, 328-334 (2020)", "context" : "dictionary" }, { "text" : "Entry Average Q-Score", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "EM Method Details", "priority_order" : 10 } ], "rcsb_current_maximum_value" : 0.99, "rcsb_current_minimum_value" : -0.104 }, "atom_inclusion_all_atoms" : { "type" : "number", "description" : "The proportion of all non hydrogen atoms within density.", "rcsb_description" : [ { "text" : "The proportion of all non hydrogen atoms within density.", "context" : "dictionary" } ] }, "atom_inclusion_backbone" : { "type" : "number", "description" : "The proportion of backbone atoms within density.", "rcsb_description" : [ { "text" : "The proportion of backbone atoms within density.", "context" : "dictionary" } ] }, "author_provided_fsc_resolution_by_cutoff_halfbit" : { "type" : "number", "description" : "The resolution from the intersection of the author provided fsc and the indicator curve halfbit.", "rcsb_description" : [ { "text" : "The resolution from the intersection of the author provided fsc and the indicator curve halfbit.", "context" : "dictionary" } ] }, "author_provided_fsc_resolution_by_cutoff_onebit" : { "type" : "number", "description" : "The resolution from the intersection of the author provided fsc and the indicator curve onebit.", "rcsb_description" : [ { "text" : "The resolution from the intersection of the author provided fsc and the indicator curve onebit.", "context" : "dictionary" } ] }, "author_provided_fsc_resolution_by_cutoff_pt_143" : { "type" : "number", "description" : "The resolution from the intersection of the author provided fsc and the indicator curve 0.143.", "rcsb_description" : [ { "text" : "The resolution from the intersection of the author provided fsc and the indicator curve 0.143.", "context" : "dictionary" } ] }, "author_provided_fsc_resolution_by_cutoff_pt_333" : { "type" : "number", "description" : "The resolution from the intersection of the author provided fsc and the indicator curve 0.333.", "rcsb_description" : [ { "text" : "The resolution from the intersection of the author provided fsc and the indicator curve 0.333.", "context" : "dictionary" } ] }, "author_provided_fsc_resolution_by_cutoff_pt_5" : { "type" : "number", "description" : "The resolution from the intersection of the author provided fsc and the indicator curve 0.5.", "rcsb_description" : [ { "text" : "The resolution from the intersection of the author provided fsc and the indicator curve 0.5.", "context" : "dictionary" } ] }, "author_provided_fsc_resolution_by_cutoff_threesigma" : { "type" : "number", "description" : "The resolution from the intersection of the author provided fsc and the indicator curve threesigma.", "rcsb_description" : [ { "text" : "The resolution from the intersection of the author provided fsc and the indicator curve threesigma.", "context" : "dictionary" } ] }, "calculated_fsc_resolution_by_cutoff_halfbit" : { "type" : "number", "description" : "The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve halfbit.", "rcsb_description" : [ { "text" : "The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve halfbit.", "context" : "dictionary" } ] }, "calculated_fsc_resolution_by_cutoff_onebit" : { "type" : "number", "description" : "The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve onebit.", "rcsb_description" : [ { "text" : "The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve onebit.", "context" : "dictionary" } ] }, "calculated_fsc_resolution_by_cutoff_pt_143" : { "type" : "number", "description" : "The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve 0.143.", "rcsb_description" : [ { "text" : "The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve 0.143.", "context" : "dictionary" } ] }, "calculated_fsc_resolution_by_cutoff_pt_333" : { "type" : "number", "description" : "The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve 0.333.", "rcsb_description" : [ { "text" : "The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve 0.333.", "context" : "dictionary" } ] }, "calculated_fsc_resolution_by_cutoff_pt_5" : { "type" : "number", "description" : "The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve 0.5.", "rcsb_description" : [ { "text" : "The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve 0.5.", "context" : "dictionary" } ] }, "calculated_fsc_resolution_by_cutoff_threesigma" : { "type" : "number", "description" : "The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve threesigma.", "rcsb_description" : [ { "text" : "The resolution from the intersection of the fsc curve generated by from the provided halfmaps and the indicator curve threesigma.", "context" : "dictionary" } ] }, "contour_level_primary_map" : { "type" : "number", "description" : "The recommended contour level for the primary map of this deposition.", "rcsb_description" : [ { "text" : "The recommended contour level for the primary map of this deposition.", "context" : "dictionary" } ] }, "exp_method" : { "type" : "string", "description" : "Experimental method for statistics", "rcsb_description" : [ { "text" : "Experimental method for statistics", "context" : "dictionary" } ] } }, "additionalProperties" : false }, "minItems" : 1, "uniqueItems" : true }, "pdbx_vrpt_summary_geometry" : { "type" : "array", "items" : { "type" : "object", "properties" : { "angles_RMSZ" : { "type" : "number", "description" : "The overall root mean square of the Z-score for deviations of bond angles in comparison to \n\"standard geometry\" made using the MolProbity dangle program.\nStandard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996).\nThis value is for all chains in the structure.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The overall root mean square of the Z-score for deviations of bond angles in comparison to \n\"standard geometry\" made using the MolProbity dangle program.\nStandard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996).\nThis value is for all chains in the structure.", "context" : "dictionary" }, { "text" : "Molprobity Angles RMSZ", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Entry Features", "priority_order" : 100 } ], "rcsb_current_maximum_value" : 26.71, "rcsb_current_minimum_value" : 0.0 }, "bonds_RMSZ" : { "type" : "number", "description" : "The overall root mean square of the Z-score for deviations of bond lengths in comparison to \n\"standard geometry\" made using the MolProbity dangle program.\nStandard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996).\nThis value is for all chains in the structure.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The overall root mean square of the Z-score for deviations of bond lengths in comparison to \n\"standard geometry\" made using the MolProbity dangle program.\nStandard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996).\nThis value is for all chains in the structure.", "context" : "dictionary" }, { "text" : "Molprobity Bonds RMSZ", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Entry Features", "priority_order" : 105 } ], "rcsb_current_maximum_value" : 150.87, "rcsb_current_minimum_value" : 0.01 }, "clashscore" : { "type" : "number", "description" : "This score is derived from the number of pairs of atoms in the PDB_model_num that are unusually close to each other. \nIt is calculated by the MolProbity pdbx_vrpt_software and expressed as the number or such clashes per thousand atoms.\nFor structures determined by NMR the clashscore value here will only consider label_atom_id pairs in the \nwell-defined (core) residues from ensemble analysis.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "This score is derived from the number of pairs of atoms in the PDB_model_num that are unusually close to each other. \nIt is calculated by the MolProbity pdbx_vrpt_software and expressed as the number or such clashes per thousand atoms.\nFor structures determined by NMR the clashscore value here will only consider label_atom_id pairs in the \nwell-defined (core) residues from ensemble analysis.", "context" : "dictionary" }, { "text" : "Molprobity Clashscore", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Entry Features", "priority_order" : 110 } ], "rcsb_current_maximum_value" : 1061.71, "rcsb_current_minimum_value" : -1.0 }, "clashscore_full_length" : { "type" : "number", "description" : "Only given for structures determined by NMR. The MolProbity pdbx_vrpt_instance_clashes score for all label_atom_id pairs.", "rcsb_description" : [ { "text" : "Only given for structures determined by NMR. The MolProbity pdbx_vrpt_instance_clashes score for all label_atom_id pairs.", "context" : "dictionary" } ] }, "num_H_reduce" : { "type" : "integer", "description" : "This is the number of hydrogen atoms added and optimized by the MolProbity reduce pdbx_vrpt_software as part of the\nall-atom clashscore.", "rcsb_description" : [ { "text" : "This is the number of hydrogen atoms added and optimized by the MolProbity reduce pdbx_vrpt_software as part of the\nall-atom clashscore.", "context" : "dictionary" } ] }, "num_angles_RMSZ" : { "type" : "integer", "description" : "The number of bond angles compared to \"standard geometry\" made using the MolProbity dangle program.\nStandard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996).\nThis value is for all chains in the structure.", "rcsb_description" : [ { "text" : "The number of bond angles compared to \"standard geometry\" made using the MolProbity dangle program.\nStandard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996).\nThis value is for all chains in the structure.", "context" : "dictionary" } ] }, "num_bonds_RMSZ" : { "type" : "integer", "description" : "The number of bond lengths compared to \"standard geometry\" made using the MolProbity dangle program.\nStandard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996).\nThis value is for all chains in the structure.", "rcsb_description" : [ { "text" : "The number of bond lengths compared to \"standard geometry\" made using the MolProbity dangle program.\nStandard geometry parameters are taken from Engh and Huber (2001) and Parkinson et al. (1996).\nThis value is for all chains in the structure.", "context" : "dictionary" } ] }, "percent_ramachandran_outliers" : { "type" : "number", "description" : "The percentage of residues with Ramachandran outliers.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The percentage of residues with Ramachandran outliers.", "context" : "dictionary" }, { "text" : "Molprobity Percentage Ramachandran Outliers", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Entry Features", "priority_order" : 115 } ], "rcsb_current_maximum_value" : 100.0, "rcsb_current_minimum_value" : 0.0 }, "percent_ramachandran_outliers_full_length" : { "type" : "number", "description" : "Only given for structures determined by NMR. The MolProbity Ramachandran outlier score\nfor all atoms in the structure rather than just the well-defined (core) residues.", "rcsb_description" : [ { "text" : "Only given for structures determined by NMR. The MolProbity Ramachandran outlier score\nfor all atoms in the structure rather than just the well-defined (core) residues.", "context" : "dictionary" } ] }, "percent_rotamer_outliers" : { "type" : "number", "description" : "The MolProbity sidechain outlier score (a percentage).\nProtein sidechains mostly adopt certain (combinations of) preferred torsion angle values \n(called rotamers or rotameric conformers), much like their backbone torsion angles \n(as assessed in the Ramachandran analysis). MolProbity considers the sidechain conformation \nof a residue to be an outlier if its set of torsion angles is not similar to any preferred \ncombination. The sidechain outlier score is calculated as the percentage of residues \nwith an unusual sidechain conformation with respect to the total number of residues for \nwhich the assessment is available.\nExample: percent-rota-outliers=\"2.44\".\nSpecific to structure that contain protein chains and have sidechains modelled.\nFor NMR structures only the well-defined (core) residues from ensemble analysis will be considered.\nThe percentage of residues with rotamer outliers.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The MolProbity sidechain outlier score (a percentage).\nProtein sidechains mostly adopt certain (combinations of) preferred torsion angle values \n(called rotamers or rotameric conformers), much like their backbone torsion angles \n(as assessed in the Ramachandran analysis). MolProbity considers the sidechain conformation \nof a residue to be an outlier if its set of torsion angles is not similar to any preferred \ncombination. The sidechain outlier score is calculated as the percentage of residues \nwith an unusual sidechain conformation with respect to the total number of residues for \nwhich the assessment is available.\nExample: percent-rota-outliers=\"2.44\".\nSpecific to structure that contain protein chains and have sidechains modelled.\nFor NMR structures only the well-defined (core) residues from ensemble analysis will be considered.\nThe percentage of residues with rotamer outliers.", "context" : "dictionary" }, { "text" : "Molprobity Percentage Rotamer Outliers", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Entry Features", "priority_order" : 120 } ], "rcsb_current_maximum_value" : 100.0, "rcsb_current_minimum_value" : 0.0 }, "percent_rotamer_outliers_full_length" : { "type" : "number", "description" : "Only given for structures determined by NMR. The MolProbity sidechain outlier score\nfor all atoms in the structure rather than just the well-defined (core) residues.", "rcsb_description" : [ { "text" : "Only given for structures determined by NMR. The MolProbity sidechain outlier score\nfor all atoms in the structure rather than just the well-defined (core) residues.", "context" : "dictionary" } ] } }, "additionalProperties" : false }, "minItems" : 1, "uniqueItems" : true }, "pdbx_vrpt_summary_nmr" : { "type" : "array", "items" : { "type" : "object", "properties" : { "chemical_shift_completeness" : { "type" : "number", "description" : "Overall completeness of the chemical shift assignments for the well-defined \nregions of the structure.", "rcsb_description" : [ { "text" : "Overall completeness of the chemical shift assignments for the well-defined \nregions of the structure.", "context" : "dictionary" } ] }, "chemical_shift_completeness_full_length" : { "type" : "number", "description" : "Overall completeness of the chemical shift assignments for the full \nmacromolecule or complex as suggested by the molecular description of an entry\n(whether some portion of it is modelled or not).", "rcsb_description" : [ { "text" : "Overall completeness of the chemical shift assignments for the full \nmacromolecule or complex as suggested by the molecular description of an entry\n(whether some portion of it is modelled or not).", "context" : "dictionary" } ] }, "cyrange_error" : { "type" : "string", "description" : "Diagnostic message from the wrapper of Cyrange software which identifies the \nwell-defined cores (domains) of NMR protein structures.", "rcsb_description" : [ { "text" : "Diagnostic message from the wrapper of Cyrange software which identifies the \nwell-defined cores (domains) of NMR protein structures.", "context" : "dictionary" } ] }, "cyrange_number_of_domains" : { "type" : "integer", "description" : "Total number of well-defined cores (domains) identified by Cyrange", "rcsb_description" : [ { "text" : "Total number of well-defined cores (domains) identified by Cyrange", "context" : "dictionary" } ] }, "exp_method" : { "type" : "string", "description" : "Experimental method for statistics", "rcsb_description" : [ { "text" : "Experimental method for statistics", "context" : "dictionary" } ] }, "medoid_model" : { "type" : "integer", "description" : "For each Cyrange well-defined core (\"cyrange_domain\") the id of the PDB_model_num which is most \nsimilar to other models as measured by pairwise RMSDs over the domain. \nFor the whole entry (\"Entry\"), the medoid PDB_model_num of the largest core is taken as an overall\nrepresentative of the structure.", "rcsb_description" : [ { "text" : "For each Cyrange well-defined core (\"cyrange_domain\") the id of the PDB_model_num which is most \nsimilar to other models as measured by pairwise RMSDs over the domain. \nFor the whole entry (\"Entry\"), the medoid PDB_model_num of the largest core is taken as an overall\nrepresentative of the structure.", "context" : "dictionary" } ] }, "nmr_models_consistency_flag" : { "type" : "string", "description" : "A flag indicating if all models in the NMR ensemble contain the exact \nsame atoms (\"True\") or if the models differ in this respect (\"False\").", "rcsb_description" : [ { "text" : "A flag indicating if all models in the NMR ensemble contain the exact \nsame atoms (\"True\") or if the models differ in this respect (\"False\").", "context" : "dictionary" } ] }, "nmrclust_error" : { "type" : "string", "description" : "Diagnostic message from the wrapper of NMRClust software which clusters NMR models.", "rcsb_description" : [ { "text" : "Diagnostic message from the wrapper of NMRClust software which clusters NMR models.", "context" : "dictionary" } ] }, "nmrclust_number_of_clusters" : { "type" : "integer", "description" : "Total number of clusters in the NMR ensemble identified by NMRClust.", "rcsb_description" : [ { "text" : "Total number of clusters in the NMR ensemble identified by NMRClust.", "context" : "dictionary" } ] }, "nmrclust_number_of_models" : { "type" : "integer", "description" : "Number of models analysed by NMRClust - should in almost all cases be the\nsame as the number of models in the NMR ensemble.", "rcsb_description" : [ { "text" : "Number of models analysed by NMRClust - should in almost all cases be the\nsame as the number of models in the NMR ensemble.", "context" : "dictionary" } ] }, "nmrclust_number_of_outliers" : { "type" : "integer", "description" : "Number of models that do not belong to any cluster as deemed by NMRClust.", "rcsb_description" : [ { "text" : "Number of models that do not belong to any cluster as deemed by NMRClust.", "context" : "dictionary" } ] }, "nmrclust_representative_model" : { "type" : "integer", "description" : "Overall representative PDB_model_num of the NMR ensemble as identified by NMRClust.", "rcsb_description" : [ { "text" : "Overall representative PDB_model_num of the NMR ensemble as identified by NMRClust.", "context" : "dictionary" } ] } }, "additionalProperties" : false }, "minItems" : 1, "uniqueItems" : true }, "rcsb_accession_info" : { "type" : "object", "properties" : { "deposit_date" : { "type" : "string", "format" : "date", "examples" : [ "2020-07-11", "2013-10-01" ], "description" : "The entry deposition date.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The entry deposition date.", "context" : "dictionary" }, { "text" : "Deposit Date", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Structure Details", "priority_order" : 20 } ], "rcsb_current_maximum_value" : 1.7834688E12, "rcsb_current_minimum_value" : 8.23392E10 }, "has_released_experimental_data" : { "type" : "string", "enum" : [ "N", "Y" ], "examples" : [ "Y", "N" ], "description" : "A code indicating the current availibility of experimental data in the repository.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "A code indicating the current availibility of experimental data in the repository.", "context" : "dictionary" }, { "text" : "Has Experimental Data", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Structure Details", "priority_order" : 50 } ] }, "initial_release_date" : { "type" : "string", "format" : "date", "examples" : [ "2020-01-10", "2018-01-23" ], "description" : "The entry initial release date.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The entry initial release date.", "context" : "dictionary" }, { "text" : "Release Date", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Structure Details", "priority_order" : 25 } ], "rcsb_current_maximum_value" : 1.7840736E12, "rcsb_current_minimum_value" : 2.01312E11 }, "major_revision" : { "type" : "integer", "description" : "The latest entry major revision number.", "rcsb_description" : [ { "text" : "The latest entry major revision number.", "context" : "dictionary" } ] }, "minor_revision" : { "type" : "integer", "description" : "The latest entry minor revision number.", "rcsb_description" : [ { "text" : "The latest entry minor revision number.", "context" : "dictionary" } ] }, "revision_date" : { "type" : "string", "format" : "date", "examples" : [ "2020-02-11", "2018-10-23" ], "description" : "The latest entry revision date.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The latest entry revision date.", "context" : "dictionary" }, { "text" : "Revision Date", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Structure Details", "priority_order" : 30 } ], "rcsb_current_maximum_value" : 1.7840736E12, "rcsb_current_minimum_value" : 1.4726016E12 }, "status_code" : { "type" : "string", "enum" : [ "AUCO", "AUTH", "HOLD", "HPUB", "POLC", "PROC", "REFI", "REL", "REPL", "WAIT", "WDRN" ], "examples" : [ "REL" ], "description" : "The release status for the entry.", "rcsb_description" : [ { "text" : "The release status for the entry.", "context" : "dictionary" } ] } }, "additionalProperties" : false }, "rcsb_binding_affinity" : { "type" : "array", "items" : { "type" : "object", "properties" : { "comp_id" : { "type" : "string", "examples" : [ "0WE", "SPE", "CL" ], "description" : "Ligand identifier.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Ligand identifier.", "context" : "dictionary" }, { "text" : "Comp Id (Binding Affinity)", "context" : "brief" } ] }, "link" : { "type" : "string", "description" : "Link to external resource referencing the data.", "rcsb_description" : [ { "text" : "Link to external resource referencing the data.", "context" : "dictionary" } ] }, "provenance_code" : { "type" : "string", "enum" : [ "Binding MOAD", "BindingDB", "PDBBind" ], "description" : "The resource name for the related binding affinity reference.", "rcsb_description" : [ { "text" : "The resource name for the related binding affinity reference.", "context" : "dictionary" } ] }, "reference_sequence_identity" : { "type" : "integer", "description" : "Data point provided by BindingDB. Percent identity between PDB sequence and reference sequence.", "rcsb_description" : [ { "text" : "Data point provided by BindingDB. Percent identity between PDB sequence and reference sequence.", "context" : "dictionary" } ] }, "symbol" : { "type" : "string", "examples" : [ "~", "=", ">", "<", ">=", "<=" ], "description" : "Binding affinity symbol indicating approximate or precise strength of the binding.", "rcsb_description" : [ { "text" : "Binding affinity symbol indicating approximate or precise strength of the binding.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "enum" : [ "ΔG", "ΔH", "-TΔS", "EC50", "IC50", "Ka", "Kd", "Ki" ], "examples" : [ "IC50", "EC50", "Kd", "Ka", "Ki" ], "description" : "Binding affinity measurement given in one of the following types: The concentration constants: IC50: the concentration of ligand that reduces enzyme activity by 50%; EC50: the concentration of compound that generates a half-maximal response; The binding constant: Kd: dissociation constant; Ka: association constant; Ki: enzyme inhibition constant; The thermodynamic parameters: delta G: Gibbs free energy of binding (for association reaction); delta H: change in enthalpy associated with a chemical reaction; delta S: change in entropy associated with a chemical reaction.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "ΔG", "detail" : "Gibbs free energy of binding (for association reaction)", "name" : "dG", "units" : "kilojoule_per_mole" }, { "value" : "ΔH", "detail" : "Change in enthalpy associated with a chemical reaction", "name" : "dH", "units" : "kilojoule_per_mole" }, { "value" : "-TΔS", "detail" : "Change in entropy associated with a chemical reaction", "name" : "-TdS", "units" : "kilojoule_per_mole" }, { "value" : "EC50", "detail" : "The concentration of compound that generates a half-maximal response", "name" : "EC50", "units" : "nanomole" }, { "value" : "IC50", "detail" : "The concentration of ligand that reduces enzyme activity by 50%", "name" : "IC50", "units" : "nanomole" }, { "value" : "Ka", "detail" : "Association constant", "name" : "Ka", "units" : "per_mole" }, { "value" : "Kd", "detail" : "Dissociation constant", "name" : "Kd", "units" : "nanomole" }, { "value" : "Ki", "detail" : "Enzyme inhibition constant", "name" : "Ki", "units" : "nanomole" } ], "rcsb_description" : [ { "text" : "Binding affinity measurement given in one of the following types: The concentration constants: IC50: the concentration of ligand that reduces enzyme activity by 50%; EC50: the concentration of compound that generates a half-maximal response; The binding constant: Kd: dissociation constant; Ka: association constant; Ki: enzyme inhibition constant; The thermodynamic parameters: delta G: Gibbs free energy of binding (for association reaction); delta H: change in enthalpy associated with a chemical reaction; delta S: change in entropy associated with a chemical reaction.", "context" : "dictionary" }, { "text" : "Binding Affinity Type", "context" : "brief" } ] }, "unit" : { "type" : "string", "examples" : [ "nM", "kJ/mol" ], "description" : "Binding affinity unit. Dissociation constant Kd is normally in molar units (or millimolar , micromolar, nanomolar, etc). Association constant Ka is normally expressed in inverse molar units (e.g. M-1).", "rcsb_description" : [ { "text" : "Binding affinity unit. Dissociation constant Kd is normally in molar units (or millimolar , micromolar, nanomolar, etc). Association constant Ka is normally expressed in inverse molar units (e.g. M-1).", "context" : "dictionary" } ] }, "value" : { "type" : "number", "description" : "Binding affinity value between a ligand and its target molecule.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Binding affinity value between a ligand and its target molecule.", "context" : "dictionary" }, { "text" : "Binding Affinity Value", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Nonpolymer Molecular Features", "priority_order" : 25 } ] } }, "additionalProperties" : false, "required" : [ "comp_id", "link", "provenance_code", "type", "unit", "value" ] }, "minItems" : 1, "uniqueItems" : true, "rcsb_nested_indexing" : true, "rcsb_nested_indexing_context" : [ { "category_name" : "binding_affinity_type", "category_path" : "rcsb_binding_affinity.type", "context_attributes" : [ { "context_value" : "IC50", "attributes" : [ { "examples" : [ 0.8, 14.0 ], "path" : "rcsb_binding_affinity.value", "rcsb_current_minimum_value" : 0.0, "rcsb_current_maximum_value" : 5.0E8 } ] }, { "context_value" : "EC50", "attributes" : [ { "examples" : [ 0.18, 23000.0 ], "path" : "rcsb_binding_affinity.value", "rcsb_current_minimum_value" : 0.006000000052154064, "rcsb_current_maximum_value" : 5.0E7 } ] }, { "context_value" : "Kd", "attributes" : [ { "examples" : [ 6.5, 220000.0 ], "path" : "rcsb_binding_affinity.value", "rcsb_current_minimum_value" : 0.0, "rcsb_current_maximum_value" : 2.62E7 } ] }, { "context_value" : "Ka", "attributes" : [ { "examples" : [ 7.5, 1700.0 ], "path" : "rcsb_binding_affinity.value" } ] }, { "context_value" : "Ki", "attributes" : [ { "examples" : [ 4.0, 390000.0 ], "path" : "rcsb_binding_affinity.value", "rcsb_current_minimum_value" : 7.999999797903001E-4, "rcsb_current_maximum_value" : 3.0E8 } ] }, { "context_value" : "ΔG", "attributes" : [ { "examples" : [ 17.2, 21.4 ], "path" : "rcsb_binding_affinity.value", "rcsb_current_minimum_value" : -123.00959777832031, "rcsb_current_maximum_value" : 1683.699951171875 } ] }, { "context_value" : "ΔH", "attributes" : [ { "examples" : [ 66.9, 123.0 ], "path" : "rcsb_binding_affinity.value" } ] }, { "context_value" : "-TΔS", "attributes" : [ { "examples" : [ 18.1, 47.2 ], "path" : "rcsb_binding_affinity.value" } ] } ] } ] }, "rcsb_comp_model_provenance" : { "type" : "object", "properties" : { "entry_id" : { "type" : "string", "examples" : [ "AF-P60325-F1", "ma-bak-cepc-0019" ], "description" : "Entry identifier corresponding to the computed structure model.", "rcsb_search_context" : [ "exact-match", "suggest" ], "rcsb_full_text_priority" : 20, "rcsb_description" : [ { "text" : "Entry identifier corresponding to the computed structure model.", "context" : "dictionary" }, { "text" : "Computed Structure Model ID(s)", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Computed Structure Model Details", "priority_order" : 5 } ] }, "source_db" : { "type" : "string", "enum" : [ "AlphaFoldDB", "ModelArchive" ], "description" : "Source database for the computed structure model.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "AlphaFoldDB", "detail" : "AlphaFoldDB" }, { "value" : "ModelArchive", "detail" : "ModelArchive" } ], "rcsb_description" : [ { "text" : "Source database for the computed structure model.", "context" : "dictionary" }, { "text" : "Source Database", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Computed Structure Model Details", "priority_order" : 10 } ] }, "source_filename" : { "type" : "string", "description" : "Source filename for the computed structure model.", "rcsb_description" : [ { "text" : "Source filename for the computed structure model.", "context" : "dictionary" } ] }, "source_pae_url" : { "type" : "string", "description" : "Source URL for computed structure model predicted aligned error (PAE) json file.", "rcsb_description" : [ { "text" : "Source URL for computed structure model predicted aligned error (PAE) json file.", "context" : "dictionary" } ] }, "source_url" : { "type" : "string", "description" : "Source URL for computed structure model file.", "rcsb_description" : [ { "text" : "Source URL for computed structure model file.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "entry_id" ] }, "rcsb_entry_container_identifiers" : { "type" : "object", "properties" : { "assembly_ids" : { "type" : "array", "items" : { "type" : "string", "description" : "List of identifiers for assemblies generated from the entry.", "rcsb_description" : [ { "text" : "List of identifiers for assemblies generated from the entry.", "context" : "dictionary" } ] }, "uniqueItems" : false }, "branched_entity_ids" : { "type" : "array", "items" : { "type" : "string", "description" : "List of identifiers for the branched entity constituents for the entry.", "rcsb_description" : [ { "text" : "List of identifiers for the branched entity constituents for the entry.", "context" : "dictionary" } ] }, "uniqueItems" : false }, "emdb_ids" : { "type" : "array", "items" : { "type" : "string", "examples" : [ "EMD-21578", "EMD-30168" ], "description" : "List of EMDB identifiers for the 3D electron microscopy density maps\n used in the production of the structure model.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "List of EMDB identifiers for the 3D electron microscopy density maps\n used in the production of the structure model.", "context" : "dictionary" }, { "text" : "EMDB ID(s) for Maps Used in Structure Modeling", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "ID(s) and Keywords", "priority_order" : 35 } ] }, "uniqueItems" : false }, "entity_ids" : { "type" : "array", "items" : { "type" : "string", "description" : "List of identifiers or the entity constituents for the entry.", "rcsb_description" : [ { "text" : "List of identifiers or the entity constituents for the entry.", "context" : "dictionary" } ] }, "uniqueItems" : false }, "entry_id" : { "type" : "string", "examples" : [ "4HHB", "AF_AFP60325F1", "MA_MABAKCEPC0019" ], "description" : "Entry identifier for the container.", "rcsb_search_context" : [ "exact-match", "suggest" ], "rcsb_full_text_priority" : 20, "rcsb_description" : [ { "text" : "Entry identifier for the container.", "context" : "dictionary" }, { "text" : "Entry ID(s)", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "ID(s) and Keywords", "priority_order" : 5 } ] }, "model_ids" : { "type" : "array", "items" : { "type" : "integer", "description" : "List of PDB model identifiers for the entry.", "rcsb_description" : [ { "text" : "List of PDB model identifiers for the entry.", "context" : "dictionary" } ] }, "uniqueItems" : false }, "non_polymer_entity_ids" : { "type" : "array", "items" : { "type" : "string", "description" : "List of identifiers for the non-polymer entity constituents for the entry.", "rcsb_description" : [ { "text" : "List of identifiers for the non-polymer entity constituents for the entry.", "context" : "dictionary" } ] }, "uniqueItems" : false }, "polymer_entity_ids" : { "type" : "array", "items" : { "type" : "string", "description" : "List of identifiers for the polymer entity constituents for the entry.", "rcsb_description" : [ { "text" : "List of identifiers for the polymer entity constituents for the entry.", "context" : "dictionary" } ] }, "uniqueItems" : false }, "pubmed_id" : { "type" : "integer", "description" : "Unique integer value assigned to each PubMed record.", "rcsb_description" : [ { "text" : "Unique integer value assigned to each PubMed record.", "context" : "dictionary" } ] }, "rcsb_id" : { "type" : "string", "examples" : [ "1KIP" ], "description" : "A unique identifier for each object in this entry container.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "A unique identifier for each object in this entry container.", "context" : "dictionary" }, { "text" : "Id (Entry Container Identifiers)", "context" : "brief" } ] }, "related_emdb_ids" : { "type" : "array", "items" : { "type" : "string", "examples" : [ "EMD-21578", "EMD-30168" ], "description" : "List of EMDB identifiers for the 3D electron microscopy density maps\n related to the structure model.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "List of EMDB identifiers for the 3D electron microscopy density maps\n related to the structure model.", "context" : "dictionary" }, { "text" : "EMDB ID(s) for Related Maps", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "ID(s) and Keywords", "priority_order" : 40 } ] }, "uniqueItems" : false }, "water_entity_ids" : { "type" : "array", "items" : { "type" : "string", "description" : "List of identifiers for the solvent/water entity constituents for the entry.", "rcsb_description" : [ { "text" : "List of identifiers for the solvent/water entity constituents for the entry.", "context" : "dictionary" } ] }, "uniqueItems" : false } }, "additionalProperties" : false, "required" : [ "entry_id" ] }, "rcsb_entry_group_membership" : { "type" : "array", "items" : { "type" : "object", "properties" : { "aggregation_method" : { "type" : "string", "enum" : [ "matching_deposit_group_id" ], "description" : "Method used to establish group membership", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Method used to establish group membership", "context" : "dictionary" }, { "text" : "Aggregation Method (Entry Group Membership)", "context" : "brief" } ] }, "group_id" : { "type" : "string", "examples" : [ "G_1001001" ], "description" : "A unique identifier for a group of entries", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "A unique identifier for a group of entries", "context" : "dictionary" }, { "text" : "Entry Group ID(s)", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "ID(s) and Keywords", "priority_order" : 60 } ] } }, "additionalProperties" : false, "required" : [ "aggregation_method", "group_id" ] }, "minItems" : 1, "uniqueItems" : true, "rcsb_nested_indexing" : true }, "rcsb_entry_info" : { "type" : "object", "properties" : { "assembly_count" : { "type" : "integer", "description" : "The number of assemblies defined for this entry including the deposited assembly.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of assemblies defined for this entry including the deposited assembly.", "context" : "dictionary" }, { "text" : "Number of Assemblies", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Entry Features", "priority_order" : 20 } ], "rcsb_current_maximum_value" : 44.0, "rcsb_current_minimum_value" : 1.0 }, "branched_entity_count" : { "type" : "integer", "description" : "The number of distinct branched entities in the structure entry.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of distinct branched entities in the structure entry.", "context" : "dictionary" }, { "text" : "Branched Entity Count (Entry Info)", "context" : "brief" } ], "rcsb_current_maximum_value" : 22.0, "rcsb_current_minimum_value" : 0.0 }, "branched_molecular_weight_maximum" : { "type" : "number", "examples" : [ 0.4, 1.2 ], "description" : "The maximum molecular mass (KDa) of a branched entity in the deposited structure entry.", "rcsb_units" : "kilodaltons", "rcsb_description" : [ { "text" : "The maximum molecular mass (KDa) of a branched entity in the deposited structure entry.", "context" : "dictionary" } ] }, "branched_molecular_weight_minimum" : { "type" : "number", "examples" : [ 0.4, 1.2 ], "description" : "The minimum molecular mass (KDa) of a branched entity in the deposited structure entry.", "rcsb_units" : "kilodaltons", "rcsb_description" : [ { "text" : "The minimum molecular mass (KDa) of a branched entity in the deposited structure entry.", "context" : "dictionary" } ] }, "cis_peptide_count" : { "type" : "integer", "description" : "The number of cis-peptide linkages per deposited structure model.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of cis-peptide linkages per deposited structure model.", "context" : "dictionary" }, { "text" : "Cis Peptide Count (Entry Info)", "context" : "brief" } ], "rcsb_current_maximum_value" : 1320.0, "rcsb_current_minimum_value" : 0.0 }, "deposited_atom_count" : { "type" : "integer", "description" : "The number of heavy atom coordinates records per deposited structure model.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of heavy atom coordinates records per deposited structure model.", "context" : "dictionary" }, { "text" : "Number of Non-Hydrogen Atoms per Deposited Model", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Entry Features", "priority_order" : 70 } ], "rcsb_current_maximum_value" : 4527463.0, "rcsb_current_minimum_value" : 28.0 }, "deposited_deuterated_water_count" : { "type" : "integer", "description" : "The number of deuterated water molecules per deposited structure model.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of deuterated water molecules per deposited structure model.", "context" : "dictionary" }, { "text" : "Number of Deuterated Water Molecules per Deposited Model", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Entry Features", "priority_order" : 85 } ], "rcsb_current_maximum_value" : 1114.0, "rcsb_current_minimum_value" : 0.0 }, "deposited_hydrogen_atom_count" : { "type" : "integer", "description" : "The number of hydrogen atom coordinates records per deposited structure model.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of hydrogen atom coordinates records per deposited structure model.", "context" : "dictionary" }, { "text" : "Number of Hydrogen Atoms per Deposited Model", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Entry Features", "priority_order" : 75 } ], "rcsb_current_maximum_value" : 680778.0, "rcsb_current_minimum_value" : 0.0 }, "deposited_model_count" : { "type" : "integer", "description" : "The number of model structures deposited.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of model structures deposited.", "context" : "dictionary" }, { "text" : "Deposited Model Count", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Entry Features", "priority_order" : 90 } ], "rcsb_current_maximum_value" : 1012.0, "rcsb_current_minimum_value" : 1.0 }, "deposited_modeled_polymer_monomer_count" : { "type" : "integer", "description" : "The number of modeled polymer monomers in the deposited coordinate data.\n This is the total count of monomers with reported coordinate data for all polymer\n entity instances in the deposited coordinate data.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of modeled polymer monomers in the deposited coordinate data.\n This is the total count of monomers with reported coordinate data for all polymer\n entity instances in the deposited coordinate data.", "context" : "dictionary" }, { "text" : "Deposited Modeled Polymer Monomer Count (Entry Info)", "context" : "brief" } ], "rcsb_current_maximum_value" : 566508.0, "rcsb_current_minimum_value" : 0.0 }, "deposited_nonpolymer_entity_instance_count" : { "type" : "integer", "description" : "The number of non-polymer instances in the deposited data set.\n This is the total count of non-polymer entity instances reported\n per deposited structure model.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of non-polymer instances in the deposited data set.\n This is the total count of non-polymer entity instances reported\n per deposited structure model.", "context" : "dictionary" }, { "text" : "Total Number of Non-polymer Instances", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Entry Features", "priority_order" : 60 } ], "rcsb_current_maximum_value" : 5351.0, "rcsb_current_minimum_value" : 0.0 }, "deposited_polymer_entity_instance_count" : { "type" : "integer", "description" : "The number of polymer instances in the deposited data set.\n This is the total count of polymer entity instances reported\n per deposited structure model.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of polymer instances in the deposited data set.\n This is the total count of polymer entity instances reported\n per deposited structure model.", "context" : "dictionary" }, { "text" : "Total Number of Polymer Instances (Chains)", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Entry Features", "priority_order" : 55 } ], "rcsb_current_maximum_value" : 1996.0, "rcsb_current_minimum_value" : 0.0 }, "deposited_polymer_monomer_count" : { "type" : "integer", "description" : "The number of polymer monomers in sample entity instances in the deposited data set.\n This is the total count of monomers for all polymer entity instances reported\n per deposited structure model.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of polymer monomers in sample entity instances in the deposited data set.\n This is the total count of monomers for all polymer entity instances reported\n per deposited structure model.", "context" : "dictionary" }, { "text" : "Total Number of Polymer Residues per Deposited Model", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Entry Features", "priority_order" : 65 } ], "rcsb_current_maximum_value" : 761922.0, "rcsb_current_minimum_value" : 0.0 }, "deposited_solvent_atom_count" : { "type" : "integer", "description" : "The number of heavy solvent atom coordinates records per deposited structure model.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of heavy solvent atom coordinates records per deposited structure model.", "context" : "dictionary" }, { "text" : "Number of Water Molecules per Deposited Model", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Entry Features", "priority_order" : 80 } ], "rcsb_current_maximum_value" : 21388.0, "rcsb_current_minimum_value" : 0.0 }, "deposited_unmodeled_polymer_monomer_count" : { "type" : "integer", "description" : "The number of unmodeled polymer monomers in the deposited coordinate data. This is\n the total count of monomers with unreported coordinate data for all polymer\n entity instances per deposited structure model.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of unmodeled polymer monomers in the deposited coordinate data. This is\n the total count of monomers with unreported coordinate data for all polymer\n entity instances per deposited structure model.", "context" : "dictionary" }, { "text" : "Deposited Unmodeled Polymer Monomer Count (Entry Info)", "context" : "brief" } ], "rcsb_current_maximum_value" : 195414.0, "rcsb_current_minimum_value" : 0.0 }, "diffrn_radiation_wavelength_maximum" : { "type" : "number", "description" : "The maximum radiation wavelength in angstroms.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "The maximum radiation wavelength in angstroms.", "context" : "dictionary" }, { "text" : "Maximum Diffraction Wavelength", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "X-ray Data Collection Details", "priority_order" : 65 } ], "rcsb_current_maximum_value" : 12.812, "rcsb_current_minimum_value" : 0.0 }, "diffrn_radiation_wavelength_minimum" : { "type" : "number", "description" : "The minimum radiation wavelength in angstroms.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "The minimum radiation wavelength in angstroms.", "context" : "dictionary" }, { "text" : "Minimum Diffraction Wavelength", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "X-ray Data Collection Details", "priority_order" : 60 } ], "rcsb_current_maximum_value" : 12.812, "rcsb_current_minimum_value" : 0.0 }, "disulfide_bond_count" : { "type" : "integer", "description" : "The number of disulfide bonds per deposited structure model.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of disulfide bonds per deposited structure model.", "context" : "dictionary" }, { "text" : "Disulfide Bond Count per Deposited Model", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Entry Features", "priority_order" : 95 } ], "rcsb_current_maximum_value" : 1356.0, "rcsb_current_minimum_value" : 0.0 }, "entity_count" : { "type" : "integer", "description" : "The number of distinct polymer, non-polymer, branched molecular, and solvent entities per deposited structure model.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of distinct polymer, non-polymer, branched molecular, and solvent entities per deposited structure model.", "context" : "dictionary" }, { "text" : "Number of Distinct Molecular Entities", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Entry Features", "priority_order" : 25 } ], "rcsb_current_maximum_value" : 455.0, "rcsb_current_minimum_value" : 1.0 }, "experimental_method" : { "type" : "string", "enum" : [ "EM", "Integrative", "Multiple methods", "NMR", "Neutron", "Other", "X-ray" ], "examples" : [ "X-ray" ], "description" : "The category of experimental method(s) used to determine the structure entry.", "rcsb_search_context" : [ "exact-match", "suggest" ], "rcsb_full_text_priority" : 20, "rcsb_enum_annotated" : [ { "value" : "EM", "detail" : "ELECTRON MICROSCOPY or ELECTRON CRYSTALLOGRAPHY or ELECTRON TOMOGRAPHY" }, { "value" : "Integrative", "detail" : "Integrative methods" }, { "value" : "Multiple methods", "detail" : "Multiple experimental methods" }, { "value" : "NMR", "detail" : "SOLUTION NMR or SOLID-STATE NMR" }, { "value" : "Neutron", "detail" : "NEUTRON DIFFRACTION" }, { "value" : "Other", "detail" : "SOLUTION SCATTERING, EPR, INFRARED SPECTROSCOPY or FLUORESCENCE TRANSFER" }, { "value" : "X-ray", "detail" : "X-RAY DIFFRACTION, FIBER DIFFRACTION, or POWDER DIFFRACTION" } ], "rcsb_description" : [ { "text" : "The category of experimental method(s) used to determine the structure entry.", "context" : "dictionary" }, { "text" : "Experimental Method (Broader Categories)", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Methods", "priority_order" : 5 } ] }, "experimental_method_count" : { "type" : "integer", "description" : "The number of experimental methods contributing data to the structure determination.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of experimental methods contributing data to the structure determination.", "context" : "dictionary" }, { "text" : "Number of Experimental Methods", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Methods", "priority_order" : 15 } ], "rcsb_current_maximum_value" : 6.0, "rcsb_current_minimum_value" : 1.0 }, "ihm_multi_scale_flag" : { "type" : "string", "enum" : [ "N", "Y" ], "description" : "Multi-scale modeling flag for integrative structures.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Multi-scale modeling flag for integrative structures.", "context" : "dictionary" }, { "text" : "IHM Multi-Scale Flag", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Integrative/Hybrid Method Details", "priority_order" : 5 } ] }, "ihm_multi_state_flag" : { "type" : "string", "enum" : [ "N", "Y" ], "description" : "Multi-state modeling flag for integrative structures.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Multi-state modeling flag for integrative structures.", "context" : "dictionary" }, { "text" : "IHM Multi-State Flag", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Integrative/Hybrid Method Details", "priority_order" : 10 } ] }, "ihm_ordered_state_flag" : { "type" : "string", "enum" : [ "N", "Y" ], "description" : "Ordered-state modeling flag for integrative structures.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Ordered-state modeling flag for integrative structures.", "context" : "dictionary" }, { "text" : "IHM Ordered-State Flag", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Integrative/Hybrid Method Details", "priority_order" : 15 } ] }, "ihm_structure_description" : { "type" : "string", "description" : "Description of the integrative structure.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Description of the integrative structure.", "context" : "dictionary" }, { "text" : "Ihm Structure Description (Entry Info)", "context" : "brief" } ] }, "inter_mol_covalent_bond_count" : { "type" : "integer", "description" : "The number of intermolecular covalent bonds.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of intermolecular covalent bonds.", "context" : "dictionary" }, { "text" : "Inter Mol Covalent Bond Count (Entry Info)", "context" : "brief" } ], "rcsb_current_maximum_value" : 3559.0, "rcsb_current_minimum_value" : 0.0 }, "inter_mol_metalic_bond_count" : { "type" : "integer", "description" : "The number of intermolecular metalic bonds.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of intermolecular metalic bonds.", "context" : "dictionary" }, { "text" : "Inter Mol Metalic Bond Count (Entry Info)", "context" : "brief" } ], "rcsb_current_maximum_value" : 11045.0, "rcsb_current_minimum_value" : 0.0 }, "molecular_weight" : { "type" : "number", "examples" : [ 33.43, 45.53 ], "description" : "The molecular mass (KDa) of polymer and non-polymer entities (exclusive of solvent) in the deposited structure entry.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "kilodaltons", "rcsb_description" : [ { "text" : "The molecular mass (KDa) of polymer and non-polymer entities (exclusive of solvent) in the deposited structure entry.", "context" : "dictionary" }, { "text" : "Molecular Weight per Deposited Model", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Entry Features", "priority_order" : 15 } ], "rcsb_current_maximum_value" : 86760.19, "rcsb_current_minimum_value" : 0.0 }, "na_polymer_entity_types" : { "type" : "string", "enum" : [ "DNA (only)", "DNA/RNA (only)", "NA-hybrid (only)", "Other", "RNA (only)" ], "examples" : [ "DNA (only)" ], "description" : "Nucleic acid polymer entity type categories describing the entry.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "DNA (only)", "detail" : "DNA entity/entities only" }, { "value" : "DNA/RNA (only)", "detail" : "Both DNA and RNA polymer entities" }, { "value" : "NA-hybrid (only)", "detail" : "NA-hybrid entity/entities only" }, { "value" : "Other", "detail" : "Another polymer type composition" }, { "value" : "RNA (only)", "detail" : "RNA entity/entities only" } ], "rcsb_description" : [ { "text" : "Nucleic acid polymer entity type categories describing the entry.", "context" : "dictionary" }, { "text" : "Na Polymer Entity Types (Entry Info)", "context" : "brief" } ] }, "ndb_struct_conf_na_feature_combined" : { "type" : "array", "items" : { "type" : "string", "enum" : [ "a-form double helix", "b-form double helix", "bulge loop", "double helix", "four-way junction", "hairpin loop", "internal loop", "mismatched base pair", "other right-handed double helix", "parallel strands", "quadruple helix", "tetraloop", "three-way junction", "triple helix", "two-way junction", "z-form double helix" ], "examples" : [ "four-way junction" ], "description" : "This data item identifies secondary structure\n features of nucleic acids in the entry.", "rcsb_description" : [ { "text" : "This data item identifies secondary structure\n features of nucleic acids in the entry.", "context" : "dictionary" } ] }, "uniqueItems" : false }, "nonpolymer_bound_components" : { "type" : "array", "items" : { "type" : "string", "description" : "Bound nonpolymer components in this entry.", "rcsb_description" : [ { "text" : "Bound nonpolymer components in this entry.", "context" : "dictionary" } ] }, "uniqueItems" : false }, "nonpolymer_entity_count" : { "type" : "integer", "description" : "The number of distinct non-polymer entities in the structure entry exclusive of solvent.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of distinct non-polymer entities in the structure entry exclusive of solvent.", "context" : "dictionary" }, { "text" : "Number of Distinct Non-polymer Entities", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Entry Features", "priority_order" : 30 } ], "rcsb_current_maximum_value" : 30.0, "rcsb_current_minimum_value" : 0.0 }, "nonpolymer_molecular_weight_maximum" : { "type" : "number", "examples" : [ 0.43, 0.91 ], "description" : "The maximum molecular mass (KDa) of a non-polymer entity in the deposited structure entry.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "kilodaltons", "rcsb_description" : [ { "text" : "The maximum molecular mass (KDa) of a non-polymer entity in the deposited structure entry.", "context" : "dictionary" }, { "text" : "Nonpolymer Molecular Weight Maximum (Entry Info)", "context" : "brief" } ], "rcsb_current_maximum_value" : 12.02, "rcsb_current_minimum_value" : 0.0 }, "nonpolymer_molecular_weight_minimum" : { "type" : "number", "examples" : [ 0.07, 0.12 ], "description" : "The minimum molecular mass (KDa) of a non-polymer entity in the deposited structure entry.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "kilodaltons", "rcsb_description" : [ { "text" : "The minimum molecular mass (KDa) of a non-polymer entity in the deposited structure entry.", "context" : "dictionary" }, { "text" : "Nonpolymer Molecular Weight Minimum (Entry Info)", "context" : "brief" } ], "rcsb_current_maximum_value" : 12.02, "rcsb_current_minimum_value" : 0.0 }, "polymer_composition" : { "type" : "string", "enum" : [ "DNA", "DNA/RNA", "NA-hybrid", "NA/oligosaccharide", "RNA", "heteromeric protein", "homomeric protein", "oligosaccharide", "other", "other type composition", "other type pair", "protein/NA", "protein/NA/oligosaccharide", "protein/oligosaccharide" ], "examples" : [ "homomeric protein" ], "description" : "Categories describing the polymer entity composition for the entry.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "DNA", "detail" : "DNA entity/entities only" }, { "value" : "DNA/RNA", "detail" : "Both DNA and RNA polymer entities" }, { "value" : "NA-hybrid", "detail" : "DNA/RNA hybrid entity/entities only" }, { "value" : "NA/oligosaccharide", "detail" : "Both NA and oligosaccharide entities" }, { "value" : "RNA", "detail" : "RNA entity/entities only" }, { "value" : "heteromeric protein", "detail" : "multiple protein entities" }, { "value" : "homomeric protein", "detail" : "single protein entity" }, { "value" : "oligosaccharide", "detail" : "One of more oligosaccharide entities" }, { "value" : "other", "detail" : "Neither an individual protein, nucleic acid polymer nor oligosaccharide entity" }, { "value" : "other type composition", "detail" : "Other combinations of 3 or more polymer types" }, { "value" : "other type pair", "detail" : "Other combinations of 2 polymer types" }, { "value" : "protein/NA", "detail" : "Both protein and nucleic acid polymer entities" }, { "value" : "protein/NA/oligosaccharide", "detail" : "Protein, nucleic acid, and oligosaccharide entities" }, { "value" : "protein/oligosaccharide", "detail" : "Both protein and oligosaccharide entities" } ], "rcsb_description" : [ { "text" : "Categories describing the polymer entity composition for the entry.", "context" : "dictionary" }, { "text" : "Entry Polymer Composition", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Entry Features", "priority_order" : 10 } ] }, "polymer_entity_count" : { "type" : "integer", "description" : "The number of distinct polymer entities in the structure entry.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of distinct polymer entities in the structure entry.", "context" : "dictionary" }, { "text" : "Polymer Entity Count (Entry Info)", "context" : "brief" } ], "rcsb_current_maximum_value" : 455.0, "rcsb_current_minimum_value" : 0.0 }, "polymer_entity_count_DNA" : { "type" : "integer", "description" : "The number of distinct DNA polymer entities.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of distinct DNA polymer entities.", "context" : "dictionary" }, { "text" : "Number of Distinct DNA Entities", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Entry Features", "priority_order" : 45 } ], "rcsb_current_maximum_value" : 455.0, "rcsb_current_minimum_value" : 0.0 }, "polymer_entity_count_RNA" : { "type" : "integer", "description" : "The number of distinct RNA polymer entities.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of distinct RNA polymer entities.", "context" : "dictionary" }, { "text" : "Number of Distinct RNA Entities", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Entry Features", "priority_order" : 40 } ], "rcsb_current_maximum_value" : 36.0, "rcsb_current_minimum_value" : 0.0 }, "polymer_entity_count_nucleic_acid" : { "type" : "integer", "description" : "The number of distinct nucleic acid polymer entities (DNA or RNA).", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of distinct nucleic acid polymer entities (DNA or RNA).", "context" : "dictionary" }, { "text" : "Polymer Entity Count Nucleic Acid (Entry Info)", "context" : "brief" } ], "rcsb_current_maximum_value" : 455.0, "rcsb_current_minimum_value" : 0.0 }, "polymer_entity_count_nucleic_acid_hybrid" : { "type" : "integer", "description" : "The number of distinct hybrid nucleic acid polymer entities.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of distinct hybrid nucleic acid polymer entities.", "context" : "dictionary" }, { "text" : "Number of Distinct NA Hybrid Entities", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Entry Features", "priority_order" : 50 } ], "rcsb_current_maximum_value" : 3.0, "rcsb_current_minimum_value" : 0.0 }, "polymer_entity_count_protein" : { "type" : "integer", "description" : "The number of distinct protein polymer entities.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of distinct protein polymer entities.", "context" : "dictionary" }, { "text" : "Number of Distinct Protein Entities", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Entry Features", "priority_order" : 35 } ], "rcsb_current_maximum_value" : 165.0, "rcsb_current_minimum_value" : 0.0 }, "polymer_entity_taxonomy_count" : { "type" : "integer", "description" : "The number of distinct taxonomies represented among the polymer entities in the entry.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of distinct taxonomies represented among the polymer entities in the entry.", "context" : "dictionary" }, { "text" : "Total Polymer Entity Taxonomy Count", "context" : "brief" } ], "rcsb_current_maximum_value" : 455.0, "rcsb_current_minimum_value" : 0.0 }, "polymer_molecular_weight_maximum" : { "type" : "number", "examples" : [ 33.43, 45.53 ], "description" : "The maximum molecular mass (KDa) of a polymer entity in the deposited structure entry.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "kilodaltons", "rcsb_description" : [ { "text" : "The maximum molecular mass (KDa) of a polymer entity in the deposited structure entry.", "context" : "dictionary" }, { "text" : "Polymer Molecular Weight Maximum (Entry Info)", "context" : "brief" } ], "rcsb_current_maximum_value" : 13596.14, "rcsb_current_minimum_value" : 0.18 }, "polymer_molecular_weight_minimum" : { "type" : "number", "examples" : [ 33.43, 45.53 ], "description" : "The minimum molecular mass (KDa) of a polymer entity in the deposited structure entry.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "kilodaltons", "rcsb_description" : [ { "text" : "The minimum molecular mass (KDa) of a polymer entity in the deposited structure entry.", "context" : "dictionary" }, { "text" : "Polymer Molecular Weight Minimum (Entry Info)", "context" : "brief" } ], "rcsb_current_maximum_value" : 1222.87, "rcsb_current_minimum_value" : 0.08 }, "polymer_monomer_count_maximum" : { "type" : "integer", "description" : "The maximum monomer count of a polymer entity per deposited structure model.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The maximum monomer count of a polymer entity per deposited structure model.", "context" : "dictionary" }, { "text" : "Polymer Monomer Count Maximum (Entry Info)", "context" : "brief" } ], "rcsb_current_maximum_value" : 43864.0, "rcsb_current_minimum_value" : 2.0 }, "polymer_monomer_count_minimum" : { "type" : "integer", "description" : "The minimum monomer count of a polymer entity per deposited structure model.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The minimum monomer count of a polymer entity per deposited structure model.", "context" : "dictionary" }, { "text" : "Polymer Monomer Count Minimum (Entry Info)", "context" : "brief" } ], "rcsb_current_maximum_value" : 5898.0, "rcsb_current_minimum_value" : 1.0 }, "representative_model" : { "type" : "integer", "description" : "The chosen representative model.", "rcsb_description" : [ { "text" : "The chosen representative model.", "context" : "dictionary" } ] }, "resolution_combined" : { "type" : "array", "items" : { "type" : "number", "examples" : [ 1.11, 2.05 ], "description" : "Combined estimates of experimental resolution contributing to the refined structural model.\n Resolution reported in \"refine.ls_d_res_high\" is used for X-RAY DIFFRACTION, FIBER DIFFRACTION, \n POWDER DIFFRACTION, ELECTRON CRYSTALLOGRAPHY, and NEUTRON DIFFRACTION as identified in\n \"refine.pdbx_refine_id\". \n Resolution reported in \"em_3d_reconstruction.resolution\" is used for ELECTRON MICROSCOPY. \n The best value corresponding to \"em_3d_reconstruction.resolution_method\" == \"FSC 0.143 CUT-OFF\" \n is used, if available. If not, the best \"em_3d_reconstruction.resolution\" value is used. \n For structures that are not obtained from diffraction-based methods, the resolution values in \n \"refine.ls_d_res_high\" are ignored.\n Multiple values are reported only if multiple methods are used in the structure determination.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "Combined estimates of experimental resolution contributing to the refined structural model.\n Resolution reported in \"refine.ls_d_res_high\" is used for X-RAY DIFFRACTION, FIBER DIFFRACTION, \n POWDER DIFFRACTION, ELECTRON CRYSTALLOGRAPHY, and NEUTRON DIFFRACTION as identified in\n \"refine.pdbx_refine_id\". \n Resolution reported in \"em_3d_reconstruction.resolution\" is used for ELECTRON MICROSCOPY. \n The best value corresponding to \"em_3d_reconstruction.resolution_method\" == \"FSC 0.143 CUT-OFF\" \n is used, if available. If not, the best \"em_3d_reconstruction.resolution\" value is used. \n For structures that are not obtained from diffraction-based methods, the resolution values in \n \"refine.ls_d_res_high\" are ignored.\n Multiple values are reported only if multiple methods are used in the structure determination.", "context" : "dictionary" }, { "text" : "Refinement Resolution", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Methods", "priority_order" : 20 } ], "rcsb_current_maximum_value" : 70.0, "rcsb_current_minimum_value" : 0.48 }, "uniqueItems" : false }, "selected_polymer_entity_types" : { "type" : "string", "enum" : [ "Nucleic acid (only)", "Oligosaccharide (only)", "Other", "Protein (only)", "Protein/NA", "Protein/Oligosaccharide" ], "examples" : [ "Protein (only)" ], "description" : "Selected polymer entity type categories describing the entry.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "Nucleic acid (only)", "detail" : "Nucleic acid (DNA, RNA, NA-hybrid entity/entities only" }, { "value" : "Oligosaccharide (only)", "detail" : "oligosaccharide/branched polymer entities only" }, { "value" : "Other", "detail" : "Another polymer type composition" }, { "value" : "Protein (only)", "detail" : "protein entity/entities only" }, { "value" : "Protein/NA", "detail" : "Both protein and nucleic acid (DNA or RNA) polymer entities" }, { "value" : "Protein/Oligosaccharide", "detail" : "Both protein and oligosaccharide/branched polymer entities" } ], "rcsb_description" : [ { "text" : "Selected polymer entity type categories describing the entry.", "context" : "dictionary" }, { "text" : "Entry Polymer Types", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Entry Features", "priority_order" : 5 } ] }, "software_programs_combined" : { "type" : "array", "items" : { "type" : "string", "examples" : [ "PHASER", "PHENIX", "REFMAC" ], "description" : "Combined list of software programs names reported in connection with the production of this entry.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Combined list of software programs names reported in connection with the production of this entry.", "context" : "dictionary" }, { "text" : "Software", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Methods", "priority_order" : 25 } ] }, "uniqueItems" : false }, "solvent_entity_count" : { "type" : "integer", "description" : "The number of distinct solvent entities per deposited structure model.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of distinct solvent entities per deposited structure model.", "context" : "dictionary" }, { "text" : "Number of Distinct Solvent Entities", "context" : "brief" } ], "rcsb_current_maximum_value" : 1.0, "rcsb_current_minimum_value" : 0.0 }, "structure_determination_methodology" : { "type" : "string", "enum" : [ "computational", "experimental", "integrative" ], "examples" : [ "experimental" ], "description" : "Indicates if the structure was determined using experimental or computational methods.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "computational", "detail" : "Computational modeling" }, { "value" : "experimental", "detail" : "Experimentally based structure determination" }, { "value" : "integrative", "detail" : "Integrative/Hybrid methods" } ], "rcsb_description" : [ { "text" : "Indicates if the structure was determined using experimental or computational methods.", "context" : "dictionary" }, { "text" : "Structure Determination Methodology", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Structure Details", "priority_order" : 90 } ] }, "structure_determination_methodology_priority" : { "type" : "integer", "description" : "Indicates the priority of the value in _rcsb_entry_info.structure_determination_methodology.\n The lower the number the higher the priority.\n Priority values for \"experimental\" structures is currently set to 10 and\n the values for \"computational\" structures is set to 100.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Indicates the priority of the value in _rcsb_entry_info.structure_determination_methodology.\n The lower the number the higher the priority.\n Priority values for \"experimental\" structures is currently set to 10 and\n the values for \"computational\" structures is set to 100.", "context" : "dictionary" }, { "text" : "Structure Determination Methodology Priority (Entry Info)", "context" : "brief" } ], "rcsb_current_maximum_value" : 100.0, "rcsb_current_minimum_value" : 10.0 }, "diffrn_resolution_high" : { "type" : "object", "properties" : { "provenance_source" : { "type" : "string", "enum" : [ "Depositor assigned", "From refinement resolution cutoff", "From the high resolution shell" ], "description" : "The provenence source for the high resolution limit of data collection.", "rcsb_enum_annotated" : [ { "value" : "Depositor assigned", "detail" : "Depositor assigned resolution limit" }, { "value" : "From refinement resolution cutoff", "detail" : "No data collection resolution limit specified, inferred from refinement cutoff" }, { "value" : "From the high resolution shell", "detail" : "Depositor assigned resolution limit for high resolution shell" } ], "rcsb_description" : [ { "text" : "The provenence source for the high resolution limit of data collection.", "context" : "dictionary" } ] }, "value" : { "type" : "number", "description" : "The high resolution limit of data collection.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "The high resolution limit of data collection.", "context" : "dictionary" }, { "text" : "Data Collection Resolution", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "X-ray Data Collection Details", "priority_order" : 5 } ], "rcsb_current_maximum_value" : 15.0, "rcsb_current_minimum_value" : 0.48 } }, "additionalProperties" : false } }, "additionalProperties" : false, "required" : [ "structure_determination_methodology" ] }, "rcsb_external_references" : { "type" : "array", "items" : { "type" : "object", "properties" : { "id" : { "type" : "string", "examples" : [ "1BMR" ], "description" : "ID (accession) from external resource linked to this entry.", "rcsb_description" : [ { "text" : "ID (accession) from external resource linked to this entry.", "context" : "dictionary" } ] }, "link" : { "type" : "string", "description" : "Link to this entry in external resource", "rcsb_description" : [ { "text" : "Link to this entry in external resource", "context" : "dictionary" } ] }, "type" : { "type" : "string", "enum" : [ "BMRB", "EM DATA RESOURCE", "NAKB", "NDB", "OLDERADO", "PROTEIN DIFFRACTION", "SB GRID" ], "examples" : [ "OLDERADO" ], "description" : "Internal identifier for external resources", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "BMRB", "detail" : "A Repository for data from NMR spectroscopy on proteins, peptides, nucleic acids, and other biomolecules", "name" : "BMRB" }, { "value" : "EM DATA RESOURCE", "detail" : "Global resource for 3-dimensional Electron Microscopy (3DEM) structure data", "name" : "EMDataResource" }, { "value" : "NAKB", "detail" : "Three-dimensional structural information about nucleic acids", "name" : "NAKB" }, { "value" : "NDB", "detail" : "Three-dimensional structural information about nucleic acids", "name" : "NDB" }, { "value" : "OLDERADO", "detail" : "OLDERADO provides analysis of clustering and domain composition for NMR structure ensembles", "name" : "OLDERADO" }, { "value" : "PROTEIN DIFFRACTION", "detail" : "Integrated resource for reproducibility in macromolecular crystallography", "name" : "Protein Diffraction" }, { "value" : "SB GRID", "detail" : "Supports publication of X-ray diffraction, MicroED, LLSM datasets, as well as structural models", "name" : "SBGrid" } ], "rcsb_description" : [ { "text" : "Internal identifier for external resources", "context" : "dictionary" }, { "text" : "Experimental Data Resource", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Linked External Resources", "priority_order" : 5 } ] } }, "additionalProperties" : false, "required" : [ "id", "type" ] }, "minItems" : 1, "uniqueItems" : true }, "rcsb_ihm_dataset_list" : { "type" : "array", "items" : { "type" : "object", "properties" : { "count" : { "type" : "integer", "description" : "Number of input datasets used in integrative modeling.", "rcsb_description" : [ { "text" : "Number of input datasets used in integrative modeling.", "context" : "dictionary" } ] }, "name" : { "type" : "string", "enum" : [ "2DEM class average", "3DEM volume", "CX-MS data", "Comparative model", "Crosslinking-MS data", "DNA footprinting data", "De Novo model", "EM raw micrographs", "EPR data", "Ensemble FRET data", "Experimental model", "H/D exchange data", "Hydroxyl radical footprinting data", "Integrative model", "Mass Spectrometry data", "Mutagenesis data", "NMR data", "Other", "Predicted contacts", "Quantitative measurements of genetic interactions", "SAS data", "Single molecule FRET data", "X-ray diffraction data", "Yeast two-hybrid screening data" ], "description" : "Name of input dataset used in integrative modeling.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Name of input dataset used in integrative modeling.", "context" : "dictionary" }, { "text" : "IHM Dataset Name", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Integrative/Hybrid Method Details", "priority_order" : 20 } ] }, "type" : { "type" : "string", "enum" : [ "Computed restraints", "Experimental data", "Other", "Starting model" ], "description" : "Type of input dataset used in integrative modeling.", "rcsb_description" : [ { "text" : "Type of input dataset used in integrative modeling.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "name" ] }, "minItems" : 1, "uniqueItems" : true }, "rcsb_ihm_dataset_source_db_reference" : { "type" : "array", "items" : { "type" : "object", "properties" : { "accession_code" : { "type" : "string", "examples" : [ "5FM1", "EMD-2799", "SASDA82", "PXD003381", "MA-CO2KC" ], "description" : "Accession code for the input dataset.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Accession code for the input dataset.", "context" : "dictionary" }, { "text" : "IHM Dataset Source DB Accession Code", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Integrative/Hybrid Method Details", "priority_order" : 25 } ] }, "db_name" : { "type" : "string", "enum" : [ "AlphaFoldDB", "BMRB", "BMRbig", "BioGRID", "EMDB", "EMPIAR", "MASSIVE", "ModelArchive", "Other", "PDB", "PDB-Dev", "PRIDE", "ProXL", "ProteomeXchange", "SASBDB", "iProX", "jPOSTrepo" ], "description" : "Name of the source database for the input dataset.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "AlphaFoldDB", "detail" : "AlphaFold Protein Structure Database", "name" : "AlphaFoldDB" }, { "value" : "BMRB", "detail" : "Biological Magnetic Resonance Bank", "name" : "BMRB" }, { "value" : "BMRbig", "detail" : "Biological Magnetic Resonance Bank BMRbig Project", "name" : "BMRbig" }, { "value" : "BioGRID", "detail" : "Biological General Repository for Interaction Datasets", "name" : "BioGRID" }, { "value" : "EMDB", "detail" : "Electron Microscopy Data Bank", "name" : "EMDB" }, { "value" : "EMPIAR", "detail" : "Electron Microscopy Public Image Archive", "name" : "EMPIAR" }, { "value" : "MASSIVE", "detail" : "Mass Spectrometry Interactive Virtual Environment", "name" : "MASSIVE" }, { "value" : "ModelArchive", "detail" : "ModelArchive Repository for Computed Structure Models", "name" : "ModelArchive" }, { "value" : "Other", "detail" : "Other type of database", "name" : "Other" }, { "value" : "PDB", "detail" : "Protein Data Bank", "name" : "PDB" }, { "value" : "PDB-Dev", "detail" : "PDB prototype repository for integrative structures", "name" : "PDB-Dev" }, { "value" : "PRIDE", "detail" : "Proteomics Identification Database", "name" : "PRIDE" }, { "value" : "ProXL", "detail" : "Protein Cross-linking Database", "name" : "ProXL" }, { "value" : "ProteomeXchange", "detail" : "ProteomeXchange Consortium", "name" : "ProteomeXchange" }, { "value" : "SASBDB", "detail" : "Small Angle Scattering Biological Data Bank", "name" : "SASBDB" }, { "value" : "iProX", "detail" : "Integrated Proteome Resource Center", "name" : "iProX" }, { "value" : "jPOSTrepo", "detail" : "Japan Proteome Standard Repository", "name" : "jPOSTrepo" } ], "rcsb_description" : [ { "text" : "Name of the source database for the input dataset.", "context" : "dictionary" }, { "text" : "IHM Dataset Source DB Name", "context" : "brief" } ] } }, "additionalProperties" : false, "required" : [ "accession_code", "db_name" ] }, "minItems" : 1, "uniqueItems" : true, "rcsb_nested_indexing" : true, "rcsb_nested_indexing_context" : [ { "category_name" : "source_database_name", "category_path" : "rcsb_ihm_dataset_source_db_reference.db_name", "context_attributes" : [ { "context_value" : "PDB", "attributes" : [ { "examples" : [ "5FM1", "7CKA" ], "path" : "rcsb_ihm_dataset_source_db_reference.accession_code" } ] }, { "context_value" : "BMRB", "attributes" : [ { "examples" : [ "27171", "27600" ], "path" : "rcsb_ihm_dataset_source_db_reference.accession_code" } ] }, { "context_value" : "EMDB", "attributes" : [ { "examples" : [ "EMD-2634", "EMD-7321" ], "path" : "rcsb_ihm_dataset_source_db_reference.accession_code" } ] }, { "context_value" : "EMPIAR", "attributes" : [ { "examples" : [ "EMPIAR-10155", "EMPIAR-10162" ], "path" : "rcsb_ihm_dataset_source_db_reference.accession_code" } ] }, { "context_value" : "SASBDB", "attributes" : [ { "examples" : [ "SASDKU3", "SASDBX9" ], "path" : "rcsb_ihm_dataset_source_db_reference.accession_code" } ] }, { "context_value" : "PRIDE", "attributes" : [ { "examples" : [ "PXD012723", "PXD016595" ], "path" : "rcsb_ihm_dataset_source_db_reference.accession_code" } ] }, { "context_value" : "ProteomeXchange", "attributes" : [ { "examples" : [ "PXD032818" ], "path" : "rcsb_ihm_dataset_source_db_reference.accession_code" } ] }, { "context_value" : "ModelArchive", "attributes" : [ { "examples" : [ "ma-fejd6", "ma-2chon" ], "path" : "rcsb_ihm_dataset_source_db_reference.accession_code" } ] }, { "context_value" : "AlphaFoldDB", "attributes" : [ { "examples" : [ "AF-Q12445-F1", "AF-Q6P0N0-F1" ], "path" : "rcsb_ihm_dataset_source_db_reference.accession_code" } ] }, { "context_value" : "MASSIVE", "attributes" : [ { "examples" : [ "MSV000079237", "MSV000084311" ], "path" : "rcsb_ihm_dataset_source_db_reference.accession_code" } ] }, { "context_value" : "ProXL", "attributes" : [ { "examples" : [ "RJAZ180", "RJAZ110" ], "path" : "rcsb_ihm_dataset_source_db_reference.accession_code" } ] }, { "context_value" : "jPOSTrepo", "attributes" : [ { "examples" : [ "JPST001851" ], "path" : "rcsb_ihm_dataset_source_db_reference.accession_code" } ] }, { "context_value" : "iProX", "attributes" : [ { "examples" : [ "IPX0004576001" ], "path" : "rcsb_ihm_dataset_source_db_reference.accession_code" } ] }, { "context_value" : "BMRbig", "attributes" : [ { "examples" : [ "bmrbig94", "bmrbig101" ], "path" : "rcsb_ihm_dataset_source_db_reference.accession_code" } ] } ] } ] }, "rcsb_ma_qa_metric_global" : { "type" : "array", "items" : { "type" : "object", "properties" : { "model_id" : { "type" : "integer", "description" : "The model identifier.", "rcsb_description" : [ { "text" : "The model identifier.", "context" : "dictionary" } ] }, "ma_qa_metric_global" : { "type" : "array", "items" : { "type" : "object", "properties" : { "description" : { "type" : "string", "examples" : [ "confidence score predicting accuracy according to the CA-only Local Distance Difference Test (lDDT-CA) in [0,100]" ], "description" : "Description of the global QA metric.", "rcsb_description" : [ { "text" : "Description of the global QA metric.", "context" : "dictionary" } ] }, "name" : { "type" : "string", "examples" : [ "pLDDT" ], "description" : "Name of the global QA metric.", "rcsb_description" : [ { "text" : "Name of the global QA metric.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "enum" : [ "PAE", "contact probability", "distance", "energy", "ipTM", "normalized score", "other", "pLDDT", "pLDDT all-atom", "pLDDT all-atom in [0,1]", "pLDDT in [0,1]", "pTM", "zscore" ], "examples" : [ "pLDDT" ], "description" : "The type of global QA metric.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "PAE", "detail" : "predicted aligned error (in Angstroms)" }, { "value" : "contact probability", "detail" : "the contact probability of a pairwise interaction" }, { "value" : "distance", "detail" : "the lower the distance, the better the quality" }, { "value" : "energy", "detail" : "the lower the energy, the better the quality" }, { "value" : "ipTM", "detail" : "confidence score of protein-protein interface based on the template modeling score in [0,1]" }, { "value" : "normalized score", "detail" : "normalized score ranging from 0 to 1" }, { "value" : "other", "detail" : "other type of QA metric" }, { "value" : "pLDDT", "detail" : "confidence score predicting accuracy according to the CA-only Local Distance Difference Test (lDDT-CA) in [0,100]" }, { "value" : "pLDDT all-atom", "detail" : "confidence score predicting accuracy according to the all-atom Local Distance Difference Test (lDDT) in [0,100]" }, { "value" : "pLDDT all-atom in [0,1]", "detail" : "confidence score predicting accuracy according to the all-atom Local Distance Difference Test (lDDT) in [0,1]" }, { "value" : "pLDDT in [0,1]", "detail" : "confidence score predicting accuracy according to the CA-only Local Distance Difference Test (lDDT-CA) in [0,1]" }, { "value" : "pTM", "detail" : "confidence score predicting accuracy according to the template modeling score in [0,1]" }, { "value" : "zscore", "detail" : "number of standard deviations from optimal/best" } ], "rcsb_description" : [ { "text" : "The type of global QA metric.", "context" : "dictionary" }, { "text" : "Type (Ma Qa Metric Global)", "context" : "brief" } ] }, "type_other_details" : { "type" : "string", "description" : "Details for other type of global QA metric.", "rcsb_description" : [ { "text" : "Details for other type of global QA metric.", "context" : "dictionary" } ] }, "value" : { "type" : "number", "examples" : [ 81.23 ], "description" : "Value of the global QA metric.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Value of the global QA metric.", "context" : "dictionary" }, { "text" : "Global Quality Score", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Computed Structure Model Details", "priority_order" : 15 } ] } }, "additionalProperties" : false, "required" : [ "name", "type", "value" ] }, "uniqueItems" : false, "rcsb_nested_indexing" : true, "rcsb_nested_indexing_context" : [ { "category_name" : "ma_qa_metric_global", "category_path" : "rcsb_ma_qa_metric_global.ma_qa_metric_global.type", "context_attributes" : [ { "context_value" : "pLDDT", "attributes" : [ { "examples" : [ 83.02, 29.14 ], "path" : "rcsb_ma_qa_metric_global.ma_qa_metric_global.value", "rcsb_current_minimum_value" : 23.42, "rcsb_current_maximum_value" : 98.75 } ] } ] } ] } }, "additionalProperties" : false, "required" : [ "model_id" ] }, "minItems" : 1, "uniqueItems" : true }, "rcsb_primary_citation" : { "type" : "object", "properties" : { "book_id_ISBN" : { "type" : "string", "description" : "The International Standard Book Number (ISBN) code assigned to\n the book cited; relevant for books or book chapters.", "rcsb_description" : [ { "text" : "The International Standard Book Number (ISBN) code assigned to\n the book cited; relevant for books or book chapters.", "context" : "dictionary" } ] }, "book_publisher" : { "type" : "string", "examples" : [ "John Wiley and Sons" ], "description" : "The name of the publisher of the citation; relevant\n for books or book chapters.", "rcsb_description" : [ { "text" : "The name of the publisher of the citation; relevant\n for books or book chapters.", "context" : "dictionary" } ] }, "book_publisher_city" : { "type" : "string", "examples" : [ "London" ], "description" : "The location of the publisher of the citation; relevant\n for books or book chapters.", "rcsb_description" : [ { "text" : "The location of the publisher of the citation; relevant\n for books or book chapters.", "context" : "dictionary" } ] }, "book_title" : { "type" : "string", "description" : "The title of the book in which the citation appeared; relevant\n for books or book chapters.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The title of the book in which the citation appeared; relevant\n for books or book chapters.", "context" : "dictionary" }, { "text" : "Book Title (Primary Citation)", "context" : "brief" } ] }, "coordinate_linkage" : { "type" : "string", "enum" : [ "n", "no", "y", "yes" ], "description" : "_rcsb_primary_citation.coordinate_linkage states whether this citation\n is concerned with precisely the set of coordinates given in the\n data block. If, for instance, the publication described the same\n structure, but the coordinates had undergone further refinement\n prior to the creation of the data block, the value of this data\n item would be 'no'.", "rcsb_enum_annotated" : [ { "value" : "n", "detail" : "abbreviation for \"no\"" }, { "value" : "no", "detail" : "citation unrelated to current coordinates" }, { "value" : "y", "detail" : "abbreviation for \"yes\"" }, { "value" : "yes", "detail" : "citation related to current coordinates" } ], "rcsb_description" : [ { "text" : "_rcsb_primary_citation.coordinate_linkage states whether this citation\n is concerned with precisely the set of coordinates given in the\n data block. If, for instance, the publication described the same\n structure, but the coordinates had undergone further refinement\n prior to the creation of the data block, the value of this data\n item would be 'no'.", "context" : "dictionary" } ] }, "country" : { "type" : "string", "description" : "The country/region of publication; relevant for books\n and book chapters.", "rcsb_description" : [ { "text" : "The country/region of publication; relevant for books\n and book chapters.", "context" : "dictionary" } ] }, "id" : { "type" : "string", "examples" : [ "primary" ], "description" : "The value of _rcsb_primary_citation.id must uniquely identify a record in the\n CITATION list.\n\n The _rcsb_primary_citation.id 'primary' should be used to indicate the\n citation that the author(s) consider to be the most pertinent to\n the contents of the data block.\n\n Note that this item need not be a number; it can be any unique\n identifier.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The value of _rcsb_primary_citation.id must uniquely identify a record in the\n CITATION list.\n\n The _rcsb_primary_citation.id 'primary' should be used to indicate the\n citation that the author(s) consider to be the most pertinent to\n the contents of the data block.\n\n Note that this item need not be a number; it can be any unique\n identifier.", "context" : "dictionary" }, { "text" : "Id (Primary Citation)", "context" : "brief" } ] }, "journal_abbrev" : { "type" : "string", "examples" : [ "J.Mol.Biol.", "J. Mol. Biol." ], "description" : "Abbreviated name of the cited journal as given in the\n Chemical Abstracts Service Source Index.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Abbreviated name of the cited journal as given in the\n Chemical Abstracts Service Source Index.", "context" : "dictionary" }, { "text" : "The PDB (i.e., the Chemical Abstracts) abbreviation for a journal. If you do not know the abbreviation, then give the complete name of the journal and we will try and find it for you. If it is a book or other monographic work, state the full title.", "context" : "deposition" }, { "text" : "Primary Citation Journal Name", "context" : "brief" } ] }, "journal_id_ASTM" : { "type" : "string", "description" : "The American Society for Testing and Materials (ASTM) code\n assigned to the journal cited (also referred to as the CODEN\n designator of the Chemical Abstracts Service); relevant for\n journal articles.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The American Society for Testing and Materials (ASTM) code\n assigned to the journal cited (also referred to as the CODEN\n designator of the Chemical Abstracts Service); relevant for\n journal articles.", "context" : "dictionary" }, { "text" : "Journal Id Astm (Primary Citation)", "context" : "brief" } ] }, "journal_id_CSD" : { "type" : "string", "examples" : [ "0070" ], "description" : "The Cambridge Structural Database (CSD) code assigned to the\n journal cited; relevant for journal articles. This is also the\n system used at the Protein Data Bank (PDB).", "rcsb_description" : [ { "text" : "The Cambridge Structural Database (CSD) code assigned to the\n journal cited; relevant for journal articles. This is also the\n system used at the Protein Data Bank (PDB).", "context" : "dictionary" } ] }, "journal_id_ISSN" : { "type" : "string", "description" : "The International Standard Serial Number (ISSN) code assigned to\n the journal cited; relevant for journal articles.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The International Standard Serial Number (ISSN) code assigned to\n the journal cited; relevant for journal articles.", "context" : "dictionary" }, { "text" : "Journal Id Issn (Primary Citation)", "context" : "brief" } ] }, "journal_issue" : { "type" : "string", "examples" : [ "2" ], "description" : "Issue number of the journal cited; relevant for journal\n articles.", "rcsb_description" : [ { "text" : "Issue number of the journal cited; relevant for journal\n articles.", "context" : "dictionary" } ] }, "journal_volume" : { "type" : "string", "examples" : [ "174" ], "description" : "Volume number of the journal cited; relevant for journal\n articles.", "rcsb_description" : [ { "text" : "Volume number of the journal cited; relevant for journal\n articles.", "context" : "dictionary" }, { "text" : "The volume number of the journal in which the article appeared. Example: 317", "context" : "deposition" } ] }, "language" : { "type" : "string", "examples" : [ "German" ], "description" : "Language in which the cited article is written.", "rcsb_description" : [ { "text" : "Language in which the cited article is written.", "context" : "dictionary" } ] }, "page_first" : { "type" : "string", "description" : "The first page of the citation; relevant for journal\n articles, books and book chapters.", "rcsb_description" : [ { "text" : "The first page of the citation; relevant for journal\n articles, books and book chapters.", "context" : "dictionary" }, { "text" : "The starting page number of this article.", "context" : "deposition" } ] }, "page_last" : { "type" : "string", "description" : "The last page of the citation; relevant for journal\n articles, books and book chapters.", "rcsb_description" : [ { "text" : "The last page of the citation; relevant for journal\n articles, books and book chapters.", "context" : "dictionary" }, { "text" : "The last page number of this article.", "context" : "deposition" } ] }, "pdbx_database_id_DOI" : { "type" : "string", "examples" : [ "10.2345/S1384107697000225" ], "description" : "Document Object Identifier used by doi.org to uniquely\n specify bibliographic entry.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Document Object Identifier used by doi.org to uniquely\n specify bibliographic entry.", "context" : "dictionary" }, { "text" : "The document Object Identifier used by doi.org to uniquely specify bibliographic entry", "context" : "deposition" }, { "text" : "Primary Citation DOI", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Publications Primary", "priority_order" : 25 } ] }, "pdbx_database_id_PubMed" : { "type" : "integer", "description" : "Ascession number used by PubMed to categorize a specific\n bibliographic entry.", "rcsb_description" : [ { "text" : "Ascession number used by PubMed to categorize a specific\n bibliographic entry.", "context" : "dictionary" }, { "text" : "The accession number used by PubMed to categorize a specific bibliographic entry", "context" : "deposition" } ] }, "rcsb_ORCID_identifiers" : { "type" : "array", "items" : { "type" : "string", "examples" : [ "0000-0002-6681-547X" ], "description" : "The Open Researcher and Contributor ID (ORCID) identifiers for the citation authors.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The Open Researcher and Contributor ID (ORCID) identifiers for the citation authors.", "context" : "dictionary" }, { "text" : "Primary Citation Author ORCID", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Publications Primary", "priority_order" : 30 } ] }, "uniqueItems" : false }, "rcsb_authors" : { "type" : "array", "items" : { "type" : "string", "examples" : [ "Bleary, Percival R." ], "description" : "Names of the authors of the citation; relevant for journal\n articles, books and book chapters. Names are separated by vertical bars.\n\n The family name(s), followed by a comma and including any\n dynastic components, precedes the first name(s) or initial(s).", "rcsb_search_context" : [ "exact-match", "full-text", "suggest" ], "rcsb_full_text_priority" : 20, "rcsb_description" : [ { "text" : "Names of the authors of the citation; relevant for journal\n articles, books and book chapters. Names are separated by vertical bars.\n\n The family name(s), followed by a comma and including any\n dynastic components, precedes the first name(s) or initial(s).", "context" : "dictionary" }, { "text" : "Primary Citation Author", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Publications Primary", "priority_order" : 5 } ] }, "uniqueItems" : false }, "rcsb_journal_abbrev" : { "type" : "string", "examples" : [ "Nat Struct Mol Biol" ], "description" : "Normalized journal abbreviation.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Normalized journal abbreviation.", "context" : "dictionary" }, { "text" : "Primary Citation Journal Name (Abbreviated)", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Publications Primary", "priority_order" : 15 } ] }, "title" : { "type" : "string", "examples" : [ "Structure of diferric duck ovotransferrin\n at 2.35 Angstroms resolution." ], "description" : "The title of the citation; relevant for journal articles, books\n and book chapters.", "rcsb_search_context" : [ "full-text", "suggest" ], "rcsb_full_text_priority" : 20, "rcsb_description" : [ { "text" : "The title of the citation; relevant for journal articles, books\n and book chapters.", "context" : "dictionary" }, { "text" : "Title of the article or chapter or part of a book. This should be marked NULL if the author(s) listed wrote the entire book (or other work) and no sub-section of the book is being cited. Example: The Structure of Crystalline Profilin-Beta-Actin", "context" : "deposition" }, { "text" : "Primary Citation Title", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Publications Primary", "priority_order" : 10 } ] }, "year" : { "type" : "integer", "description" : "The year of the citation; relevant for journal articles, books\n and book chapters.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The year of the citation; relevant for journal articles, books\n and book chapters.", "context" : "dictionary" }, { "text" : "The year of publication of the article. Example: 2002", "context" : "deposition" }, { "text" : "Primary Citation Publication Year", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Publications Primary", "priority_order" : 20 } ], "rcsb_current_maximum_value" : 2026.0, "rcsb_current_minimum_value" : 1969.0 } }, "additionalProperties" : false, "required" : [ "id" ] }, "refine" : { "type" : "array", "items" : { "type" : "object", "properties" : { "B_iso_max" : { "type" : "number", "description" : "The maximum isotropic displacement parameter (B value)\n found in the coordinate set.", "rcsb_units" : "angstroms_squared", "rcsb_description" : [ { "text" : "The maximum isotropic displacement parameter (B value)\n found in the coordinate set.", "context" : "dictionary" } ] }, "B_iso_mean" : { "type" : "number", "description" : "The mean isotropic displacement parameter (B value)\n for the coordinate set.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "angstroms_squared", "rcsb_description" : [ { "text" : "The mean isotropic displacement parameter (B value)\n for the coordinate set.", "context" : "dictionary" }, { "text" : "The mean isotropic displacement parameter (B value) for the coordinate set", "context" : "deposition" }, { "text" : "Average B Factor", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "X-ray Method Details", "priority_order" : 10 } ], "rcsb_current_maximum_value" : 1274.1, "rcsb_current_minimum_value" : -13.7642 }, "B_iso_min" : { "type" : "number", "description" : "The minimum isotropic displacement parameter (B value)\n found in the coordinate set.", "rcsb_units" : "angstroms_squared", "rcsb_description" : [ { "text" : "The minimum isotropic displacement parameter (B value)\n found in the coordinate set.", "context" : "dictionary" } ] }, "aniso_B_1_1" : { "type" : "number", "description" : "The [1][1] element of the matrix that defines the overall\n anisotropic displacement model if one was refined for this\n structure.", "rcsb_units" : "angstroms_squared", "rcsb_description" : [ { "text" : "The [1][1] element of the matrix that defines the overall\n anisotropic displacement model if one was refined for this\n structure.", "context" : "dictionary" }, { "text" : "The [1][1] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure", "context" : "deposition" } ] }, "aniso_B_1_2" : { "type" : "number", "description" : "The [1][2] element of the matrix that defines the overall\n anisotropic displacement model if one was refined for this\n structure.", "rcsb_units" : "angstroms_squared", "rcsb_description" : [ { "text" : "The [1][2] element of the matrix that defines the overall\n anisotropic displacement model if one was refined for this\n structure.", "context" : "dictionary" } ] }, "aniso_B_1_3" : { "type" : "number", "description" : "The [1][3] element of the matrix that defines the overall\n anisotropic displacement model if one was refined for this\n structure.", "rcsb_units" : "angstroms_squared", "rcsb_description" : [ { "text" : "The [1][3] element of the matrix that defines the overall\n anisotropic displacement model if one was refined for this\n structure.", "context" : "dictionary" }, { "text" : "The [1][3] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure", "context" : "deposition" } ] }, "aniso_B_2_2" : { "type" : "number", "description" : "The [2][2] element of the matrix that defines the overall\n anisotropic displacement model if one was refined for this\n structure.", "rcsb_units" : "angstroms_squared", "rcsb_description" : [ { "text" : "The [2][2] element of the matrix that defines the overall\n anisotropic displacement model if one was refined for this\n structure.", "context" : "dictionary" }, { "text" : "The [2][2] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure", "context" : "deposition" } ] }, "aniso_B_2_3" : { "type" : "number", "description" : "The [2][3] element of the matrix that defines the overall\n anisotropic displacement model if one was refined for this\n structure.", "rcsb_units" : "angstroms_squared", "rcsb_description" : [ { "text" : "The [2][3] element of the matrix that defines the overall\n anisotropic displacement model if one was refined for this\n structure.", "context" : "dictionary" }, { "text" : "The [2][3] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure", "context" : "deposition" } ] }, "aniso_B_3_3" : { "type" : "number", "description" : "The [3][3] element of the matrix that defines the overall\n anisotropic displacement model if one was refined for this\n structure.", "rcsb_units" : "angstroms_squared", "rcsb_description" : [ { "text" : "The [3][3] element of the matrix that defines the overall\n anisotropic displacement model if one was refined for this\n structure.", "context" : "dictionary" }, { "text" : "The [3][3] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure", "context" : "deposition" } ] }, "correlation_coeff_Fo_to_Fc" : { "type" : "number", "description" : "The correlation coefficient between the observed and\n calculated structure factors for reflections included in\n the refinement.\n\n The correlation coefficient is scale-independent and gives\n an idea of the quality of the refined model.\n\n sum~i~(Fo~i~ Fc~i~ - )\nR~corr~ = ------------------------------------------------------------\n SQRT{sum~i~(Fo~i~)^2^-^2^} SQRT{sum~i~(Fc~i~)^2^-^2^}\n\n Fo = observed structure factors\n Fc = calculated structure factors\n <> denotes average value\n\n summation is over reflections included in the refinement", "rcsb_description" : [ { "text" : "The correlation coefficient between the observed and\n calculated structure factors for reflections included in\n the refinement.\n\n The correlation coefficient is scale-independent and gives\n an idea of the quality of the refined model.\n\n sum~i~(Fo~i~ Fc~i~ - )\nR~corr~ = ------------------------------------------------------------\n SQRT{sum~i~(Fo~i~)^2^-^2^} SQRT{sum~i~(Fc~i~)^2^-^2^}\n\n Fo = observed structure factors\n Fc = calculated structure factors\n <> denotes average value\n\n summation is over reflections included in the refinement", "context" : "dictionary" } ] }, "correlation_coeff_Fo_to_Fc_free" : { "type" : "number", "description" : "The correlation coefficient between the observed and\n calculated structure factors for reflections not included\n in the refinement (free reflections).\n\n The correlation coefficient is scale-independent and gives\n an idea of the quality of the refined model.\n\n sum~i~(Fo~i~ Fc~i~ - )\nR~corr~ = ------------------------------------------------------------\n SQRT{sum~i~(Fo~i~)^2^-^2^} SQRT{sum~i~(Fc~i~)^2^-^2^}\n\n Fo = observed structure factors\n Fc = calculated structure factors\n <> denotes average value\n\n summation is over reflections not included\n in the refinement (free reflections)", "rcsb_description" : [ { "text" : "The correlation coefficient between the observed and\n calculated structure factors for reflections not included\n in the refinement (free reflections).\n\n The correlation coefficient is scale-independent and gives\n an idea of the quality of the refined model.\n\n sum~i~(Fo~i~ Fc~i~ - )\nR~corr~ = ------------------------------------------------------------\n SQRT{sum~i~(Fo~i~)^2^-^2^} SQRT{sum~i~(Fc~i~)^2^-^2^}\n\n Fo = observed structure factors\n Fc = calculated structure factors\n <> denotes average value\n\n summation is over reflections not included\n in the refinement (free reflections)", "context" : "dictionary" } ] }, "details" : { "type" : "string", "examples" : [ "HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS" ], "description" : "Description of special aspects of the refinement process.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Description of special aspects of the refinement process.", "context" : "dictionary" }, { "text" : "Description of special aspects of the refinement process", "context" : "deposition" }, { "text" : "Structure Refinement Details", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "X-ray Method Details", "priority_order" : 35 } ] }, "ls_R_factor_R_free" : { "type" : "number", "description" : "Residual factor R for reflections that satisfy the resolution\n limits established by _refine.ls_d_res_high and\n _refine.ls_d_res_low and the observation limit established by\n _reflns.observed_criterion, and that were used as the test\n reflections (i.e. were excluded from the refinement) when the\n refinement included the calculation of a 'free' R factor.\n Details of how reflections were assigned to the working and\n test sets are given in _reflns.R_free_details.\n\n sum|F~obs~ - F~calc~|\n R = ---------------------\n sum|F~obs~|\n\n F~obs~ = the observed structure-factor amplitudes\n F~calc~ = the calculated structure-factor amplitudes\n\n sum is taken over the specified reflections", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Residual factor R for reflections that satisfy the resolution\n limits established by _refine.ls_d_res_high and\n _refine.ls_d_res_low and the observation limit established by\n _reflns.observed_criterion, and that were used as the test\n reflections (i.e. were excluded from the refinement) when the\n refinement included the calculation of a 'free' R factor.\n Details of how reflections were assigned to the working and\n test sets are given in _reflns.R_free_details.\n\n sum|F~obs~ - F~calc~|\n R = ---------------------\n sum|F~obs~|\n\n F~obs~ = the observed structure-factor amplitudes\n F~calc~ = the calculated structure-factor amplitudes\n\n sum is taken over the specified reflections", "context" : "dictionary" }, { "text" : "Sum(abs((abs(F-obs)-abs(F-calc)))/Sum(abs(F-obs)) on pre-allocated cross-validation testing data that were not used in structure solution process", "context" : "deposition" }, { "text" : "Refinement R Factors (R Free)", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "X-ray Method Details", "priority_order" : 30 } ], "rcsb_current_maximum_value" : 0.5568, "rcsb_current_minimum_value" : 0.04439 }, "ls_R_factor_R_free_error" : { "type" : "number", "description" : "The estimated error in _refine.ls_R_factor_R_free.\n The method used to estimate the error is described in the\n item _refine.ls_R_factor_R_free_error_details.", "rcsb_description" : [ { "text" : "The estimated error in _refine.ls_R_factor_R_free.\n The method used to estimate the error is described in the\n item _refine.ls_R_factor_R_free_error_details.", "context" : "dictionary" }, { "text" : "The estimated error of R-free", "context" : "deposition" } ] }, "ls_R_factor_R_free_error_details" : { "type" : "string", "description" : "Special aspects of the method used to estimated the error in\n _refine.ls_R_factor_R_free.", "rcsb_description" : [ { "text" : "Special aspects of the method used to estimated the error in\n _refine.ls_R_factor_R_free.", "context" : "dictionary" } ] }, "ls_R_factor_R_work" : { "type" : "number", "description" : "Residual factor R for reflections that satisfy the resolution\n limits established by _refine.ls_d_res_high and\n _refine.ls_d_res_low and the observation limit established by\n _reflns.observed_criterion, and that were used as the working\n reflections (i.e. were included in the refinement) when the\n refinement included the calculation of a 'free' R factor.\n Details of how reflections were assigned to the working and\n test sets are given in _reflns.R_free_details.\n\n _refine.ls_R_factor_obs should not be confused with\n _refine.ls_R_factor_R_work; the former reports the results of a\n refinement in which all observed reflections were used, the\n latter a refinement in which a subset of the observed\n reflections were excluded from refinement for the calculation\n of a 'free' R factor. However, it would be meaningful to quote\n both values if a 'free' R factor were calculated for most of\n the refinement, but all of the observed reflections were used\n in the final rounds of refinement; such a protocol should be\n explained in _refine.details.\n\n sum|F~obs~ - F~calc~|\n R = ---------------------\n sum|F~obs~|\n\n F~obs~ = the observed structure-factor amplitudes\n F~calc~ = the calculated structure-factor amplitudes\n\n sum is taken over the specified reflections", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Residual factor R for reflections that satisfy the resolution\n limits established by _refine.ls_d_res_high and\n _refine.ls_d_res_low and the observation limit established by\n _reflns.observed_criterion, and that were used as the working\n reflections (i.e. were included in the refinement) when the\n refinement included the calculation of a 'free' R factor.\n Details of how reflections were assigned to the working and\n test sets are given in _reflns.R_free_details.\n\n _refine.ls_R_factor_obs should not be confused with\n _refine.ls_R_factor_R_work; the former reports the results of a\n refinement in which all observed reflections were used, the\n latter a refinement in which a subset of the observed\n reflections were excluded from refinement for the calculation\n of a 'free' R factor. However, it would be meaningful to quote\n both values if a 'free' R factor were calculated for most of\n the refinement, but all of the observed reflections were used\n in the final rounds of refinement; such a protocol should be\n explained in _refine.details.\n\n sum|F~obs~ - F~calc~|\n R = ---------------------\n sum|F~obs~|\n\n F~obs~ = the observed structure-factor amplitudes\n F~calc~ = the calculated structure-factor amplitudes\n\n sum is taken over the specified reflections", "context" : "dictionary" }, { "text" : "Sum(abs((abs(F-obs)-abs(F-calc)))/Sum(abs(F-obs)) on working data, i.e. the data used in calculating the structural model throughout the structure solution and refinement process", "context" : "deposition" }, { "text" : "Refinement R Factors (R Work)", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "X-ray Method Details", "priority_order" : 25 } ], "rcsb_current_maximum_value" : 0.615, "rcsb_current_minimum_value" : 0.03602 }, "ls_R_factor_all" : { "type" : "number", "description" : "Residual factor R for all reflections that satisfy the resolution\n limits established by _refine.ls_d_res_high and\n _refine.ls_d_res_low.\n\n sum|F~obs~ - F~calc~|\n R = ---------------------\n sum|F~obs~|\n\n F~obs~ = the observed structure-factor amplitudes\n F~calc~ = the calculated structure-factor amplitudes\n\n sum is taken over the specified reflections", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Residual factor R for all reflections that satisfy the resolution\n limits established by _refine.ls_d_res_high and\n _refine.ls_d_res_low.\n\n sum|F~obs~ - F~calc~|\n R = ---------------------\n sum|F~obs~|\n\n F~obs~ = the observed structure-factor amplitudes\n F~calc~ = the calculated structure-factor amplitudes\n\n sum is taken over the specified reflections", "context" : "dictionary" }, { "text" : "Refinement R Factors (All)", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "X-ray Method Details", "priority_order" : 20 } ], "rcsb_current_maximum_value" : 0.999, "rcsb_current_minimum_value" : 0.0 }, "ls_R_factor_obs" : { "type" : "number", "description" : "Residual factor R for reflections that satisfy the resolution\n limits established by _refine.ls_d_res_high and\n _refine.ls_d_res_low and the observation limit established by\n _reflns.observed_criterion.\n\n _refine.ls_R_factor_obs should not be confused with\n _refine.ls_R_factor_R_work; the former reports the results of a\n refinement in which all observed reflections were used, the\n latter a refinement in which a subset of the observed\n reflections were excluded from refinement for the calculation\n of a 'free' R factor. However, it would be meaningful to quote\n both values if a 'free' R factor were calculated for most of\n the refinement, but all of the observed reflections were used\n in the final rounds of refinement; such a protocol should be\n explained in _refine.details.\n\n sum|F~obs~ - F~calc~|\n R = ---------------------\n sum|F~obs~|\n\n F~obs~ = the observed structure-factor amplitudes\n F~calc~ = the calculated structure-factor amplitudes\n\n sum is taken over the specified reflections", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Residual factor R for reflections that satisfy the resolution\n limits established by _refine.ls_d_res_high and\n _refine.ls_d_res_low and the observation limit established by\n _reflns.observed_criterion.\n\n _refine.ls_R_factor_obs should not be confused with\n _refine.ls_R_factor_R_work; the former reports the results of a\n refinement in which all observed reflections were used, the\n latter a refinement in which a subset of the observed\n reflections were excluded from refinement for the calculation\n of a 'free' R factor. However, it would be meaningful to quote\n both values if a 'free' R factor were calculated for most of\n the refinement, but all of the observed reflections were used\n in the final rounds of refinement; such a protocol should be\n explained in _refine.details.\n\n sum|F~obs~ - F~calc~|\n R = ---------------------\n sum|F~obs~|\n\n F~obs~ = the observed structure-factor amplitudes\n F~calc~ = the calculated structure-factor amplitudes\n\n sum is taken over the specified reflections", "context" : "dictionary" }, { "text" : "Residual factor R for reflections that satisfy the high and low resolution limits and the observed criterion", "context" : "deposition" }, { "text" : "Refinement R Factors (Observed)", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "X-ray Method Details", "priority_order" : 15 } ], "rcsb_current_maximum_value" : 0.981485, "rcsb_current_minimum_value" : 0.035 }, "ls_d_res_high" : { "type" : "number", "description" : "The smallest value for the interplanar spacings for the\n reflection data used in the refinement in angstroms. This is\n called the highest resolution.", "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "The smallest value for the interplanar spacings for the\n reflection data used in the refinement in angstroms. This is\n called the highest resolution.", "context" : "dictionary" }, { "text" : "The smallest value(in angstroms) for the interplanar spacings for the reflection data used in the refinement.", "context" : "deposition" } ] }, "ls_d_res_low" : { "type" : "number", "description" : "The largest value for the interplanar spacings for\n the reflection data used in the refinement in angstroms.\n This is called the lowest resolution.", "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "The largest value for the interplanar spacings for\n the reflection data used in the refinement in angstroms.\n This is called the lowest resolution.", "context" : "dictionary" }, { "text" : "The largest value(in angstroms) for the interplanar spacings for the reflection data used in the refinement.", "context" : "deposition" } ] }, "ls_matrix_type" : { "type" : "string", "enum" : [ "atomblock", "diagonal", "full", "fullcycle", "sparse", "userblock" ], "description" : "Type of matrix used to accumulate the least-squares derivatives.", "rcsb_enum_annotated" : [ { "value" : "atomblock", "detail" : "block diagonal per atom" }, { "value" : "diagonal", "detail" : "diagonal elements only" }, { "value" : "full", "detail" : "full" }, { "value" : "fullcycle", "detail" : "full with fixed elements per cycle" }, { "value" : "sparse", "detail" : "selected elements only" }, { "value" : "userblock", "detail" : "user-defined blocks" } ], "rcsb_description" : [ { "text" : "Type of matrix used to accumulate the least-squares derivatives.", "context" : "dictionary" } ] }, "ls_number_parameters" : { "type" : "integer", "description" : "The number of parameters refined in the least-squares process.\n If possible, this number should include some contribution from\n the restrained parameters. The restrained parameters are\n distinct from the constrained parameters (where one or more\n parameters are linearly dependent on the refined value of\n another). Least-squares restraints often depend on geometry or\n energy considerations and this makes their direct contribution\n to this number, and to the goodness-of-fit calculation,\n difficult to assess.", "rcsb_description" : [ { "text" : "The number of parameters refined in the least-squares process.\n If possible, this number should include some contribution from\n the restrained parameters. The restrained parameters are\n distinct from the constrained parameters (where one or more\n parameters are linearly dependent on the refined value of\n another). Least-squares restraints often depend on geometry or\n energy considerations and this makes their direct contribution\n to this number, and to the goodness-of-fit calculation,\n difficult to assess.", "context" : "dictionary" } ] }, "ls_number_reflns_R_free" : { "type" : "integer", "description" : "The number of reflections that satisfy the resolution limits\n established by _refine.ls_d_res_high and _refine.ls_d_res_low\n and the observation limit established by\n _reflns.observed_criterion, and that were used as the test\n reflections (i.e. were excluded from the refinement) when the\n refinement included the calculation of a 'free' R factor.\n Details of how reflections were assigned to the working and\n test sets are given in _reflns.R_free_details.", "rcsb_description" : [ { "text" : "The number of reflections that satisfy the resolution limits\n established by _refine.ls_d_res_high and _refine.ls_d_res_low\n and the observation limit established by\n _reflns.observed_criterion, and that were used as the test\n reflections (i.e. were excluded from the refinement) when the\n refinement included the calculation of a 'free' R factor.\n Details of how reflections were assigned to the working and\n test sets are given in _reflns.R_free_details.", "context" : "dictionary" }, { "text" : "The number of reflections that satisfy both resolution limits and observation criterion, and that were pre-allocated as the cross-validation test reflections. These data were not used in the structure solution and refinement process and were used to calculate the 'free' R factor", "context" : "deposition" } ] }, "ls_number_reflns_R_work" : { "type" : "integer", "description" : "The number of reflections that satisfy the resolution limits\n established by _refine.ls_d_res_high and _refine.ls_d_res_low\n and the observation limit established by\n _reflns.observed_criterion, and that were used as the working\n reflections (i.e. were included in the refinement) when the\n refinement included the calculation of a 'free' R factor.\n Details of how reflections were assigned to the working and\n test sets are given in _reflns.R_free_details.", "rcsb_description" : [ { "text" : "The number of reflections that satisfy the resolution limits\n established by _refine.ls_d_res_high and _refine.ls_d_res_low\n and the observation limit established by\n _reflns.observed_criterion, and that were used as the working\n reflections (i.e. were included in the refinement) when the\n refinement included the calculation of a 'free' R factor.\n Details of how reflections were assigned to the working and\n test sets are given in _reflns.R_free_details.", "context" : "dictionary" } ] }, "ls_number_reflns_all" : { "type" : "integer", "description" : "The number of reflections that satisfy the resolution limits\n established by _refine.ls_d_res_high and _refine.ls_d_res_low.", "rcsb_description" : [ { "text" : "The number of reflections that satisfy the resolution limits\n established by _refine.ls_d_res_high and _refine.ls_d_res_low.", "context" : "dictionary" } ] }, "ls_number_reflns_obs" : { "type" : "integer", "description" : "The number of reflections that satisfy the resolution limits\n established by _refine.ls_d_res_high and _refine.ls_d_res_low\n and the observation limit established by\n _reflns.observed_criterion.", "rcsb_description" : [ { "text" : "The number of reflections that satisfy the resolution limits\n established by _refine.ls_d_res_high and _refine.ls_d_res_low\n and the observation limit established by\n _reflns.observed_criterion.", "context" : "dictionary" }, { "text" : "The number of reflections that satisfy both resolution limits and observation criterion (such as sigma cutoffs)", "context" : "deposition" } ] }, "ls_number_restraints" : { "type" : "integer", "description" : "The number of restrained parameters. These are parameters which\n are not directly dependent on another refined parameter.\n Restrained parameters often involve geometry or energy\n dependencies.\n See also _atom_site.constraints and _atom_site.refinement_flags.\n A general description of refinement constraints may appear in\n _refine.details.", "rcsb_description" : [ { "text" : "The number of restrained parameters. These are parameters which\n are not directly dependent on another refined parameter.\n Restrained parameters often involve geometry or energy\n dependencies.\n See also _atom_site.constraints and _atom_site.refinement_flags.\n A general description of refinement constraints may appear in\n _refine.details.", "context" : "dictionary" } ] }, "ls_percent_reflns_R_free" : { "type" : "number", "description" : "The number of reflections that satisfy the resolution limits\n established by _refine.ls_d_res_high and _refine.ls_d_res_low\n and the observation limit established by\n _reflns.observed_criterion, and that were used as the test\n reflections (i.e. were excluded from the refinement) when the\n refinement included the calculation of a 'free' R factor,\n expressed as a percentage of the number of geometrically\n observable reflections that satisfy the resolution limits.", "rcsb_description" : [ { "text" : "The number of reflections that satisfy the resolution limits\n established by _refine.ls_d_res_high and _refine.ls_d_res_low\n and the observation limit established by\n _reflns.observed_criterion, and that were used as the test\n reflections (i.e. were excluded from the refinement) when the\n refinement included the calculation of a 'free' R factor,\n expressed as a percentage of the number of geometrically\n observable reflections that satisfy the resolution limits.", "context" : "dictionary" }, { "text" : "The percent of reflections that satisfy both resolution limits and observation criterion, and that were pre-allocated as the cross-validation test reflections. These data were not used in the structure solution and refinement process and were used to calculate the 'free' R factor. In percentage to the overall reflections used for refinement.", "context" : "deposition" } ] }, "ls_percent_reflns_obs" : { "type" : "number", "description" : "The number of reflections that satisfy the resolution limits\n established by _refine.ls_d_res_high and _refine.ls_d_res_low\n and the observation limit established by\n _reflns.observed_criterion, expressed as a percentage of the\n number of geometrically observable reflections that satisfy\n the resolution limits.", "rcsb_description" : [ { "text" : "The number of reflections that satisfy the resolution limits\n established by _refine.ls_d_res_high and _refine.ls_d_res_low\n and the observation limit established by\n _reflns.observed_criterion, expressed as a percentage of the\n number of geometrically observable reflections that satisfy\n the resolution limits.", "context" : "dictionary" }, { "text" : "The number of reflections that satisfy both resolution limits and observation criterion, expressed as a percentage of the number of geometrically observable reflections that satisfy the resolution limits.", "context" : "deposition" } ] }, "ls_redundancy_reflns_all" : { "type" : "number", "description" : "The ratio of the total number of observations of the\n reflections that satisfy the resolution limits established by\n _refine.ls_d_res_high and _refine.ls_d_res_low to the number\n of crystallographically unique reflections that satisfy the\n same limits.", "rcsb_description" : [ { "text" : "The ratio of the total number of observations of the\n reflections that satisfy the resolution limits established by\n _refine.ls_d_res_high and _refine.ls_d_res_low to the number\n of crystallographically unique reflections that satisfy the\n same limits.", "context" : "dictionary" } ] }, "ls_redundancy_reflns_obs" : { "type" : "number", "description" : "The ratio of the total number of observations of the\n reflections that satisfy the resolution limits established by\n _refine.ls_d_res_high and _refine.ls_d_res_low and the\n observation limit established by _reflns.observed_criterion to\n the number of crystallographically unique reflections that\n satisfy the same limits.", "rcsb_description" : [ { "text" : "The ratio of the total number of observations of the\n reflections that satisfy the resolution limits established by\n _refine.ls_d_res_high and _refine.ls_d_res_low and the\n observation limit established by _reflns.observed_criterion to\n the number of crystallographically unique reflections that\n satisfy the same limits.", "context" : "dictionary" } ] }, "ls_wR_factor_R_free" : { "type" : "number", "description" : "Weighted residual factor wR for reflections that satisfy the\n resolution limits established by _refine.ls_d_res_high and\n _refine.ls_d_res_low and the observation limit established by\n _reflns.observed_criterion, and that were used as the test\n reflections (i.e. were excluded from the refinement) when the\n refinement included the calculation of a 'free' R factor.\n Details of how reflections were assigned to the working and\n test sets are given in _reflns.R_free_details.\n\n ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^\n wR = ( ---------------------------- )\n ( sum|w Y~obs~^2^| )\n\n Y~obs~ = the observed amplitude specified by\n _refine.ls_structure_factor_coef\n Y~calc~ = the calculated amplitude specified by\n _refine.ls_structure_factor_coef\n w = the least-squares weight\n\n sum is taken over the specified reflections", "rcsb_description" : [ { "text" : "Weighted residual factor wR for reflections that satisfy the\n resolution limits established by _refine.ls_d_res_high and\n _refine.ls_d_res_low and the observation limit established by\n _reflns.observed_criterion, and that were used as the test\n reflections (i.e. were excluded from the refinement) when the\n refinement included the calculation of a 'free' R factor.\n Details of how reflections were assigned to the working and\n test sets are given in _reflns.R_free_details.\n\n ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^\n wR = ( ---------------------------- )\n ( sum|w Y~obs~^2^| )\n\n Y~obs~ = the observed amplitude specified by\n _refine.ls_structure_factor_coef\n Y~calc~ = the calculated amplitude specified by\n _refine.ls_structure_factor_coef\n w = the least-squares weight\n\n sum is taken over the specified reflections", "context" : "dictionary" } ] }, "ls_wR_factor_R_work" : { "type" : "number", "description" : "Weighted residual factor wR for reflections that satisfy the\n resolution limits established by _refine.ls_d_res_high and\n _refine.ls_d_res_low and the observation limit established by\n _reflns.observed_criterion, and that were used as the working\n reflections (i.e. were included in the refinement) when the\n refinement included the calculation of a 'free' R factor.\n Details of how reflections were assigned to the working and\n test sets are given in _reflns.R_free_details.\n\n ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^\n wR = ( ---------------------------- )\n ( sum|w Y~obs~^2^| )\n\n Y~obs~ = the observed amplitude specified by\n _refine.ls_structure_factor_coef\n Y~calc~ = the calculated amplitude specified by\n _refine.ls_structure_factor_coef\n w = the least-squares weight\n\n sum is taken over the specified reflections", "rcsb_description" : [ { "text" : "Weighted residual factor wR for reflections that satisfy the\n resolution limits established by _refine.ls_d_res_high and\n _refine.ls_d_res_low and the observation limit established by\n _reflns.observed_criterion, and that were used as the working\n reflections (i.e. were included in the refinement) when the\n refinement included the calculation of a 'free' R factor.\n Details of how reflections were assigned to the working and\n test sets are given in _reflns.R_free_details.\n\n ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^\n wR = ( ---------------------------- )\n ( sum|w Y~obs~^2^| )\n\n Y~obs~ = the observed amplitude specified by\n _refine.ls_structure_factor_coef\n Y~calc~ = the calculated amplitude specified by\n _refine.ls_structure_factor_coef\n w = the least-squares weight\n\n sum is taken over the specified reflections", "context" : "dictionary" } ] }, "occupancy_max" : { "type" : "number", "description" : "The maximum value for occupancy found in the coordinate set.", "rcsb_description" : [ { "text" : "The maximum value for occupancy found in the coordinate set.", "context" : "dictionary" } ] }, "occupancy_min" : { "type" : "number", "description" : "The minimum value for occupancy found in the coordinate set.", "rcsb_description" : [ { "text" : "The minimum value for occupancy found in the coordinate set.", "context" : "dictionary" } ] }, "overall_FOM_free_R_set" : { "type" : "number", "description" : "Average figure of merit of phases of reflections not included\n in the refinement.\n\n This value is derived from the likelihood function.\n\n FOM = I~1~(X)/I~0~(X)\n\n I~0~, I~1~ = zero- and first-order modified Bessel functions\n of the first kind\n X = sigma~A~ |E~o~| |E~c~|/SIGMA\n E~o~, E~c~ = normalized observed and calculated structure\n factors\n sigma~A~ = SQRT(Sigma~P~/Sigma~N~)\n estimated using maximum likelihood\n Sigma~P~ = sum~{atoms in model}~ f^2^\n Sigma~N~ = sum~{atoms in crystal}~ f^2^\n f = form factor of atoms\n delta~x~ = expected error\n SIGMA = (sigma~{E;exp}~)^2^ + epsilon [1-(sigma~A~)^2^]\n sigma~{E;exp}~ = uncertainties of normalized observed\n structure factors\n epsilon = multiplicity of the diffracting plane\n\n Ref: Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997).\n Acta Cryst. D53, 240-255.", "rcsb_description" : [ { "text" : "Average figure of merit of phases of reflections not included\n in the refinement.\n\n This value is derived from the likelihood function.\n\n FOM = I~1~(X)/I~0~(X)\n\n I~0~, I~1~ = zero- and first-order modified Bessel functions\n of the first kind\n X = sigma~A~ |E~o~| |E~c~|/SIGMA\n E~o~, E~c~ = normalized observed and calculated structure\n factors\n sigma~A~ = SQRT(Sigma~P~/Sigma~N~)\n estimated using maximum likelihood\n Sigma~P~ = sum~{atoms in model}~ f^2^\n Sigma~N~ = sum~{atoms in crystal}~ f^2^\n f = form factor of atoms\n delta~x~ = expected error\n SIGMA = (sigma~{E;exp}~)^2^ + epsilon [1-(sigma~A~)^2^]\n sigma~{E;exp}~ = uncertainties of normalized observed\n structure factors\n epsilon = multiplicity of the diffracting plane\n\n Ref: Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997).\n Acta Cryst. D53, 240-255.", "context" : "dictionary" } ] }, "overall_FOM_work_R_set" : { "type" : "number", "description" : "Average figure of merit of phases of reflections included in\n the refinement.\n\n This value is derived from the likelihood function.\n\n FOM = I~1~(X)/I~0~(X)\n\n I~0~, I~1~ = zero- and first-order modified Bessel functions\n of the first kind\n X = sigma~A~ |E~o~| |E~c~|/SIGMA\n E~o~, E~c~ = normalized observed and calculated structure\n factors\n sigma~A~ = SQRT(Sigma~P~/Sigma~N~)\n estimated using maximum likelihood\n Sigma~P~ = sum~{atoms in model}~ f^2^\n Sigma~N~ = sum~{atoms in crystal}~ f^2^\n f = form factor of atoms\n delta~x~ = expected error\n SIGMA = (sigma~{E;exp}~)^2^ + epsilon [1-(sigma~A~)^2^]\n sigma~{E;exp}~ = uncertainties of normalized observed\n structure factors\n epsilon = multiplicity of the diffracting plane\n\n Ref: Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997).\n Acta Cryst. D53, 240-255.", "rcsb_description" : [ { "text" : "Average figure of merit of phases of reflections included in\n the refinement.\n\n This value is derived from the likelihood function.\n\n FOM = I~1~(X)/I~0~(X)\n\n I~0~, I~1~ = zero- and first-order modified Bessel functions\n of the first kind\n X = sigma~A~ |E~o~| |E~c~|/SIGMA\n E~o~, E~c~ = normalized observed and calculated structure\n factors\n sigma~A~ = SQRT(Sigma~P~/Sigma~N~)\n estimated using maximum likelihood\n Sigma~P~ = sum~{atoms in model}~ f^2^\n Sigma~N~ = sum~{atoms in crystal}~ f^2^\n f = form factor of atoms\n delta~x~ = expected error\n SIGMA = (sigma~{E;exp}~)^2^ + epsilon [1-(sigma~A~)^2^]\n sigma~{E;exp}~ = uncertainties of normalized observed\n structure factors\n epsilon = multiplicity of the diffracting plane\n\n Ref: Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997).\n Acta Cryst. D53, 240-255.", "context" : "dictionary" } ] }, "overall_SU_B" : { "type" : "number", "description" : "The overall standard uncertainty (estimated standard deviation)\n of the displacement parameters based on a maximum-likelihood\n residual.\n\n The overall standard uncertainty (sigma~B~)^2^ gives an idea\n of the uncertainty in the B values of averagely defined\n atoms (atoms with B values equal to the average B value).\n\n N~a~\n(sigma~B~)^2^ = 8 ----------------------------------------------\n sum~i~ {[1/Sigma - (E~o~)^2^ (1-m^2^)](SUM_AS)s^4^}\n\n N~a~ = number of atoms\n E~o~ = normalized structure factors\n m = figure of merit of phases of reflections\n included in the summation\n s = reciprocal-space vector\n\n SUM_AS = (sigma~A~)^2^/Sigma^2^\n Sigma = (sigma~{E;exp}~)^2^ + epsilon [1-(sigma~A~)^2^]\n sigma~{E;exp}~ = experimental uncertainties of normalized\n structure factors\n sigma~A~ = SQRT(Sigma~P~/Sigma~N~)\n estimated using maximum likelihood\n Sigma~P~ = sum~{atoms in model}~ f^2^\n Sigma~N~ = sum~{atoms in crystal}~ f^2^\n f = atom form factor\n delta~x~ = expected error\n epsilon = multiplicity of diffracting plane\n\n summation is over all reflections included in refinement\n\n Ref: (sigma~A~ estimation) \"Refinement of macromolecular\n structures by the maximum-likelihood method\",\n Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997).\n Acta Cryst. D53, 240-255.\n\n (SU B estimation) Murshudov, G. N. & Dodson,\n E. J. (1997). Simplified error estimation a la\n Cruickshank in macromolecular crystallography.\n CCP4 Newsletter on Protein Crystallography, No. 33,\n January 1997, pp. 31-39.\n\n http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html", "rcsb_description" : [ { "text" : "The overall standard uncertainty (estimated standard deviation)\n of the displacement parameters based on a maximum-likelihood\n residual.\n\n The overall standard uncertainty (sigma~B~)^2^ gives an idea\n of the uncertainty in the B values of averagely defined\n atoms (atoms with B values equal to the average B value).\n\n N~a~\n(sigma~B~)^2^ = 8 ----------------------------------------------\n sum~i~ {[1/Sigma - (E~o~)^2^ (1-m^2^)](SUM_AS)s^4^}\n\n N~a~ = number of atoms\n E~o~ = normalized structure factors\n m = figure of merit of phases of reflections\n included in the summation\n s = reciprocal-space vector\n\n SUM_AS = (sigma~A~)^2^/Sigma^2^\n Sigma = (sigma~{E;exp}~)^2^ + epsilon [1-(sigma~A~)^2^]\n sigma~{E;exp}~ = experimental uncertainties of normalized\n structure factors\n sigma~A~ = SQRT(Sigma~P~/Sigma~N~)\n estimated using maximum likelihood\n Sigma~P~ = sum~{atoms in model}~ f^2^\n Sigma~N~ = sum~{atoms in crystal}~ f^2^\n f = atom form factor\n delta~x~ = expected error\n epsilon = multiplicity of diffracting plane\n\n summation is over all reflections included in refinement\n\n Ref: (sigma~A~ estimation) \"Refinement of macromolecular\n structures by the maximum-likelihood method\",\n Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997).\n Acta Cryst. D53, 240-255.\n\n (SU B estimation) Murshudov, G. N. & Dodson,\n E. J. (1997). Simplified error estimation a la\n Cruickshank in macromolecular crystallography.\n CCP4 Newsletter on Protein Crystallography, No. 33,\n January 1997, pp. 31-39.\n\n http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html", "context" : "dictionary" }, { "text" : "The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on B factors.", "context" : "deposition" } ] }, "overall_SU_ML" : { "type" : "number", "description" : "The overall standard uncertainty (estimated standard deviation)\n of the positional parameters based on a maximum likelihood\n residual.\n\n The overall standard uncertainty (sigma~X~)^2^ gives an\n idea of the uncertainty in the position of averagely\n defined atoms (atoms with B values equal to average B value)\n\n 3 N~a~\n(sigma~X~)^2^ = ---------------------------------------------------------\n 8 pi^2^ sum~i~ {[1/Sigma - (E~o~)^2^ (1-m^2^)](SUM_AS)s^2^}\n\n N~a~ = number of atoms\n E~o~ = normalized structure factors\n m = figure of merit of phases of reflections\n included in the summation\n s = reciprocal-space vector\n\n SUM_AS = (sigma~A~)^2^/Sigma^2^\n Sigma = (sigma~{E;exp}~)^2^ + epsilon [1-(sigma~A~)^2^]\n sigma~{E;exp}~ = experimental uncertainties of normalized\n structure factors\n sigma~A~ = SQRT(Sigma~P~/Sigma~N~)\n estimated using maximum likelihood\n Sigma~P~ = sum~{atoms in model}~ f^2^\n Sigma~N~ = sum~{atoms in crystal}~ f^2^\n f = atom form factor\n delta~x~ = expected error\n epsilon = multiplicity of diffracting plane\n\n summation is over all reflections included in refinement\n\n Ref: (sigma_A estimation) \"Refinement of macromolecular\n structures by the maximum-likelihood method\",\n Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997).\n Acta Cryst. D53, 240-255.\n\n (SU ML estimation) Murshudov, G. N. & Dodson,\n E. J. (1997). Simplified error estimation a la\n Cruickshank in macromolecular crystallography.\n CCP4 Newsletter on Protein Crystallography, No. 33,\n January 1997, pp. 31-39.\n\n http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html", "rcsb_description" : [ { "text" : "The overall standard uncertainty (estimated standard deviation)\n of the positional parameters based on a maximum likelihood\n residual.\n\n The overall standard uncertainty (sigma~X~)^2^ gives an\n idea of the uncertainty in the position of averagely\n defined atoms (atoms with B values equal to average B value)\n\n 3 N~a~\n(sigma~X~)^2^ = ---------------------------------------------------------\n 8 pi^2^ sum~i~ {[1/Sigma - (E~o~)^2^ (1-m^2^)](SUM_AS)s^2^}\n\n N~a~ = number of atoms\n E~o~ = normalized structure factors\n m = figure of merit of phases of reflections\n included in the summation\n s = reciprocal-space vector\n\n SUM_AS = (sigma~A~)^2^/Sigma^2^\n Sigma = (sigma~{E;exp}~)^2^ + epsilon [1-(sigma~A~)^2^]\n sigma~{E;exp}~ = experimental uncertainties of normalized\n structure factors\n sigma~A~ = SQRT(Sigma~P~/Sigma~N~)\n estimated using maximum likelihood\n Sigma~P~ = sum~{atoms in model}~ f^2^\n Sigma~N~ = sum~{atoms in crystal}~ f^2^\n f = atom form factor\n delta~x~ = expected error\n epsilon = multiplicity of diffracting plane\n\n summation is over all reflections included in refinement\n\n Ref: (sigma_A estimation) \"Refinement of macromolecular\n structures by the maximum-likelihood method\",\n Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997).\n Acta Cryst. D53, 240-255.\n\n (SU ML estimation) Murshudov, G. N. & Dodson,\n E. J. (1997). Simplified error estimation a la\n Cruickshank in macromolecular crystallography.\n CCP4 Newsletter on Protein Crystallography, No. 33,\n January 1997, pp. 31-39.\n\n http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html", "context" : "dictionary" }, { "text" : "The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on a maximum likelihood residual.", "context" : "deposition" } ] }, "overall_SU_R_Cruickshank_DPI" : { "type" : "number", "description" : "The overall standard uncertainty (estimated standard deviation)\n of the displacement parameters based on the crystallographic\n R value, expressed in a formalism known as the dispersion\n precision indicator (DPI).\n\n The overall standard uncertainty (sigma~B~) gives an idea\n of the uncertainty in the B values of averagely defined\n atoms (atoms with B values equal to the average B value).\n\n N~a~\n (sigma~B~)^2^ = 0.65 ---------- (R~value~)^2^ (D~min~)^2^ C^-2/3^\n (N~o~-N~p~)\n\n\n N~a~ = number of atoms included in refinement\n N~o~ = number of observations\n N~p~ = number of parameters refined\n R~value~ = conventional crystallographic R value\n D~min~ = maximum resolution\n C = completeness of data\n\n Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601.\n\n Murshudov, G. N. & Dodson,\n E. J. (1997). Simplified error estimation a la\n Cruickshank in macromolecular crystallography.\n CCP4 Newsletter on Protein Crystallography, No. 33,\n January 1997, pp. 31-39.\n\n http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html", "rcsb_description" : [ { "text" : "The overall standard uncertainty (estimated standard deviation)\n of the displacement parameters based on the crystallographic\n R value, expressed in a formalism known as the dispersion\n precision indicator (DPI).\n\n The overall standard uncertainty (sigma~B~) gives an idea\n of the uncertainty in the B values of averagely defined\n atoms (atoms with B values equal to the average B value).\n\n N~a~\n (sigma~B~)^2^ = 0.65 ---------- (R~value~)^2^ (D~min~)^2^ C^-2/3^\n (N~o~-N~p~)\n\n\n N~a~ = number of atoms included in refinement\n N~o~ = number of observations\n N~p~ = number of parameters refined\n R~value~ = conventional crystallographic R value\n D~min~ = maximum resolution\n C = completeness of data\n\n Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601.\n\n Murshudov, G. N. & Dodson,\n E. J. (1997). Simplified error estimation a la\n Cruickshank in macromolecular crystallography.\n CCP4 Newsletter on Protein Crystallography, No. 33,\n January 1997, pp. 31-39.\n\n http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html", "context" : "dictionary" }, { "text" : "The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on the crystallographic R value, expressed in a formalism known as the dispersion precision indicator (DPI)", "context" : "deposition" } ] }, "overall_SU_R_free" : { "type" : "number", "description" : "The overall standard uncertainty (estimated standard deviation)\n of the displacement parameters based on the free R value.\n\n The overall standard uncertainty (sigma~B~) gives an idea\n of the uncertainty in the B values of averagely defined\n atoms (atoms with B values equal to the average B value).\n\n N~a~\n (sigma~B~)^2^ = 0.65 ---------- (R~free~)^2^ (D~min~)^2^ C^-2/3^\n (N~o~-N~p~)\n\n\n N~a~ = number of atoms included in refinement\n N~o~ = number of observations\n N~p~ = number of parameters refined\n R~free~ = conventional free crystallographic R value calculated\n using reflections not included in refinement\n D~min~ = maximum resolution\n C = completeness of data\n\n Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601.\n\n Murshudov, G. N. & Dodson,\n E. J. (1997). Simplified error estimation a la\n Cruickshank in macromolecular crystallography.\n CCP4 Newsletter on Protein Crystallography, No. 33,\n January 1997, pp. 31-39.\n\n http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html", "rcsb_description" : [ { "text" : "The overall standard uncertainty (estimated standard deviation)\n of the displacement parameters based on the free R value.\n\n The overall standard uncertainty (sigma~B~) gives an idea\n of the uncertainty in the B values of averagely defined\n atoms (atoms with B values equal to the average B value).\n\n N~a~\n (sigma~B~)^2^ = 0.65 ---------- (R~free~)^2^ (D~min~)^2^ C^-2/3^\n (N~o~-N~p~)\n\n\n N~a~ = number of atoms included in refinement\n N~o~ = number of observations\n N~p~ = number of parameters refined\n R~free~ = conventional free crystallographic R value calculated\n using reflections not included in refinement\n D~min~ = maximum resolution\n C = completeness of data\n\n Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601.\n\n Murshudov, G. N. & Dodson,\n E. J. (1997). Simplified error estimation a la\n Cruickshank in macromolecular crystallography.\n CCP4 Newsletter on Protein Crystallography, No. 33,\n January 1997, pp. 31-39.\n\n http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html", "context" : "dictionary" } ] }, "pdbx_R_Free_selection_details" : { "type" : "string", "examples" : [ "Random selection" ], "description" : "Details of the manner in which the cross validation\n reflections were selected.", "rcsb_description" : [ { "text" : "Details of the manner in which the cross validation\n reflections were selected.", "context" : "dictionary" }, { "text" : "Details of the manner in which the cross validation reflections were selected", "context" : "deposition" } ] }, "pdbx_TLS_residual_ADP_flag" : { "type" : "string", "enum" : [ "LIKELY RESIDUAL", "UNVERIFIED" ], "description" : "A flag for TLS refinements identifying the type of atomic displacement parameters stored\n in _atom_site.B_iso_or_equiv.", "rcsb_enum_annotated" : [ { "value" : "LIKELY RESIDUAL", "detail" : "Residual B values (excluding TLS contributions) are likely specified for some or all atom sites" }, { "value" : "UNVERIFIED" } ], "rcsb_description" : [ { "text" : "A flag for TLS refinements identifying the type of atomic displacement parameters stored\n in _atom_site.B_iso_or_equiv.", "context" : "dictionary" } ] }, "pdbx_average_fsc_free" : { "type" : "number", "description" : "Average Fourier Shell Correlation (avgFSC) between model and\n observed structure factors for reflections not included in refinement.\n\n The average FSC is a measure of the agreement between observed\n and calculated structure factors.\n\n sum(N~i~ FSC~free-i~)\n avgFSC~free~ = ---------------------\n sum(N~i~)\n\n\n N~i~ = the number of free reflections in the resolution shell i\n FSC~free-i~ = FSC for free reflections in the i-th resolution shell calculated as:\n\n (sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~)))\n FSC~free-i~ = -------------------------------------------\n (sum(|F~o~|^2^) (sum(|F~c~|^2^)))^1/2^\n\n |F~o~| = amplitude of observed structure factor\n |F~c~| = amplitude of calculated structure factor\n phi~o~ = phase of observed structure factor\n phi~c~ = phase of calculated structure factor\n fom = figure of merit of the experimental phases.\n\n Summation of FSC~free-i~ is carried over all free reflections in the resolution shell.\n\n Summation of avgFSC~free~ is carried over all resolution shells.\n\n\n Ref: Rosenthal P.B., Henderson R.\n \"Optimal determination of particle orientation, absolute hand,\n and contrast loss in single-particle electron cryomicroscopy.\n Journal of Molecular Biology. 2003;333(4):721-745, equation (A6).", "rcsb_description" : [ { "text" : "Average Fourier Shell Correlation (avgFSC) between model and\n observed structure factors for reflections not included in refinement.\n\n The average FSC is a measure of the agreement between observed\n and calculated structure factors.\n\n sum(N~i~ FSC~free-i~)\n avgFSC~free~ = ---------------------\n sum(N~i~)\n\n\n N~i~ = the number of free reflections in the resolution shell i\n FSC~free-i~ = FSC for free reflections in the i-th resolution shell calculated as:\n\n (sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~)))\n FSC~free-i~ = -------------------------------------------\n (sum(|F~o~|^2^) (sum(|F~c~|^2^)))^1/2^\n\n |F~o~| = amplitude of observed structure factor\n |F~c~| = amplitude of calculated structure factor\n phi~o~ = phase of observed structure factor\n phi~c~ = phase of calculated structure factor\n fom = figure of merit of the experimental phases.\n\n Summation of FSC~free-i~ is carried over all free reflections in the resolution shell.\n\n Summation of avgFSC~free~ is carried over all resolution shells.\n\n\n Ref: Rosenthal P.B., Henderson R.\n \"Optimal determination of particle orientation, absolute hand,\n and contrast loss in single-particle electron cryomicroscopy.\n Journal of Molecular Biology. 2003;333(4):721-745, equation (A6).", "context" : "dictionary" } ] }, "pdbx_average_fsc_overall" : { "type" : "number", "description" : "Overall average Fourier Shell Correlation (avgFSC) between model and\n observed structure factors for all reflections.\n\n The average FSC is a measure of the agreement between observed\n and calculated structure factors.\n\n sum(N~i~ FSC~i~)\n avgFSC = ----------------\n sum(N~i~)\n\n\n N~i~ = the number of all reflections in the resolution shell i\n FSC~i~ = FSC for all reflections in the i-th resolution shell calculated as:\n\n (sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~)))\n FSC~i~ = -------------------------------------------\n (sum(|F~o~|^2^) (sum(|F~c~|^2^)))^1/2^\n\n |F~o~| = amplitude of observed structure factor\n |F~c~| = amplitude of calculated structure factor\n phi~o~ = phase of observed structure factor\n phi~c~ = phase of calculated structure factor\n fom = figure of merit of the experimental phases.\n\n Summation of FSC~i~ is carried over all reflections in the resolution shell.\n\n Summation of avgFSC is carried over all resolution shells.\n\n\n Ref: Rosenthal P.B., Henderson R.\n \"Optimal determination of particle orientation, absolute hand,\n and contrast loss in single-particle electron cryomicroscopy.\n Journal of Molecular Biology. 2003;333(4):721-745, equation (A6).", "rcsb_description" : [ { "text" : "Overall average Fourier Shell Correlation (avgFSC) between model and\n observed structure factors for all reflections.\n\n The average FSC is a measure of the agreement between observed\n and calculated structure factors.\n\n sum(N~i~ FSC~i~)\n avgFSC = ----------------\n sum(N~i~)\n\n\n N~i~ = the number of all reflections in the resolution shell i\n FSC~i~ = FSC for all reflections in the i-th resolution shell calculated as:\n\n (sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~)))\n FSC~i~ = -------------------------------------------\n (sum(|F~o~|^2^) (sum(|F~c~|^2^)))^1/2^\n\n |F~o~| = amplitude of observed structure factor\n |F~c~| = amplitude of calculated structure factor\n phi~o~ = phase of observed structure factor\n phi~c~ = phase of calculated structure factor\n fom = figure of merit of the experimental phases.\n\n Summation of FSC~i~ is carried over all reflections in the resolution shell.\n\n Summation of avgFSC is carried over all resolution shells.\n\n\n Ref: Rosenthal P.B., Henderson R.\n \"Optimal determination of particle orientation, absolute hand,\n and contrast loss in single-particle electron cryomicroscopy.\n Journal of Molecular Biology. 2003;333(4):721-745, equation (A6).", "context" : "dictionary" } ] }, "pdbx_average_fsc_work" : { "type" : "number", "description" : "Average Fourier Shell Correlation (avgFSC) between model and\n observed structure factors for reflections included in refinement.\n\n The average FSC is a measure of the agreement between observed\n and calculated structure factors.\n\n sum(N~i~ FSC~work-i~)\n avgFSC~work~ = ---------------------\n sum(N~i~)\n\n\n N~i~ = the number of working reflections in the resolution shell i\n FSC~work-i~ = FSC for working reflections in the i-th resolution shell calculated as:\n\n (sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~)))\n FSC~work-i~ = -------------------------------------------\n (sum(|F~o~|^2^) (sum(|F~c~|^2^)))^1/2^\n\n |F~o~| = amplitude of observed structure factor\n |F~c~| = amplitude of calculated structure factor\n phi~o~ = phase of observed structure factor\n phi~c~ = phase of calculated structure factor\n fom = figure of merit of the experimental phases.\n\n Summation of FSC~work-i~ is carried over all working reflections in the resolution shell.\n\n Summation of avgFSC~work~ is carried over all resolution shells.\n\n\n Ref: Rosenthal P.B., Henderson R.\n \"Optimal determination of particle orientation, absolute hand,\n and contrast loss in single-particle electron cryomicroscopy.\n Journal of Molecular Biology. 2003;333(4):721-745, equation (A6).", "rcsb_description" : [ { "text" : "Average Fourier Shell Correlation (avgFSC) between model and\n observed structure factors for reflections included in refinement.\n\n The average FSC is a measure of the agreement between observed\n and calculated structure factors.\n\n sum(N~i~ FSC~work-i~)\n avgFSC~work~ = ---------------------\n sum(N~i~)\n\n\n N~i~ = the number of working reflections in the resolution shell i\n FSC~work-i~ = FSC for working reflections in the i-th resolution shell calculated as:\n\n (sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~)))\n FSC~work-i~ = -------------------------------------------\n (sum(|F~o~|^2^) (sum(|F~c~|^2^)))^1/2^\n\n |F~o~| = amplitude of observed structure factor\n |F~c~| = amplitude of calculated structure factor\n phi~o~ = phase of observed structure factor\n phi~c~ = phase of calculated structure factor\n fom = figure of merit of the experimental phases.\n\n Summation of FSC~work-i~ is carried over all working reflections in the resolution shell.\n\n Summation of avgFSC~work~ is carried over all resolution shells.\n\n\n Ref: Rosenthal P.B., Henderson R.\n \"Optimal determination of particle orientation, absolute hand,\n and contrast loss in single-particle electron cryomicroscopy.\n Journal of Molecular Biology. 2003;333(4):721-745, equation (A6).", "context" : "dictionary" } ] }, "pdbx_data_cutoff_high_absF" : { "type" : "number", "description" : "Value of F at \"high end\" of data cutoff.", "rcsb_description" : [ { "text" : "Value of F at \"high end\" of data cutoff.", "context" : "dictionary" }, { "text" : "Value of F at \"high end\" of data cutoff", "context" : "deposition" } ] }, "pdbx_data_cutoff_high_rms_absF" : { "type" : "number", "examples" : [ 205.1 ], "description" : "Value of RMS |F| used as high data cutoff.", "rcsb_description" : [ { "text" : "Value of RMS |F| used as high data cutoff.", "context" : "dictionary" } ] }, "pdbx_data_cutoff_low_absF" : { "type" : "number", "examples" : [ 0.3 ], "description" : "Value of F at \"low end\" of data cutoff.", "rcsb_description" : [ { "text" : "Value of F at \"low end\" of data cutoff.", "context" : "dictionary" }, { "text" : "Value of F at \"low end\" of data cutoff", "context" : "deposition" } ] }, "pdbx_diffrn_id" : { "type" : "array", "items" : { "type" : "string", "description" : "An identifier for the diffraction data set used in this refinement.\n\n Multiple diffraction data sets specified as a comma separated list.", "rcsb_description" : [ { "text" : "An identifier for the diffraction data set used in this refinement.\n\n Multiple diffraction data sets specified as a comma separated list.", "context" : "dictionary" } ] }, "uniqueItems" : false }, "pdbx_isotropic_thermal_model" : { "type" : "string", "examples" : [ "Isotropic", "Overall" ], "description" : "Whether the structure was refined with indvidual\nisotropic, anisotropic or overall temperature factor.", "rcsb_description" : [ { "text" : "Whether the structure was refined with indvidual\nisotropic, anisotropic or overall temperature factor.", "context" : "dictionary" } ] }, "pdbx_ls_cross_valid_method" : { "type" : "string", "examples" : [ "FREE R-VALUE" ], "description" : "Whether the cross validataion method was used through\nout or only at the end.", "rcsb_description" : [ { "text" : "Whether the cross validataion method was used through\nout or only at the end.", "context" : "dictionary" }, { "text" : "Whether the cross validataion method was used through out or only at the end", "context" : "deposition" } ] }, "pdbx_ls_sigma_F" : { "type" : "number", "description" : "Data cutoff (SIGMA(F))", "rcsb_description" : [ { "text" : "Data cutoff (SIGMA(F))", "context" : "dictionary" }, { "text" : "Data cutoff on amplitude", "context" : "deposition" } ] }, "pdbx_ls_sigma_Fsqd" : { "type" : "number", "description" : "Data cutoff (SIGMA(F^2))", "rcsb_description" : [ { "text" : "Data cutoff (SIGMA(F^2))", "context" : "dictionary" } ] }, "pdbx_ls_sigma_I" : { "type" : "number", "description" : "Data cutoff (SIGMA(I))", "rcsb_description" : [ { "text" : "Data cutoff (SIGMA(I))", "context" : "dictionary" } ] }, "pdbx_method_to_determine_struct" : { "type" : "string", "examples" : [ "AB INITIO PHASING", "DM", "ISAS", "ISIR", "ISIRAS", "MAD", "MIR", "MIRAS", "MR", "SIR", "SIRAS" ], "description" : "Method(s) used to determine the structure.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Method(s) used to determine the structure.", "context" : "dictionary" }, { "text" : "Method(s) used to determine the structure", "context" : "deposition" }, { "text" : "Structure Determination Method", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "X-ray Method Details", "priority_order" : 5 } ] }, "pdbx_overall_ESU_R" : { "type" : "number", "description" : "Overall estimated standard uncertainties of positional\n parameters based on R value.", "rcsb_description" : [ { "text" : "Overall estimated standard uncertainties of positional\n parameters based on R value.", "context" : "dictionary" } ] }, "pdbx_overall_ESU_R_Free" : { "type" : "number", "description" : "Overall estimated standard uncertainties of positional parameters based on R free value.", "rcsb_description" : [ { "text" : "Overall estimated standard uncertainties of positional parameters based on R free value.", "context" : "dictionary" } ] }, "pdbx_overall_SU_R_Blow_DPI" : { "type" : "number", "description" : "The overall standard uncertainty (estimated standard deviation)\n of the displacement parameters based on the crystallographic\n R value, expressed in a formalism known as the dispersion\n precision indicator (DPI).\n\n Ref: Blow, D (2002) Acta Cryst. D58, 792-797", "rcsb_description" : [ { "text" : "The overall standard uncertainty (estimated standard deviation)\n of the displacement parameters based on the crystallographic\n R value, expressed in a formalism known as the dispersion\n precision indicator (DPI).\n\n Ref: Blow, D (2002) Acta Cryst. D58, 792-797", "context" : "dictionary" } ] }, "pdbx_overall_SU_R_free_Blow_DPI" : { "type" : "number", "description" : "The overall standard uncertainty (estimated standard deviation)\n of the displacement parameters based on the crystallographic\n R-free value, expressed in a formalism known as the dispersion\n precision indicator (DPI).\n\n Ref: Blow, D (2002) Acta Cryst. D58, 792-797", "rcsb_description" : [ { "text" : "The overall standard uncertainty (estimated standard deviation)\n of the displacement parameters based on the crystallographic\n R-free value, expressed in a formalism known as the dispersion\n precision indicator (DPI).\n\n Ref: Blow, D (2002) Acta Cryst. D58, 792-797", "context" : "dictionary" }, { "text" : "Precision index (DPI) by Blow to estimate the precision of coordinates obtained by structural refinement of protein diffraction data.", "context" : "deposition" } ] }, "pdbx_overall_SU_R_free_Cruickshank_DPI" : { "type" : "number", "description" : "The overall standard uncertainty (estimated standard deviation)\n of the displacement parameters based on the crystallographic\n R-free value, expressed in a formalism known as the dispersion\n precision indicator (DPI).\n\n Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601.", "rcsb_description" : [ { "text" : "The overall standard uncertainty (estimated standard deviation)\n of the displacement parameters based on the crystallographic\n R-free value, expressed in a formalism known as the dispersion\n precision indicator (DPI).\n\n Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601.", "context" : "dictionary" }, { "text" : "Precision index (DPI) by Cruickshank to estimate the precision of coordinates obtained by structural refinement of protein diffraction data.", "context" : "deposition" } ] }, "pdbx_overall_phase_error" : { "type" : "number", "examples" : [ 0.3 ], "description" : "The overall phase error for all reflections after refinement using\n the current refinement target.", "rcsb_description" : [ { "text" : "The overall phase error for all reflections after refinement using\n the current refinement target.", "context" : "dictionary" } ] }, "pdbx_refine_id" : { "type" : "string", "description" : "This data item uniquely identifies a refinement within an entry.\n _refine.pdbx_refine_id can be used to distinguish the results of\n joint refinements.", "rcsb_description" : [ { "text" : "This data item uniquely identifies a refinement within an entry.\n _refine.pdbx_refine_id can be used to distinguish the results of\n joint refinements.", "context" : "dictionary" } ] }, "pdbx_solvent_ion_probe_radii" : { "type" : "number", "description" : "For bulk solvent mask calculation, the amount that the ionic radii of atoms, which can be ions, are increased used.", "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "For bulk solvent mask calculation, the amount that the ionic radii of atoms, which can be ions, are increased used.", "context" : "dictionary" }, { "text" : "Bulk solvent ion probe radii", "context" : "deposition" } ] }, "pdbx_solvent_shrinkage_radii" : { "type" : "number", "description" : "For bulk solvent mask calculation, amount mask is shrunk after taking away atoms with new radii and a constant value assigned to this new region.", "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "For bulk solvent mask calculation, amount mask is shrunk after taking away atoms with new radii and a constant value assigned to this new region.", "context" : "dictionary" }, { "text" : "Bulk solvent shrinkage radii", "context" : "deposition" } ] }, "pdbx_solvent_vdw_probe_radii" : { "type" : "number", "description" : "For bulk solvent mask calculation, the value by which the vdw radii of non-ion atoms (like carbon) are increased and used.", "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "For bulk solvent mask calculation, the value by which the vdw radii of non-ion atoms (like carbon) are increased and used.", "context" : "dictionary" }, { "text" : "Bulk solvent probe van der Waals radii", "context" : "deposition" } ] }, "pdbx_starting_model" : { "type" : "string", "examples" : [ "1XYZ, 2XYZ", "BDL001" ], "description" : "Starting model for refinement. Starting model for\n molecular replacement should refer to a previous\n structure or experiment.", "rcsb_description" : [ { "text" : "Starting model for refinement. Starting model for\n molecular replacement should refer to a previous\n structure or experiment.", "context" : "dictionary" }, { "text" : "Starting model for refinement. Starting model for molecular replacement should refer to a previous structure or experiment", "context" : "deposition" } ] }, "pdbx_stereochem_target_val_spec_case" : { "type" : "string", "description" : "Special case of stereochemistry target values used\nin SHELXL refinement.", "rcsb_description" : [ { "text" : "Special case of stereochemistry target values used\nin SHELXL refinement.", "context" : "dictionary" } ] }, "pdbx_stereochemistry_target_values" : { "type" : "string", "description" : "Stereochemistry target values used in refinement.", "rcsb_description" : [ { "text" : "Stereochemistry target values used in refinement.", "context" : "dictionary" }, { "text" : "Stereochemistry target values used in refinement", "context" : "deposition" } ] }, "solvent_model_details" : { "type" : "string", "description" : "Special aspects of the solvent model used during refinement.", "rcsb_description" : [ { "text" : "Special aspects of the solvent model used during refinement.", "context" : "dictionary" } ] }, "solvent_model_param_bsol" : { "type" : "number", "description" : "The value of the BSOL solvent-model parameter describing\n the average isotropic displacement parameter of disordered\n solvent atoms.\n\n This is one of the two parameters (the other is\n _refine.solvent_model_param_ksol) in Tronrud's method of\n modelling the contribution of bulk solvent to the\n scattering. The standard scale factor is modified according\n to the expression\n\n k0 exp(-B0 * s^2^)[1-KSOL * exp(-BSOL * s^2^)]\n\n where k0 and B0 are the scale factors for the protein.\n\n Ref: Tronrud, D. E. (1997). Methods Enzymol. 277, 243-268.", "rcsb_description" : [ { "text" : "The value of the BSOL solvent-model parameter describing\n the average isotropic displacement parameter of disordered\n solvent atoms.\n\n This is one of the two parameters (the other is\n _refine.solvent_model_param_ksol) in Tronrud's method of\n modelling the contribution of bulk solvent to the\n scattering. The standard scale factor is modified according\n to the expression\n\n k0 exp(-B0 * s^2^)[1-KSOL * exp(-BSOL * s^2^)]\n\n where k0 and B0 are the scale factors for the protein.\n\n Ref: Tronrud, D. E. (1997). Methods Enzymol. 277, 243-268.", "context" : "dictionary" }, { "text" : "The value of the BSOL solvent-model parameter describing the average isotropic displacement parameter of disordered solvent atoms", "context" : "deposition" } ] }, "solvent_model_param_ksol" : { "type" : "number", "description" : "The value of the KSOL solvent-model parameter describing\n the ratio of the electron density in the bulk solvent to the\n electron density in the molecular solute.\n\n This is one of the two parameters (the other is\n _refine.solvent_model_param_bsol) in Tronrud's method of\n modelling the contribution of bulk solvent to the\n scattering. The standard scale factor is modified according\n to the expression\n\n k0 exp(-B0 * s^2^)[1-KSOL * exp(-BSOL * s^2^)]\n\n where k0 and B0 are the scale factors for the protein.\n\n Ref: Tronrud, D. E. (1997). Methods Enzymol. 277, 243-268.", "rcsb_description" : [ { "text" : "The value of the KSOL solvent-model parameter describing\n the ratio of the electron density in the bulk solvent to the\n electron density in the molecular solute.\n\n This is one of the two parameters (the other is\n _refine.solvent_model_param_bsol) in Tronrud's method of\n modelling the contribution of bulk solvent to the\n scattering. The standard scale factor is modified according\n to the expression\n\n k0 exp(-B0 * s^2^)[1-KSOL * exp(-BSOL * s^2^)]\n\n where k0 and B0 are the scale factors for the protein.\n\n Ref: Tronrud, D. E. (1997). Methods Enzymol. 277, 243-268.", "context" : "dictionary" }, { "text" : "The value of the KSOL solvent-model parameter describing the ratio of the electron density in the bulk solvent to the electron density in the molecular solute", "context" : "deposition" } ] } }, "additionalProperties" : false, "required" : [ "pdbx_refine_id" ] }, "minItems" : 1, "uniqueItems" : true }, "refine_analyze" : { "type" : "array", "items" : { "type" : "object", "properties" : { "Luzzati_coordinate_error_free" : { "type" : "number", "description" : "The estimated coordinate error obtained from the plot of\n the R value versus sin(theta)/lambda for the reflections\n treated as a test set during refinement.\n\n Ref: Luzzati, V. (1952). Traitement statistique des erreurs\n dans la determination des structures cristallines. Acta\n Cryst. 5, 802-810.", "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "The estimated coordinate error obtained from the plot of\n the R value versus sin(theta)/lambda for the reflections\n treated as a test set during refinement.\n\n Ref: Luzzati, V. (1952). Traitement statistique des erreurs\n dans la determination des structures cristallines. Acta\n Cryst. 5, 802-810.", "context" : "dictionary" }, { "text" : "The estimated coordinate error obtained from the plot of the R value versus sin(theta)/lambda for the reflections treated as a test set during refinement.", "context" : "deposition" } ] }, "Luzzati_coordinate_error_obs" : { "type" : "number", "description" : "The estimated coordinate error obtained from the plot of\n the R value versus sin(theta)/lambda for reflections classified\n as observed.\n\n Ref: Luzzati, V. (1952). Traitement statistique des erreurs\n dans la determination des structures cristallines. Acta\n Cryst. 5, 802-810.", "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "The estimated coordinate error obtained from the plot of\n the R value versus sin(theta)/lambda for reflections classified\n as observed.\n\n Ref: Luzzati, V. (1952). Traitement statistique des erreurs\n dans la determination des structures cristallines. Acta\n Cryst. 5, 802-810.", "context" : "dictionary" }, { "text" : "The estimated coordinate error obtained from the plot of the R value versus sin(theta)/lambda for reflections classified as observed", "context" : "deposition" } ] }, "Luzzati_d_res_low_free" : { "type" : "number", "description" : "The value of the low-resolution cutoff used in constructing the\n Luzzati plot for reflections treated as a test set during\n refinement.\n\n Ref: Luzzati, V. (1952). Traitement statistique des erreurs\n dans la determination des structures cristallines. Acta\n Cryst. 5, 802-810.", "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "The value of the low-resolution cutoff used in constructing the\n Luzzati plot for reflections treated as a test set during\n refinement.\n\n Ref: Luzzati, V. (1952). Traitement statistique des erreurs\n dans la determination des structures cristallines. Acta\n Cryst. 5, 802-810.", "context" : "dictionary" } ] }, "Luzzati_d_res_low_obs" : { "type" : "number", "description" : "The value of the low-resolution cutoff used in\n constructing the Luzzati plot for reflections classified as\n observed.\n\n Ref: Luzzati, V. (1952). Traitement statistique des erreurs\n dans la determination des structures cristallines. Acta\n Cryst. 5, 802-810.", "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "The value of the low-resolution cutoff used in\n constructing the Luzzati plot for reflections classified as\n observed.\n\n Ref: Luzzati, V. (1952). Traitement statistique des erreurs\n dans la determination des structures cristallines. Acta\n Cryst. 5, 802-810.", "context" : "dictionary" }, { "text" : "The value of the low-resolution cutoff used in constructing the Luzzati plot for reflections classified as observed.", "context" : "deposition" } ] }, "Luzzati_sigma_a_free" : { "type" : "number", "description" : "The value of sigma~a~ used in constructing the Luzzati plot for\n the reflections treated as a test set during refinement.\n Details of the estimation of sigma~a~ can be specified\n in _refine_analyze.Luzzati_sigma_a_free_details.\n\n Ref: Luzzati, V. (1952). Traitement statistique des erreurs\n dans la determination des structures cristallines. Acta\n Cryst. 5, 802-810.", "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "The value of sigma~a~ used in constructing the Luzzati plot for\n the reflections treated as a test set during refinement.\n Details of the estimation of sigma~a~ can be specified\n in _refine_analyze.Luzzati_sigma_a_free_details.\n\n Ref: Luzzati, V. (1952). Traitement statistique des erreurs\n dans la determination des structures cristallines. Acta\n Cryst. 5, 802-810.", "context" : "dictionary" } ] }, "Luzzati_sigma_a_obs" : { "type" : "number", "description" : "The value of sigma~a~ used in constructing the Luzzati plot for\n reflections classified as observed. Details of the\n estimation of sigma~a~ can be specified in\n _refine_analyze.Luzzati_sigma_a_obs_details.\n\n Ref: Luzzati, V. (1952). Traitement statistique des erreurs\n dans la determination des structures cristallines. Acta\n Cryst. 5, 802-810.", "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "The value of sigma~a~ used in constructing the Luzzati plot for\n reflections classified as observed. Details of the\n estimation of sigma~a~ can be specified in\n _refine_analyze.Luzzati_sigma_a_obs_details.\n\n Ref: Luzzati, V. (1952). Traitement statistique des erreurs\n dans la determination des structures cristallines. Acta\n Cryst. 5, 802-810.", "context" : "dictionary" }, { "text" : "The value of sigma~a~ used in constructing the Luzzati plot for reflections classified as observed.", "context" : "deposition" } ] }, "number_disordered_residues" : { "type" : "number", "description" : "The number of discretely disordered residues in the refined\n model.", "rcsb_description" : [ { "text" : "The number of discretely disordered residues in the refined\n model.", "context" : "dictionary" } ] }, "occupancy_sum_hydrogen" : { "type" : "number", "description" : "The sum of the occupancies of the hydrogen atoms in the refined\n model.", "rcsb_description" : [ { "text" : "The sum of the occupancies of the hydrogen atoms in the refined\n model.", "context" : "dictionary" } ] }, "occupancy_sum_non_hydrogen" : { "type" : "number", "description" : "The sum of the occupancies of the non-hydrogen atoms in the\n refined model.", "rcsb_description" : [ { "text" : "The sum of the occupancies of the non-hydrogen atoms in the\n refined model.", "context" : "dictionary" } ] }, "pdbx_Luzzati_d_res_high_obs" : { "type" : "number", "description" : "record the high resolution for calculating Luzzati statistics.", "rcsb_description" : [ { "text" : "record the high resolution for calculating Luzzati statistics.", "context" : "dictionary" } ] }, "pdbx_refine_id" : { "type" : "string", "description" : "This data item uniquely identifies a refinement within an entry.\n _refine_analyze.pdbx_refine_id can be used to distinguish the results\n of joint refinements.", "rcsb_description" : [ { "text" : "This data item uniquely identifies a refinement within an entry.\n _refine_analyze.pdbx_refine_id can be used to distinguish the results\n of joint refinements.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "pdbx_refine_id" ] }, "minItems" : 1, "uniqueItems" : true }, "refine_hist" : { "type" : "array", "items" : { "type" : "object", "properties" : { "cycle_id" : { "type" : "string", "description" : "The value of _refine_hist.cycle_id must uniquely identify a\n record in the REFINE_HIST list.\n\n Note that this item need not be a number; it can be any unique\n identifier.", "rcsb_description" : [ { "text" : "The value of _refine_hist.cycle_id must uniquely identify a\n record in the REFINE_HIST list.\n\n Note that this item need not be a number; it can be any unique\n identifier.", "context" : "dictionary" } ] }, "d_res_high" : { "type" : "number", "description" : "The lowest value for the interplanar spacings for the\n reflection data for this cycle of refinement. This is called\n the highest resolution.", "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "The lowest value for the interplanar spacings for the\n reflection data for this cycle of refinement. This is called\n the highest resolution.", "context" : "dictionary" } ] }, "d_res_low" : { "type" : "number", "description" : "The highest value for the interplanar spacings for the\n reflection data for this cycle of refinement. This is\n called the lowest resolution.", "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "The highest value for the interplanar spacings for the\n reflection data for this cycle of refinement. This is\n called the lowest resolution.", "context" : "dictionary" } ] }, "number_atoms_solvent" : { "type" : "integer", "description" : "The number of solvent atoms that were included in the model at\n this cycle of the refinement.", "rcsb_description" : [ { "text" : "The number of solvent atoms that were included in the model at\n this cycle of the refinement.", "context" : "dictionary" } ] }, "number_atoms_total" : { "type" : "integer", "description" : "The total number of atoms that were included in the model at\n this cycle of the refinement.", "rcsb_description" : [ { "text" : "The total number of atoms that were included in the model at\n this cycle of the refinement.", "context" : "dictionary" } ] }, "pdbx_B_iso_mean_ligand" : { "type" : "number", "description" : "Mean isotropic B-value for ligand molecules included in refinement.", "rcsb_description" : [ { "text" : "Mean isotropic B-value for ligand molecules included in refinement.", "context" : "dictionary" } ] }, "pdbx_B_iso_mean_solvent" : { "type" : "number", "description" : "Mean isotropic B-value for solvent molecules included in refinement.", "rcsb_description" : [ { "text" : "Mean isotropic B-value for solvent molecules included in refinement.", "context" : "dictionary" } ] }, "pdbx_number_atoms_ligand" : { "type" : "integer", "description" : "Number of ligand atoms included in refinement", "rcsb_description" : [ { "text" : "Number of ligand atoms included in refinement", "context" : "dictionary" } ] }, "pdbx_number_atoms_nucleic_acid" : { "type" : "integer", "description" : "Number of nucleic atoms included in refinement", "rcsb_description" : [ { "text" : "Number of nucleic atoms included in refinement", "context" : "dictionary" } ] }, "pdbx_number_atoms_protein" : { "type" : "integer", "description" : "Number of protein atoms included in refinement", "rcsb_description" : [ { "text" : "Number of protein atoms included in refinement", "context" : "dictionary" } ] }, "pdbx_number_residues_total" : { "type" : "integer", "description" : "Total number of polymer residues included in refinement.", "rcsb_description" : [ { "text" : "Total number of polymer residues included in refinement.", "context" : "dictionary" } ] }, "pdbx_refine_id" : { "type" : "string", "description" : "This data item uniquely identifies a refinement within an entry.\n _refine_hist.pdbx_refine_id can be used to distinguish the results\n of joint refinements.", "rcsb_description" : [ { "text" : "This data item uniquely identifies a refinement within an entry.\n _refine_hist.pdbx_refine_id can be used to distinguish the results\n of joint refinements.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "cycle_id", "pdbx_refine_id" ] }, "minItems" : 1, "uniqueItems" : true }, "refine_ls_restr" : { "type" : "array", "items" : { "type" : "object", "properties" : { "dev_ideal" : { "type" : "number", "description" : "For the given parameter type, the root-mean-square deviation\n between the ideal values used as restraints in the least-squares\n refinement and the values obtained by refinement. For instance,\n bond distances may deviate by 0.018 \\%A (r.m.s.) from ideal\n values in the current model.", "rcsb_description" : [ { "text" : "For the given parameter type, the root-mean-square deviation\n between the ideal values used as restraints in the least-squares\n refinement and the values obtained by refinement. For instance,\n bond distances may deviate by 0.018 \\%A (r.m.s.) from ideal\n values in the current model.", "context" : "dictionary" } ] }, "dev_ideal_target" : { "type" : "number", "description" : "For the given parameter type, the target root-mean-square\n deviation between the ideal values used as restraints in the\n least-squares refinement and the values obtained by refinement.", "rcsb_description" : [ { "text" : "For the given parameter type, the target root-mean-square\n deviation between the ideal values used as restraints in the\n least-squares refinement and the values obtained by refinement.", "context" : "dictionary" } ] }, "number" : { "type" : "integer", "description" : "The number of parameters of this type subjected to restraint in\n least-squares refinement.", "rcsb_description" : [ { "text" : "The number of parameters of this type subjected to restraint in\n least-squares refinement.", "context" : "dictionary" } ] }, "pdbx_refine_id" : { "type" : "string", "description" : "This data item uniquely identifies a refinement within an entry.\n _refine_ls_restr.pdbx_refine_id can be used to distinguish the results\n of joint refinements.", "rcsb_description" : [ { "text" : "This data item uniquely identifies a refinement within an entry.\n _refine_ls_restr.pdbx_refine_id can be used to distinguish the results\n of joint refinements.", "context" : "dictionary" } ] }, "pdbx_restraint_function" : { "type" : "string", "examples" : [ "SINUSOIDAL", "HARMONIC", "SEMIHARMONIC" ], "description" : "The functional form of the restraint function used in the least-squares\n refinement.", "rcsb_description" : [ { "text" : "The functional form of the restraint function used in the least-squares\n refinement.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "examples" : [ "p_bond_d", "p_angle_d", "p_planar_d", "p_xhbond_d", "p_xhangle_d", "p_hydrog_d", "p_special_d", "p_planar", "p_chiral", "p_singtor_nbd", "p_multtor_nbd", "p_xyhbond_nbd", "p_xhyhbond_nbd", "p_special_tor", "p_planar_tor", "p_staggered_tor", "p_orthonormal_tor", "p_mcbond_it", "p_mcangle_it", "p_scbond_it", "p_scangle_it", "p_xhbond_it", "p_xhangle_it", "p_special_it", "RESTRAIN_Distances < 2.12", "RESTRAIN_Distances 2.12 < D < 2.625", "RESTRAIN_Distances > 2.625", "RESTRAIN_Peptide Planes", "RESTRAIN_Ring and other planes", "RESTRAIN_rms diffs for Uiso atoms at dist 1.2-1.4", "RESTRAIN_rms diffs for Uiso atoms at dist 1.4-1.6", "RESTRAIN_rms diffs for Uiso atoms at dist 1.8-2.0", "RESTRAIN_rms diffs for Uiso atoms at dist 2.0-2.2", "RESTRAIN_rms diffs for Uiso atoms at dist 2.2-2.4", "RESTRAIN_rms diffs for Uiso atoms at dist >2.4" ], "description" : "The type of the parameter being restrained.\n Explicit sets of data values are provided for the programs\n PROTIN/PROLSQ (beginning with p_) and RESTRAIN (beginning with\n RESTRAIN_). As computer programs change, these data values\n are given as examples, not as an enumeration list. Computer\n programs that convert a data block to a refinement table will\n expect the exact form of the data values given here to be used.", "rcsb_description" : [ { "text" : "The type of the parameter being restrained.\n Explicit sets of data values are provided for the programs\n PROTIN/PROLSQ (beginning with p_) and RESTRAIN (beginning with\n RESTRAIN_). As computer programs change, these data values\n are given as examples, not as an enumeration list. Computer\n programs that convert a data block to a refinement table will\n expect the exact form of the data values given here to be used.", "context" : "dictionary" } ] }, "weight" : { "type" : "number", "description" : "The weighting value applied to this type of restraint in\n the least-squares refinement.", "rcsb_description" : [ { "text" : "The weighting value applied to this type of restraint in\n the least-squares refinement.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "pdbx_refine_id", "type" ] }, "minItems" : 1, "uniqueItems" : true }, "reflns" : { "type" : "array", "items" : { "type" : "object", "properties" : { "B_iso_Wilson_estimate" : { "type" : "number", "description" : "The value of the overall isotropic displacement parameter\n estimated from the slope of the Wilson plot.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "angstroms_squared", "rcsb_description" : [ { "text" : "The value of the overall isotropic displacement parameter\n estimated from the slope of the Wilson plot.", "context" : "dictionary" }, { "text" : "The value of the overall isotropic displacement parameter estimated from the slope of the Wilson plot", "context" : "deposition" }, { "text" : "B Wilson Estimate", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "X-ray Data Collection Details", "priority_order" : 10 } ], "rcsb_current_maximum_value" : 1119.43, "rcsb_current_minimum_value" : -288.36 }, "R_free_details" : { "type" : "string", "examples" : [ "The data set was sorted with l varying most\n rapidly and h varying least rapidly. Every\n 10th reflection in this sorted list was\n excluded from refinement and included in the\n calculation of a 'free' R factor." ], "description" : "A description of the method by which a subset of reflections was\n selected for exclusion from refinement so as to be used in the\n calculation of a 'free' R factor.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "A description of the method by which a subset of reflections was\n selected for exclusion from refinement so as to be used in the\n calculation of a 'free' R factor.", "context" : "dictionary" }, { "text" : "R Free Details (Reflns)", "context" : "brief" } ] }, "Rmerge_F_all" : { "type" : "number", "description" : "Residual factor Rmerge for all reflections that satisfy the\n resolution limits established by _reflns.d_resolution_high\n and _reflns.d_resolution_low.\n\n sum~i~(sum~j~|F~j~ - |)\n Rmerge(F) = --------------------------\n sum~i~(sum~j~)\n\n F~j~ = the amplitude of the jth observation of reflection i\n = the mean of the amplitudes of all observations of\n reflection i\n\n sum~i~ is taken over all reflections\n sum~j~ is taken over all observations of each reflection", "rcsb_description" : [ { "text" : "Residual factor Rmerge for all reflections that satisfy the\n resolution limits established by _reflns.d_resolution_high\n and _reflns.d_resolution_low.\n\n sum~i~(sum~j~|F~j~ - |)\n Rmerge(F) = --------------------------\n sum~i~(sum~j~)\n\n F~j~ = the amplitude of the jth observation of reflection i\n = the mean of the amplitudes of all observations of\n reflection i\n\n sum~i~ is taken over all reflections\n sum~j~ is taken over all observations of each reflection", "context" : "dictionary" } ] }, "Rmerge_F_obs" : { "type" : "number", "description" : "Residual factor Rmerge for reflections that satisfy the\n resolution limits established by _reflns.d_resolution_high\n and _reflns.d_resolution_low and the observation limit\n established by _reflns.observed_criterion.\n\n sum~i~(sum~j~|F~j~ - |)\n Rmerge(F) = --------------------------\n sum~i~(sum~j~)\n\n F~j~ = the amplitude of the jth observation of reflection i\n = the mean of the amplitudes of all observations of\n reflection i\n\n sum~i~ is taken over all reflections\n sum~j~ is taken over all observations of each reflection", "rcsb_description" : [ { "text" : "Residual factor Rmerge for reflections that satisfy the\n resolution limits established by _reflns.d_resolution_high\n and _reflns.d_resolution_low and the observation limit\n established by _reflns.observed_criterion.\n\n sum~i~(sum~j~|F~j~ - |)\n Rmerge(F) = --------------------------\n sum~i~(sum~j~)\n\n F~j~ = the amplitude of the jth observation of reflection i\n = the mean of the amplitudes of all observations of\n reflection i\n\n sum~i~ is taken over all reflections\n sum~j~ is taken over all observations of each reflection", "context" : "dictionary" } ] }, "d_resolution_high" : { "type" : "number", "description" : "The smallest value in angstroms for the interplanar spacings\n for the reflection data. This is called the highest resolution.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "The smallest value in angstroms for the interplanar spacings\n for the reflection data. This is called the highest resolution.", "context" : "dictionary" }, { "text" : "The high resolution limit used for data processing. The high resolution limit actually used for structure solution or model refinement might be lower than this.", "context" : "deposition" }, { "text" : "Data Collection Resolution", "context" : "brief" } ], "rcsb_current_maximum_value" : 24.0, "rcsb_current_minimum_value" : 0.0 }, "d_resolution_low" : { "type" : "number", "description" : "The largest value in angstroms for the interplanar spacings\n for the reflection data. This is called the lowest resolution.", "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "The largest value in angstroms for the interplanar spacings\n for the reflection data. This is called the lowest resolution.", "context" : "dictionary" }, { "text" : "The low resolution limit used for data processing. The low resolution limit actually used for structure solution or model refinement might be higher than this.\"", "context" : "deposition" } ] }, "data_reduction_details" : { "type" : "string", "examples" : [ "Merging and scaling based on only those\n reflections with I > sig(I)." ], "description" : "A description of special aspects of the data-reduction\n procedures.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "A description of special aspects of the data-reduction\n procedures.", "context" : "dictionary" }, { "text" : "Data Reduction Details (Reflns)", "context" : "brief" } ] }, "data_reduction_method" : { "type" : "string", "examples" : [ "Profile fitting by method of Kabsch (1987).\n Scaling used spherical harmonic coefficients." ], "description" : "The method used for data reduction.\n\n Note that this is not the computer program used, which is\n described in the SOFTWARE category, but the method\n itself.\n\n This data item should be used to describe significant\n methodological options used within the data-reduction programs.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The method used for data reduction.\n\n Note that this is not the computer program used, which is\n described in the SOFTWARE category, but the method\n itself.\n\n This data item should be used to describe significant\n methodological options used within the data-reduction programs.", "context" : "dictionary" }, { "text" : "Data Reduction Method (Reflns)", "context" : "brief" } ] }, "details" : { "type" : "string", "description" : "A description of reflection data not covered by other data\n names. This should include details of the Friedel pairs.", "rcsb_description" : [ { "text" : "A description of reflection data not covered by other data\n names. This should include details of the Friedel pairs.", "context" : "dictionary" } ] }, "limit_h_max" : { "type" : "integer", "description" : "Maximum value of the Miller index h for the reflection data. This\n need not have the same value as _diffrn_reflns.limit_h_max.", "rcsb_description" : [ { "text" : "Maximum value of the Miller index h for the reflection data. This\n need not have the same value as _diffrn_reflns.limit_h_max.", "context" : "dictionary" } ] }, "limit_h_min" : { "type" : "integer", "description" : "Minimum value of the Miller index h for the reflection data. This\n need not have the same value as _diffrn_reflns.limit_h_min.", "rcsb_description" : [ { "text" : "Minimum value of the Miller index h for the reflection data. This\n need not have the same value as _diffrn_reflns.limit_h_min.", "context" : "dictionary" } ] }, "limit_k_max" : { "type" : "integer", "description" : "Maximum value of the Miller index k for the reflection data. This\n need not have the same value as _diffrn_reflns.limit_k_max.", "rcsb_description" : [ { "text" : "Maximum value of the Miller index k for the reflection data. This\n need not have the same value as _diffrn_reflns.limit_k_max.", "context" : "dictionary" } ] }, "limit_k_min" : { "type" : "integer", "description" : "Minimum value of the Miller index k for the reflection data. This\n need not have the same value as _diffrn_reflns.limit_k_min.", "rcsb_description" : [ { "text" : "Minimum value of the Miller index k for the reflection data. This\n need not have the same value as _diffrn_reflns.limit_k_min.", "context" : "dictionary" } ] }, "limit_l_max" : { "type" : "integer", "description" : "Maximum value of the Miller index l for the reflection data. This\n need not have the same value as _diffrn_reflns.limit_l_max.", "rcsb_description" : [ { "text" : "Maximum value of the Miller index l for the reflection data. This\n need not have the same value as _diffrn_reflns.limit_l_max.", "context" : "dictionary" } ] }, "limit_l_min" : { "type" : "integer", "description" : "Minimum value of the Miller index l for the reflection data. This\n need not have the same value as _diffrn_reflns.limit_l_min.", "rcsb_description" : [ { "text" : "Minimum value of the Miller index l for the reflection data. This\n need not have the same value as _diffrn_reflns.limit_l_min.", "context" : "dictionary" } ] }, "number_all" : { "type" : "integer", "description" : "The total number of reflections in the REFLN list (not the\n DIFFRN_REFLN list). This number may contain Friedel-equivalent\n reflections according to the nature of the structure and the\n procedures used. The item _reflns.details describes the\n reflection data.", "rcsb_description" : [ { "text" : "The total number of reflections in the REFLN list (not the\n DIFFRN_REFLN list). This number may contain Friedel-equivalent\n reflections according to the nature of the structure and the\n procedures used. The item _reflns.details describes the\n reflection data.", "context" : "dictionary" }, { "text" : "The total number of unique reflections collected after merging", "context" : "deposition" } ] }, "number_obs" : { "type" : "integer", "description" : "The number of reflections in the REFLN list (not the DIFFRN_REFLN\n list) classified as observed (see _reflns.observed_criterion).\n This number may contain Friedel-equivalent reflections according\n to the nature of the structure and the procedures used.", "rcsb_description" : [ { "text" : "The number of reflections in the REFLN list (not the DIFFRN_REFLN\n list) classified as observed (see _reflns.observed_criterion).\n This number may contain Friedel-equivalent reflections according\n to the nature of the structure and the procedures used.", "context" : "dictionary" }, { "text" : "The number of unique reflections collected after using any sigma cutoffs", "context" : "deposition" } ] }, "observed_criterion" : { "type" : "string", "examples" : [ ">2sigma(I)" ], "description" : "The criterion used to classify a reflection as 'observed'. This\n criterion is usually expressed in terms of a sigma(I) or\n sigma(F) threshold.", "rcsb_description" : [ { "text" : "The criterion used to classify a reflection as 'observed'. This\n criterion is usually expressed in terms of a sigma(I) or\n sigma(F) threshold.", "context" : "dictionary" } ] }, "observed_criterion_F_max" : { "type" : "number", "description" : "The criterion used to classify a reflection as 'observed'\n expressed as an upper limit for the value of F.", "rcsb_description" : [ { "text" : "The criterion used to classify a reflection as 'observed'\n expressed as an upper limit for the value of F.", "context" : "dictionary" } ] }, "observed_criterion_F_min" : { "type" : "number", "description" : "The criterion used to classify a reflection as 'observed'\n expressed as a lower limit for the value of F.", "rcsb_description" : [ { "text" : "The criterion used to classify a reflection as 'observed'\n expressed as a lower limit for the value of F.", "context" : "dictionary" } ] }, "observed_criterion_I_max" : { "type" : "number", "description" : "The criterion used to classify a reflection as 'observed'\n expressed as an upper limit for the value of I.", "rcsb_description" : [ { "text" : "The criterion used to classify a reflection as 'observed'\n expressed as an upper limit for the value of I.", "context" : "dictionary" } ] }, "observed_criterion_I_min" : { "type" : "number", "description" : "The criterion used to classify a reflection as 'observed'\n expressed as a lower limit for the value of I.", "rcsb_description" : [ { "text" : "The criterion used to classify a reflection as 'observed'\n expressed as a lower limit for the value of I.", "context" : "dictionary" } ] }, "observed_criterion_sigma_F" : { "type" : "number", "description" : "The criterion used to classify a reflection as 'observed'\n expressed as a multiple of the value of sigma(F).", "rcsb_description" : [ { "text" : "The criterion used to classify a reflection as 'observed'\n expressed as a multiple of the value of sigma(F).", "context" : "dictionary" } ] }, "observed_criterion_sigma_I" : { "type" : "number", "description" : "The criterion used to classify a reflection as 'observed'\n expressed as a multiple of the value of sigma(I).", "rcsb_description" : [ { "text" : "The criterion used to classify a reflection as 'observed'\n expressed as a multiple of the value of sigma(I).", "context" : "dictionary" }, { "text" : "The sigma cutoff applied to intensities in scaling of data. Xengen and scalepack use -3.", "context" : "deposition" } ] }, "pdbx_CC_half" : { "type" : "number", "description" : "The Pearson's correlation coefficient expressed as a decimal value\n between the average intensities from randomly selected\n half-datasets.\n\n\t Ref: Karplus & Diederichs (2012), Science 336, 1030-33", "rcsb_description" : [ { "text" : "The Pearson's correlation coefficient expressed as a decimal value\n between the average intensities from randomly selected\n half-datasets.\n\n\t Ref: Karplus & Diederichs (2012), Science 336, 1030-33", "context" : "dictionary" } ] }, "pdbx_R_split" : { "type" : "number", "description" : "R split measures the agreement between the sets of intensities created by merging\n odd- and even-numbered images from the overall data.\n\n\t Ref: T. A. White, R. A. Kirian, A. V. Martin, A. Aquila, K. Nass, A. Barty\n and H. N. Chapman (2012), J. Appl. Cryst. 45, 335-341", "rcsb_description" : [ { "text" : "R split measures the agreement between the sets of intensities created by merging\n odd- and even-numbered images from the overall data.\n\n\t Ref: T. A. White, R. A. Kirian, A. V. Martin, A. Aquila, K. Nass, A. Barty\n and H. N. Chapman (2012), J. Appl. Cryst. 45, 335-341", "context" : "dictionary" } ] }, "pdbx_Rmerge_I_obs" : { "type" : "number", "description" : "The R value for merging intensities satisfying the observed\n criteria in this data set.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The R value for merging intensities satisfying the observed\n criteria in this data set.", "context" : "dictionary" }, { "text" : "Provide the Rmerge of data collection as a decimal number. This is sometimes referred to the linear R-factor", "context" : "deposition" }, { "text" : "R Value for Merging Intensities (Observed)", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "X-ray Data Collection Details", "priority_order" : 25 } ], "rcsb_current_maximum_value" : 9.9, "rcsb_current_minimum_value" : 0.0 }, "pdbx_Rpim_I_all" : { "type" : "number", "description" : "The precision-indicating merging R factor value Rpim,\n for merging all intensities in this data set.\n\n sum~i~ [1/(N~i~ - 1)]1/2^ sum~j~ | I~j~ - |\n Rpim = --------------------------------------------------\n sum~i~ ( sum~j~ I~j~ )\n\n I~j~ = the intensity of the jth observation of reflection i\n = the mean of the intensities of all observations\n of reflection i\n N~i~ = the redundancy (the number of times reflection i\n has been measured).\n\n sum~i~ is taken over all reflections\n sum~j~ is taken over all observations of each reflection.\n\n Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct.\n Biol. 4, 269-275.\n Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst.\n 30, 203-205.\n Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.", "rcsb_description" : [ { "text" : "The precision-indicating merging R factor value Rpim,\n for merging all intensities in this data set.\n\n sum~i~ [1/(N~i~ - 1)]1/2^ sum~j~ | I~j~ - |\n Rpim = --------------------------------------------------\n sum~i~ ( sum~j~ I~j~ )\n\n I~j~ = the intensity of the jth observation of reflection i\n = the mean of the intensities of all observations\n of reflection i\n N~i~ = the redundancy (the number of times reflection i\n has been measured).\n\n sum~i~ is taken over all reflections\n sum~j~ is taken over all observations of each reflection.\n\n Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct.\n Biol. 4, 269-275.\n Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst.\n 30, 203-205.\n Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.", "context" : "dictionary" } ] }, "pdbx_Rrim_I_all" : { "type" : "number", "description" : "The redundancy-independent merging R factor value Rrim,\n also denoted Rmeas, for merging all intensities in this\n data set.\n\n sum~i~ [N~i~/(N~i~ - 1)]1/2^ sum~j~ | I~j~ - |\n Rrim = ----------------------------------------------------\n sum~i~ ( sum~j~ I~j~ )\n\n I~j~ = the intensity of the jth observation of reflection i\n = the mean of the intensities of all observations of\n reflection i\n\t N~i~ = the redundancy (the number of times reflection i\n has been measured).\n\n sum~i~ is taken over all reflections\n sum~j~ is taken over all observations of each reflection.\n\n Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct.\n Biol. 4, 269-275.\n Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst.\n 30, 203-205.\n Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.", "rcsb_description" : [ { "text" : "The redundancy-independent merging R factor value Rrim,\n also denoted Rmeas, for merging all intensities in this\n data set.\n\n sum~i~ [N~i~/(N~i~ - 1)]1/2^ sum~j~ | I~j~ - |\n Rrim = ----------------------------------------------------\n sum~i~ ( sum~j~ I~j~ )\n\n I~j~ = the intensity of the jth observation of reflection i\n = the mean of the intensities of all observations of\n reflection i\n\t N~i~ = the redundancy (the number of times reflection i\n has been measured).\n\n sum~i~ is taken over all reflections\n sum~j~ is taken over all observations of each reflection.\n\n Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct.\n Biol. 4, 269-275.\n Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst.\n 30, 203-205.\n Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.", "context" : "dictionary" } ] }, "pdbx_Rsym_value" : { "type" : "number", "examples" : [ 0.02 ], "description" : "The R sym value as a decimal number.", "rcsb_description" : [ { "text" : "The R sym value as a decimal number.", "context" : "dictionary" } ] }, "pdbx_chi_squared" : { "type" : "number", "description" : "Overall Chi-squared statistic.", "rcsb_description" : [ { "text" : "Overall Chi-squared statistic.", "context" : "dictionary" } ] }, "pdbx_diffrn_id" : { "type" : "array", "items" : { "type" : "string", "description" : "An identifier for the diffraction data set for this set of summary statistics.\n\n Multiple diffraction data sets entered as a comma separated list.", "rcsb_description" : [ { "text" : "An identifier for the diffraction data set for this set of summary statistics.\n\n Multiple diffraction data sets entered as a comma separated list.", "context" : "dictionary" } ] }, "uniqueItems" : false }, "pdbx_netI_over_av_sigmaI" : { "type" : "number", "description" : "The ratio of the average intensity to the average uncertainty,\n /.", "rcsb_description" : [ { "text" : "The ratio of the average intensity to the average uncertainty,\n /.", "context" : "dictionary" }, { "text" : "The ratio of the average intensity to the average uncertainty, average(I)/average(sigma(I))", "context" : "deposition" } ] }, "pdbx_netI_over_sigmaI" : { "type" : "number", "description" : "The mean of the ratio of the intensities to their\n standard uncertainties, .", "rcsb_description" : [ { "text" : "The mean of the ratio of the intensities to their\n standard uncertainties, .", "context" : "dictionary" }, { "text" : "The overall average(I/sigma(I)) of data collection", "context" : "deposition" } ] }, "pdbx_number_measured_all" : { "type" : "integer", "description" : "Total number of measured reflections.", "rcsb_description" : [ { "text" : "Total number of measured reflections.", "context" : "dictionary" } ] }, "pdbx_ordinal" : { "type" : "integer", "description" : "An ordinal identifier for this set of reflection statistics.", "rcsb_description" : [ { "text" : "An ordinal identifier for this set of reflection statistics.", "context" : "dictionary" } ] }, "pdbx_redundancy" : { "type" : "number", "description" : "Overall redundancy for this data set.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Overall redundancy for this data set.", "context" : "dictionary" }, { "text" : "Overall reduncancy of the data collection", "context" : "deposition" }, { "text" : "Overall Redundancy", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "X-ray Data Collection Details", "priority_order" : 15 } ], "rcsb_current_maximum_value" : 26558.0, "rcsb_current_minimum_value" : 0.035 }, "pdbx_scaling_rejects" : { "type" : "integer", "description" : "Number of reflections rejected in scaling operations.", "rcsb_description" : [ { "text" : "Number of reflections rejected in scaling operations.", "context" : "dictionary" } ] }, "percent_possible_obs" : { "type" : "number", "description" : "The percentage of geometrically possible reflections represented\n by reflections that satisfy the resolution limits established\n by _reflns.d_resolution_high and _reflns.d_resolution_low and\n the observation limit established by\n _reflns.observed_criterion.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The percentage of geometrically possible reflections represented\n by reflections that satisfy the resolution limits established\n by _reflns.d_resolution_high and _reflns.d_resolution_low and\n the observation limit established by\n _reflns.observed_criterion.", "context" : "dictionary" }, { "text" : "The percent of possible observed reflections collected. Do not incude the % sign", "context" : "deposition" }, { "text" : "Percentage of Possible Reflections", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "X-ray Data Collection Details", "priority_order" : 20 } ], "rcsb_current_maximum_value" : 100.0, "rcsb_current_minimum_value" : 0.045 }, "phase_calculation_details" : { "type" : "string", "examples" : [ "From model", "NCS averaging", "Solvent flipping", "Solvent flattening", "Multiple crystal averaging", "Multiple phase modification", "Other phase modification" ], "description" : "The value of _reflns.phase_calculation_details describes a\n special details about calculation of phases in _refln.phase_calc.", "rcsb_description" : [ { "text" : "The value of _reflns.phase_calculation_details describes a\n special details about calculation of phases in _refln.phase_calc.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "pdbx_ordinal" ] }, "minItems" : 1, "uniqueItems" : true }, "reflns_shell" : { "type" : "array", "items" : { "type" : "object", "properties" : { "Rmerge_F_all" : { "type" : "number", "description" : "Residual factor Rmerge for all reflections that satisfy the\n resolution limits established by _reflns_shell.d_res_high and\n _reflns_shell.d_res_low.\n\n sum~i~(sum~j~|F~j~ - |)\n Rmerge(F) = --------------------------\n sum~i~(sum~j~)\n\n F~j~ = the amplitude of the jth observation of reflection i\n = the mean of the amplitudes of all observations of\n reflection i\n\n sum~i~ is taken over all reflections\n sum~j~ is taken over all observations of each reflection", "rcsb_description" : [ { "text" : "Residual factor Rmerge for all reflections that satisfy the\n resolution limits established by _reflns_shell.d_res_high and\n _reflns_shell.d_res_low.\n\n sum~i~(sum~j~|F~j~ - |)\n Rmerge(F) = --------------------------\n sum~i~(sum~j~)\n\n F~j~ = the amplitude of the jth observation of reflection i\n = the mean of the amplitudes of all observations of\n reflection i\n\n sum~i~ is taken over all reflections\n sum~j~ is taken over all observations of each reflection", "context" : "dictionary" } ] }, "Rmerge_F_obs" : { "type" : "number", "description" : "Residual factor Rmerge for reflections that satisfy the\n resolution limits established by _reflns_shell.d_res_high and\n _reflns_shell.d_res_low and the observation criterion\n established by _reflns.observed_criterion.\n\n sum~i~(sum~j~|F~j~ - |)\n Rmerge(F) = --------------------------\n sum~i~(sum~j~)\n\n F~j~ = the amplitude of the jth observation of reflection i\n = the mean of the amplitudes of all observations of\n reflection i\n\n sum~i~ is taken over all reflections\n sum~j~ is taken over all observations of each reflection", "rcsb_description" : [ { "text" : "Residual factor Rmerge for reflections that satisfy the\n resolution limits established by _reflns_shell.d_res_high and\n _reflns_shell.d_res_low and the observation criterion\n established by _reflns.observed_criterion.\n\n sum~i~(sum~j~|F~j~ - |)\n Rmerge(F) = --------------------------\n sum~i~(sum~j~)\n\n F~j~ = the amplitude of the jth observation of reflection i\n = the mean of the amplitudes of all observations of\n reflection i\n\n sum~i~ is taken over all reflections\n sum~j~ is taken over all observations of each reflection", "context" : "dictionary" } ] }, "Rmerge_I_all" : { "type" : "number", "description" : "The value of Rmerge(I) for all reflections in a given shell.\n\n sum~i~(sum~j~|I~j~ - |)\n Rmerge(I) = --------------------------\n sum~i~(sum~j~)\n\n I~j~ = the intensity of the jth observation of reflection i\n = the mean of the intensities of all observations of\n reflection i\n\n sum~i~ is taken over all reflections\n sum~j~ is taken over all observations of each reflection", "rcsb_description" : [ { "text" : "The value of Rmerge(I) for all reflections in a given shell.\n\n sum~i~(sum~j~|I~j~ - |)\n Rmerge(I) = --------------------------\n sum~i~(sum~j~)\n\n I~j~ = the intensity of the jth observation of reflection i\n = the mean of the intensities of all observations of\n reflection i\n\n sum~i~ is taken over all reflections\n sum~j~ is taken over all observations of each reflection", "context" : "dictionary" } ] }, "Rmerge_I_obs" : { "type" : "number", "description" : "The value of Rmerge(I) for reflections classified as 'observed'\n (see _reflns.observed_criterion) in a given shell.\n\n sum~i~(sum~j~|I~j~ - |)\n Rmerge(I) = --------------------------\n sum~i~(sum~j~)\n\n I~j~ = the intensity of the jth observation of reflection i\n = the mean of the intensities of all observations of\n reflection i\n\n sum~i~ is taken over all reflections\n sum~j~ is taken over all observations of each reflection", "rcsb_description" : [ { "text" : "The value of Rmerge(I) for reflections classified as 'observed'\n (see _reflns.observed_criterion) in a given shell.\n\n sum~i~(sum~j~|I~j~ - |)\n Rmerge(I) = --------------------------\n sum~i~(sum~j~)\n\n I~j~ = the intensity of the jth observation of reflection i\n = the mean of the intensities of all observations of\n reflection i\n\n sum~i~ is taken over all reflections\n sum~j~ is taken over all observations of each reflection", "context" : "dictionary" }, { "text" : "For this resolution shell, provide the Rmerge of data collection as a decimal number", "context" : "deposition" } ] }, "d_res_high" : { "type" : "number", "description" : "The smallest value in angstroms for the interplanar spacings\n for the reflections in this shell. This is called the highest\n resolution.", "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "The smallest value in angstroms for the interplanar spacings\n for the reflections in this shell. This is called the highest\n resolution.", "context" : "dictionary" }, { "text" : "For this resolution shell, the high resolution limit processed.", "context" : "deposition" } ] }, "d_res_low" : { "type" : "number", "description" : "The highest value in angstroms for the interplanar spacings\n for the reflections in this shell. This is called the lowest\n resolution.", "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "The highest value in angstroms for the interplanar spacings\n for the reflections in this shell. This is called the lowest\n resolution.", "context" : "dictionary" }, { "text" : "For this resolution shell, the low resolution limit processed.", "context" : "deposition" } ] }, "meanI_over_sigI_all" : { "type" : "number", "description" : "The ratio of the mean of the intensities of all reflections\n in this shell to the mean of the standard uncertainties of the\n intensities of all reflections in this shell.", "rcsb_description" : [ { "text" : "The ratio of the mean of the intensities of all reflections\n in this shell to the mean of the standard uncertainties of the\n intensities of all reflections in this shell.", "context" : "dictionary" } ] }, "meanI_over_sigI_obs" : { "type" : "number", "description" : "The ratio of the mean of the intensities of the reflections\n classified as 'observed' (see _reflns.observed_criterion) in\n this shell to the mean of the standard uncertainties of the\n intensities of the 'observed' reflections in this\n shell.", "rcsb_description" : [ { "text" : "The ratio of the mean of the intensities of the reflections\n classified as 'observed' (see _reflns.observed_criterion) in\n this shell to the mean of the standard uncertainties of the\n intensities of the 'observed' reflections in this\n shell.", "context" : "dictionary" }, { "text" : "For this resolution shell, the average I/sigma(I)", "context" : "deposition" } ] }, "meanI_over_uI_all" : { "type" : "number", "description" : "The ratio of the mean of the intensities of all reflections\n in this shell to the mean of the standard uncertainties of the\n intensities of all reflections in this shell.", "rcsb_description" : [ { "text" : "The ratio of the mean of the intensities of all reflections\n in this shell to the mean of the standard uncertainties of the\n intensities of all reflections in this shell.", "context" : "dictionary" } ] }, "number_measured_all" : { "type" : "integer", "description" : "The total number of reflections measured for this\n shell.", "rcsb_description" : [ { "text" : "The total number of reflections measured for this\n shell.", "context" : "dictionary" } ] }, "number_measured_obs" : { "type" : "integer", "description" : "The number of reflections classified as 'observed'\n (see _reflns.observed_criterion) for this\n shell.", "rcsb_description" : [ { "text" : "The number of reflections classified as 'observed'\n (see _reflns.observed_criterion) for this\n shell.", "context" : "dictionary" } ] }, "number_possible" : { "type" : "integer", "description" : "The number of unique reflections it is possible to measure in\n this shell.", "rcsb_description" : [ { "text" : "The number of unique reflections it is possible to measure in\n this shell.", "context" : "dictionary" } ] }, "number_unique_all" : { "type" : "integer", "description" : "The total number of measured reflections which are symmetry-\n unique after merging for this shell.", "rcsb_description" : [ { "text" : "The total number of measured reflections which are symmetry-\n unique after merging for this shell.", "context" : "dictionary" } ] }, "number_unique_obs" : { "type" : "integer", "description" : "The total number of measured reflections classified as 'observed'\n (see _reflns.observed_criterion) which are symmetry-unique\n after merging for this shell.", "rcsb_description" : [ { "text" : "The total number of measured reflections classified as 'observed'\n (see _reflns.observed_criterion) which are symmetry-unique\n after merging for this shell.", "context" : "dictionary" } ] }, "pdbx_CC_half" : { "type" : "number", "description" : "The Pearson's correlation coefficient expressed as a decimal value\n between the average intensities from randomly selected\n half-datasets within the resolution shell.\n\n\t Ref: Karplus & Diederichs (2012), Science 336, 1030-33", "rcsb_description" : [ { "text" : "The Pearson's correlation coefficient expressed as a decimal value\n between the average intensities from randomly selected\n half-datasets within the resolution shell.\n\n\t Ref: Karplus & Diederichs (2012), Science 336, 1030-33", "context" : "dictionary" } ] }, "pdbx_R_split" : { "type" : "number", "description" : "R split measures the agreement between the sets of intensities created by merging\n odd- and even-numbered images from the data within the resolution shell.\n\n\t Ref: T. A. White, R. A. Kirian, A. V. Martin, A. Aquila, K. Nass,\n\t A. Barty and H. N. Chapman (2012), J. Appl. Cryst. 45, 335-341", "rcsb_description" : [ { "text" : "R split measures the agreement between the sets of intensities created by merging\n odd- and even-numbered images from the data within the resolution shell.\n\n\t Ref: T. A. White, R. A. Kirian, A. V. Martin, A. Aquila, K. Nass,\n\t A. Barty and H. N. Chapman (2012), J. Appl. Cryst. 45, 335-341", "context" : "dictionary" } ] }, "pdbx_Rpim_I_all" : { "type" : "number", "description" : "The precision-indicating merging R factor value Rpim,\n for merging all intensities in a given shell.\n\n sum~i~ [1/(N~i~ - 1)]1/2^ sum~j~ | I~j~ - |\n Rpim = --------------------------------------------------\n sum~i~ ( sum~j~ I~j~ )\n\n I~j~ = the intensity of the jth observation of reflection i\n = the mean of the intensities of all observations of\n reflection i\n N~i~ = the redundancy (the number of times reflection i\n has been measured).\n\n sum~i~ is taken over all reflections\n sum~j~ is taken over all observations of each reflection.\n\n Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct.\n Biol. 4, 269-275.\n Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst.\n 30, 203-205.\n Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.", "rcsb_description" : [ { "text" : "The precision-indicating merging R factor value Rpim,\n for merging all intensities in a given shell.\n\n sum~i~ [1/(N~i~ - 1)]1/2^ sum~j~ | I~j~ - |\n Rpim = --------------------------------------------------\n sum~i~ ( sum~j~ I~j~ )\n\n I~j~ = the intensity of the jth observation of reflection i\n = the mean of the intensities of all observations of\n reflection i\n N~i~ = the redundancy (the number of times reflection i\n has been measured).\n\n sum~i~ is taken over all reflections\n sum~j~ is taken over all observations of each reflection.\n\n Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct.\n Biol. 4, 269-275.\n Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst.\n 30, 203-205.\n Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.", "context" : "dictionary" } ] }, "pdbx_Rrim_I_all" : { "type" : "number", "description" : "The redundancy-independent merging R factor value Rrim,\n also denoted Rmeas, for merging all intensities in a\n given shell.\n\n sum~i~ [N~i~ /( N~i~ - 1)]1/2^ sum~j~ | I~j~ - |\n Rrim = --------------------------------------------------------\n sum~i~ ( sum~j~ I~j~ )\n\n I~j~ = the intensity of the jth observation of reflection i\n = the mean of the intensities of all observations of\n reflection i\n\t N~i~ = the redundancy (the number of times reflection i\n has been measured).\n\n sum~i~ is taken over all reflections\n sum~j~ is taken over all observations of each reflection.\n\n Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct.\n Biol. 4, 269-275.\n Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst.\n 30, 203-205.\n Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.", "rcsb_description" : [ { "text" : "The redundancy-independent merging R factor value Rrim,\n also denoted Rmeas, for merging all intensities in a\n given shell.\n\n sum~i~ [N~i~ /( N~i~ - 1)]1/2^ sum~j~ | I~j~ - |\n Rrim = --------------------------------------------------------\n sum~i~ ( sum~j~ I~j~ )\n\n I~j~ = the intensity of the jth observation of reflection i\n = the mean of the intensities of all observations of\n reflection i\n\t N~i~ = the redundancy (the number of times reflection i\n has been measured).\n\n sum~i~ is taken over all reflections\n sum~j~ is taken over all observations of each reflection.\n\n Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct.\n Biol. 4, 269-275.\n Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst.\n 30, 203-205.\n Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.", "context" : "dictionary" } ] }, "pdbx_Rsym_value" : { "type" : "number", "description" : "R sym value in percent.", "rcsb_description" : [ { "text" : "R sym value in percent.", "context" : "dictionary" } ] }, "pdbx_chi_squared" : { "type" : "number", "description" : "Chi-squared statistic for this resolution shell.", "rcsb_description" : [ { "text" : "Chi-squared statistic for this resolution shell.", "context" : "dictionary" } ] }, "pdbx_diffrn_id" : { "type" : "array", "items" : { "type" : "string", "description" : "An identifier for the diffraction data set corresponding to this resolution shell.\n\n Multiple diffraction data sets specified as a comma separated list.", "rcsb_description" : [ { "text" : "An identifier for the diffraction data set corresponding to this resolution shell.\n\n Multiple diffraction data sets specified as a comma separated list.", "context" : "dictionary" } ] }, "uniqueItems" : false }, "pdbx_netI_over_sigmaI_all" : { "type" : "number", "description" : "The mean of the ratio of the intensities to their\n standard uncertainties of all reflections in the\n resolution shell.\n\n _reflns_shell.pdbx_netI_over_sigmaI_all = ", "rcsb_description" : [ { "text" : "The mean of the ratio of the intensities to their\n standard uncertainties of all reflections in the\n resolution shell.\n\n _reflns_shell.pdbx_netI_over_sigmaI_all = ", "context" : "dictionary" } ] }, "pdbx_netI_over_sigmaI_obs" : { "type" : "number", "description" : "The mean of the ratio of the intensities to their\n standard uncertainties of observed reflections\n (see _reflns.observed_criterion) in the resolution shell.\n\n _reflns_shell.pdbx_netI_over_sigmaI_obs = ", "rcsb_description" : [ { "text" : "The mean of the ratio of the intensities to their\n standard uncertainties of observed reflections\n (see _reflns.observed_criterion) in the resolution shell.\n\n _reflns_shell.pdbx_netI_over_sigmaI_obs = ", "context" : "dictionary" } ] }, "pdbx_ordinal" : { "type" : "integer", "description" : "An ordinal identifier for this resolution shell.", "rcsb_description" : [ { "text" : "An ordinal identifier for this resolution shell.", "context" : "dictionary" } ] }, "pdbx_redundancy" : { "type" : "number", "description" : "Redundancy for the current shell.", "rcsb_description" : [ { "text" : "Redundancy for the current shell.", "context" : "dictionary" }, { "text" : "The redundancy of data collected in this resolution shell", "context" : "deposition" } ] }, "pdbx_rejects" : { "type" : "integer", "description" : "The number of rejected reflections in the resolution\n shell. Reflections may be rejected from scaling\n by setting the observation criterion,\n _reflns.observed_criterion.", "rcsb_description" : [ { "text" : "The number of rejected reflections in the resolution\n shell. Reflections may be rejected from scaling\n by setting the observation criterion,\n _reflns.observed_criterion.", "context" : "dictionary" } ] }, "percent_possible_all" : { "type" : "number", "description" : "The percentage of geometrically possible reflections represented\n by all reflections measured for this shell.", "rcsb_description" : [ { "text" : "The percentage of geometrically possible reflections represented\n by all reflections measured for this shell.", "context" : "dictionary" }, { "text" : "Percentage of possible reflections collected in this resolution shell", "context" : "deposition" } ] }, "percent_possible_obs" : { "type" : "number", "description" : "The percentage of geometrically possible reflections represented\n by reflections classified as 'observed' (see\n _reflns.observed_criterion) for this shell.", "rcsb_description" : [ { "text" : "The percentage of geometrically possible reflections represented\n by reflections classified as 'observed' (see\n _reflns.observed_criterion) for this shell.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "pdbx_ordinal" ] }, "minItems" : 1, "uniqueItems" : true }, "software" : { "type" : "array", "items" : { "type" : "object", "properties" : { "citation_id" : { "type" : "string", "description" : "This data item is a pointer to _citation.id in the CITATION\n category.", "rcsb_description" : [ { "text" : "This data item is a pointer to _citation.id in the CITATION\n category.", "context" : "dictionary" } ] }, "classification" : { "type" : "string", "examples" : [ "data collection", "data reduction", "phasing", "model building", "refinement", "validation", "other" ], "description" : "The classification of the program according to its\n major function.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The classification of the program according to its\n major function.", "context" : "dictionary" }, { "text" : "Classification (Software)", "context" : "brief" } ] }, "contact_author" : { "type" : "string", "examples" : [ "T. Alwyn Jones", "Axel Brunger" ], "description" : "The recognized contact author of the software. This could be\n the original author, someone who has modified the code or\n someone who maintains the code. It should be the person\n most commonly associated with the code.", "rcsb_description" : [ { "text" : "The recognized contact author of the software. This could be\n the original author, someone who has modified the code or\n someone who maintains the code. It should be the person\n most commonly associated with the code.", "context" : "dictionary" } ] }, "contact_author_email" : { "type" : "string", "examples" : [ "bourne@sdsc.edu" ], "description" : "The e-mail address of the person specified in\n _software.contact_author.", "rcsb_description" : [ { "text" : "The e-mail address of the person specified in\n _software.contact_author.", "context" : "dictionary" } ] }, "date" : { "type" : "string", "examples" : [ "1991-10-01", "1990-04-30" ], "description" : "The date the software was released.", "rcsb_description" : [ { "text" : "The date the software was released.", "context" : "dictionary" } ] }, "description" : { "type" : "string", "examples" : [ "Uses method of restrained least squares" ], "description" : "Description of the software.", "rcsb_description" : [ { "text" : "Description of the software.", "context" : "dictionary" } ] }, "language" : { "type" : "string", "enum" : [ "Ada", "Awk", "Basic", "C", "C++", "C/C++", "Fortran", "Fortran 77", "Fortran 90", "Fortran_77", "Java", "Java & Fortran", "Other", "Pascal", "Perl", "Python", "Python/C++", "Tcl", "assembler", "csh", "ksh", "sh" ], "description" : "The major computing language in which the software is\n coded.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The major computing language in which the software is\n coded.", "context" : "dictionary" }, { "text" : "Language (Software)", "context" : "brief" } ] }, "location" : { "type" : "string", "examples" : [ "http://rosebud.sdsc.edu/projects/pb/IUCr/software.html", "ftp://ftp.sdsc.edu/pub/sdsc/biology/" ], "description" : "The URL for an Internet address at which\n details of the software can be found.", "rcsb_description" : [ { "text" : "The URL for an Internet address at which\n details of the software can be found.", "context" : "dictionary" } ] }, "name" : { "type" : "string", "examples" : [ "Merlot", "O", "Xengen", "X-plor" ], "description" : "The name of the software.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The name of the software.", "context" : "dictionary" }, { "text" : "Select the appropriate software used in the structure determination", "context" : "deposition" }, { "text" : "Name (Software)", "context" : "brief" } ] }, "os" : { "type" : "string", "examples" : [ "Ultrix", "OpenVMS", "DOS", "Windows 95", "Windows NT", "Irix", "HPUX", "DEC Unix" ], "description" : "The name of the operating system under which the software\n runs.", "rcsb_description" : [ { "text" : "The name of the operating system under which the software\n runs.", "context" : "dictionary" } ] }, "pdbx_ordinal" : { "type" : "integer", "description" : "An ordinal index for this category", "rcsb_description" : [ { "text" : "An ordinal index for this category", "context" : "dictionary" } ] }, "type" : { "type" : "string", "enum" : [ "filter", "jiffy", "library", "other", "package", "program" ], "description" : "The classification of the software according to the most\n common types.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "filter", "detail" : " filters input and output streams" }, { "value" : "jiffy", "detail" : " short, simple program" }, { "value" : "library", "detail" : " used by a program at load time" }, { "value" : "other", "detail" : " all other kinds of software" }, { "value" : "package", "detail" : " collections of programs with multiple\n functionality" }, { "value" : "program", "detail" : " individual program with limited\n functionality" } ], "rcsb_description" : [ { "text" : "The classification of the software according to the most\n common types.", "context" : "dictionary" }, { "text" : "Type (Software)", "context" : "brief" } ] }, "version" : { "type" : "string", "examples" : [ "v1.0", "beta", "3.1-2", "unknown" ], "description" : "The version of the software.", "rcsb_description" : [ { "text" : "The version of the software.", "context" : "dictionary" }, { "text" : "The version of the refinement software", "context" : "deposition" } ] } }, "additionalProperties" : false, "required" : [ "pdbx_ordinal" ] }, "minItems" : 1, "uniqueItems" : true }, "struct" : { "type" : "object", "properties" : { "pdbx_CASP_flag" : { "type" : "string", "enum" : [ "N", "Y" ], "examples" : [ "Y" ], "description" : "The item indicates whether the entry is a CASP target, a CASD-NMR target,\n or similar target participating in methods development experiments.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "N", "detail" : "No" }, { "value" : "Y", "detail" : "Yes" } ], "rcsb_description" : [ { "text" : "The item indicates whether the entry is a CASP target, a CASD-NMR target,\n or similar target participating in methods development experiments.", "context" : "dictionary" }, { "text" : "Selecting a prediction target identifies the deposition as a CASP (Critical Assessment of Techniques for Protein Structure Prediction), CASD-NMR (Critical Assessment of Automated Structure Determination of Proteins from NMR Data), or Foldit target. When identifying a deposited protein structure as a prediction target, the depositors agree to the conditions of CASP, CASD-NMR, and Foldit: (1) the polymer sequence will be released to the public immediately, and (2) the coordinates and any related data will be released to the public after an eight week hold from the deposition date.", "context" : "deposition" }, { "text" : "Casp Flag (Struct)", "context" : "brief" } ] }, "pdbx_descriptor" : { "type" : "string", "examples" : [ "Cytochrome b5", "Regulatory protein RecX", "Uridine kinase (E.C.2.7.1.48)" ], "description" : "An automatically generated descriptor for an NDB structure or\n the unstructured content of the PDB COMPND record.", "rcsb_description" : [ { "text" : "An automatically generated descriptor for an NDB structure or\n the unstructured content of the PDB COMPND record.", "context" : "dictionary" } ] }, "pdbx_model_details" : { "type" : "string", "examples" : [ "This model was produced from a 10 nanosecond Amber/MD simulation\nstarting from PDB structure ID 1ABC." ], "description" : "Text description of the methodology which produced this\n model structure.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Text description of the methodology which produced this\n model structure.", "context" : "dictionary" }, { "text" : "Model Details (Struct)", "context" : "brief" } ] }, "pdbx_model_type_details" : { "type" : "string", "examples" : [ "MINIMIZED AVERAGE" ], "description" : "A description of the type of structure model.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "A description of the type of structure model.", "context" : "dictionary" }, { "text" : "Model Type Details (Struct)", "context" : "brief" } ] }, "title" : { "type" : "string", "examples" : [ "T4 lysozyme mutant - S32A", "Rhinovirus 16 polymerase elongation complex (r1_form)", "Crystal structure of the OXA-10 W154A mutant at pH 9.0", "Mutant structure of Thermus thermophilus HB8 uridine-cytidine kinase", "Crystal structure of xylanase from Trichoderma longibrachiatum" ], "description" : "A title for the data block. The author should attempt to convey\n the essence of the structure archived in the CIF in the title,\n and to distinguish this structural result from others.", "rcsb_search_context" : [ "full-text", "suggest" ], "rcsb_full_text_priority" : 20, "rcsb_description" : [ { "text" : "A title for the data block. The author should attempt to convey\n the essence of the structure archived in the CIF in the title,\n and to distinguish this structural result from others.", "context" : "dictionary" }, { "text" : "Provide a brief title that describes the contents of the entry and procedures or conditions which set this entry apart from others. For related entries provide unique structure titles emphasizing the underlying purpose of particular experiment.", "context" : "deposition" }, { "text" : "Structure Title", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Structure Details", "priority_order" : 5 } ] } }, "additionalProperties" : false }, "struct_keywords" : { "type" : "object", "properties" : { "pdbx_keywords" : { "type" : "string", "examples" : [ "DNA", "RNA", "T-RNA", "DNA/RNA", "RIBOZYME", "PROTEIN/DNA", "PROTEIN/RNA", "PEPTIDE NUCLEIC ACID", "PEPTIDE NUCLEIC ACID/DNA", "DNA-BINDING PROTEIN", "RNA-BINDING PROTEIN" ], "description" : "Terms characterizing the macromolecular structure.", "rcsb_search_context" : [ "full-text", "suggest" ], "rcsb_full_text_priority" : 20, "rcsb_description" : [ { "text" : "Terms characterizing the macromolecular structure.", "context" : "dictionary" }, { "text" : "Structure Keywords", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "ID(s) and Keywords", "priority_order" : 50 } ] }, "text" : { "type" : "string", "examples" : [ "Inhibitor, Complex, Isomerase...", "serine protease", "inhibited complex", "high-resolution refinement" ], "description" : "Keywords describing this structure.", "rcsb_search_context" : [ "full-text", "suggest" ], "rcsb_full_text_priority" : 20, "rcsb_description" : [ { "text" : "Keywords describing this structure.", "context" : "dictionary" }, { "text" : "Provide the list of keywords that describe your entry (functional class, metabolic role, biological or chemical activity, structural classification, etc.). These will be used to categorize your submission (assign header, function of the small molecule, etc.), and to search the entry within the archive. The keywords should not include long phrases or sentences", "context" : "deposition" }, { "text" : "Additional Structure Keywords", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "ID(s) and Keywords", "priority_order" : 55 } ] } }, "additionalProperties" : false }, "symmetry" : { "type" : "object", "properties" : { "Int_Tables_number" : { "type" : "integer", "description" : "Space-group number from International Tables for Crystallography\n Vol. A (2002).", "rcsb_description" : [ { "text" : "Space-group number from International Tables for Crystallography\n Vol. A (2002).", "context" : "dictionary" } ] }, "cell_setting" : { "type" : "string", "enum" : [ "cubic", "hexagonal", "monoclinic", "orthorhombic", "rhombohedral", "tetragonal", "triclinic", "trigonal" ], "description" : "The cell settings for this space-group symmetry.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The cell settings for this space-group symmetry.", "context" : "dictionary" }, { "text" : "Cell Setting (Symmetry)", "context" : "brief" } ] }, "pdbx_full_space_group_name_H_M" : { "type" : "string", "examples" : [ "Example: 'C 1 2 1' (instead of C 2)\n 'P 1 2 1' (instead of P 2)\n 'P 1 21 1' (instead of P 21)\n 'P 1 1 21' (instead of P 21 -unique C axis)\n 'H 3' (instead of R 3 -hexagonal)\n 'H 3 2' (instead of R 3 2 -hexagonal)" ], "description" : "Used for PDB space group:\n\n Example: 'C 1 2 1' (instead of C 2)\n 'P 1 2 1' (instead of P 2)\n 'P 1 21 1' (instead of P 21)\n 'P 1 1 21' (instead of P 21 -unique C axis)\n 'H 3' (instead of R 3 -hexagonal)\n 'H 3 2' (instead of R 3 2 -hexagonal)", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Used for PDB space group:\n\n Example: 'C 1 2 1' (instead of C 2)\n 'P 1 2 1' (instead of P 2)\n 'P 1 21 1' (instead of P 21)\n 'P 1 1 21' (instead of P 21 -unique C axis)\n 'H 3' (instead of R 3 -hexagonal)\n 'H 3 2' (instead of R 3 2 -hexagonal)", "context" : "dictionary" }, { "text" : "Full Space Group Name H M (Symmetry)", "context" : "brief" } ] }, "space_group_name_H_M" : { "type" : "string", "examples" : [ "A 1", "A 1 2 1", "A 2", "B 1 1 2", "B 2", "B 2 21 2", "C 2", "C 1 2 1", "C 21", "C 1 21 1", "C 2(A 112)", "C 2 2 2", "C 2 2 21", "C 4 21 2", "F 2 2 2", "F 2 3", "F 4 2 2", "F 4 3 2", "F 41 3 2", "I 1 2 1", "I 1 21 1", "I 2", "I 2 2 2", "I 2 3", "I 21", "I 21 3", "I 21 21 21", "I 4", "I 4 2 2", "I 4 3 2", "I 41", "I 41/a", "I 41 2 2", "I 41 3 2", "P 1", "P 1-", "P 2", "P 1 2 1", "P 1 1 2", "P 2 2 2", "P 2 3", "P 2 2 21", "P 2 21 21", "P 21", "P 1 21 1", "P 1 21/c 1", "P 1 1 21", "P 21(C)", "P 21 2 21", "P 21 3", "P 21 21 2", "P 21 21 2 A", "P 21 21 21", "P 3", "P 3 1 2", "P 3 2 1", "P 31", "P 31 1 2", "P 31 2 1", "P 32", "P 32 1 2", "P 32 2 1", "P 4", "P 4 2 2", "P 4 3 2", "P 4 21 2", "P 41", "P 41 2 2", "P 41 3 2", "P 41 21 2", "P 42", "P 42 2 2", "P 42 3 2", "P 42 21 2", "P 43", "P 43 2 2", "P 43 3 2", "P 43 21 2", "P 6", "P 6 2 2", "P 61", "P 61 2 2", "P 62", "P 62 2 2", "P 63", "P 63 2 2", "P 64", "P 64 2 2", "P 65", "P 65 2 2", "H 3", "R 3", "H 3 2", "R 3 2" ], "description" : "Hermann-Mauguin space-group symbol. Note that the\n Hermann-Mauguin symbol does not necessarily contain complete\n information about the symmetry and the space-group origin. If\n used, always supply the FULL symbol from International Tables\n for Crystallography Vol. A (2002) and indicate the origin and\n the setting if it is not implicit. If there is any doubt that\n the equivalent positions can be uniquely deduced from this\n symbol, specify the _symmetry_equiv.pos_as_xyz or\n _symmetry.space_group_name_Hall data items as well. Leave\n spaces between symbols referring to\n different axes.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Hermann-Mauguin space-group symbol. Note that the\n Hermann-Mauguin symbol does not necessarily contain complete\n information about the symmetry and the space-group origin. If\n used, always supply the FULL symbol from International Tables\n for Crystallography Vol. A (2002) and indicate the origin and\n the setting if it is not implicit. If there is any doubt that\n the equivalent positions can be uniquely deduced from this\n symbol, specify the _symmetry_equiv.pos_as_xyz or\n _symmetry.space_group_name_Hall data items as well. Leave\n spaces between symbols referring to\n different axes.", "context" : "dictionary" }, { "text" : "The full crystal space-group symbol", "context" : "deposition" }, { "text" : "Space Group", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Cell Dimensions and Space Group", "priority_order" : 35 } ] }, "space_group_name_Hall" : { "type" : "string", "examples" : [ "-P 2ac 2n", "-R 3 2\"", "P 61 2 2 (0 0 -1)" ], "description" : "Space-group symbol as described by Hall (1981). This symbol\n gives the space-group setting explicitly. Leave spaces between\n the separate components of the symbol.\n\n Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525; erratum\n (1981) A37, 921.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Space-group symbol as described by Hall (1981). This symbol\n gives the space-group setting explicitly. Leave spaces between\n the separate components of the symbol.\n\n Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525; erratum\n (1981) A37, 921.", "context" : "dictionary" }, { "text" : "Space Group Name Hall (Symmetry)", "context" : "brief" } ] } }, "additionalProperties" : false }, "rcsb_pubmed_container_identifiers" : { "type" : "object", "properties" : { "pubmed_id" : { "type" : "integer", "description" : "UID assigned to each PubMed record.", "rcsb_search_context" : [ "default-match" ], "examples" : [ 15937111 ], "rcsb_description" : [ { "text" : "PubMed ID", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "ID(s) and Keywords", "priority_order" : 18 } ], "rcsb_current_maximum_value" : 4.2415474E7, "rcsb_current_minimum_value" : 5.0 } }, "additionalProperties" : false }, "rcsb_pubmed_central_id" : { "type" : "string", "description" : "Unique integer value assigned to each PubMed Central record." }, "rcsb_pubmed_doi" : { "type" : "string", "description" : "Persistent identifier used to provide a link to an article location on the Internet." }, "rcsb_pubmed_abstract_text" : { "type" : "string", "description" : "A concise, accurate and factual mini-version of the paper contents.", "rcsb_search_context" : [ "full-text" ], "rcsb_description" : [ { "text" : "PubMed Abstract", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Publications Primary", "priority_order" : 30 } ] }, "rcsb_pubmed_affiliation_info" : { "type" : "array", "minItems" : 1, "uniqueItems" : true, "items" : { "type" : "string" }, "description" : "The institution(s) that the author is affiliated with. Multiple affiliations per author are allowed." }, "rcsb_pubmed_mesh_descriptors" : { "type" : "array", "minItems" : 1, "uniqueItems" : true, "items" : { "type" : "string" }, "description" : "NLM controlled vocabulary, Medical Subject Headings (MeSH), is used to characterize the content of the articles represented by MEDLINE citations." }, "rcsb_pubmed_mesh_descriptors_lineage" : { "type" : "array", "minItems" : 1, "uniqueItems" : true, "items" : { "type" : "object", "properties" : { "id" : { "type" : "string", "description" : "Identifier for MeSH classification term.", "rcsb_search_context" : [ "exact-match" ], "examples" : [ "E01.370.225.500.388", "H01.181" ], "rcsb_description" : [ { "text" : "MeSH Identifier", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Publications Primary", "priority_order" : 35 } ] }, "name" : { "type" : "string", "description" : "MeSH classification term.", "rcsb_search_context" : [ "exact-match", "full-text" ], "examples" : [ "Chemistry", "Mammals", "Therapeutic Uses" ], "rcsb_description" : [ { "text" : "MeSH Descriptor", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Publications Primary", "priority_order" : 36 } ] }, "depth" : { "type" : "integer", "description" : "Hierarchy depth.", "rcsb_search_context" : [ "default-match" ], "rcsb_current_maximum_value" : 13.0, "rcsb_current_minimum_value" : 0.0, "rcsb_description" : [ { "text" : "Depth (Pubmed Mesh Descriptors Lineage)", "context" : "brief" } ] } }, "additionalProperties" : false }, "rcsb_nested_indexing" : true, "description" : "Members of the MeSH classification lineage." }, "entity_poly" : { "type" : "object", "properties" : { "nstd_linkage" : { "type" : "string", "enum" : [ "n", "no", "y", "yes" ], "description" : "A flag to indicate whether the polymer contains at least\n one monomer-to-monomer link different from that implied by\n _entity_poly.type.", "rcsb_enum_annotated" : [ { "value" : "n", "detail" : "abbreviation for \"no\"" }, { "value" : "no", "detail" : "polymer contains no different links" }, { "value" : "y", "detail" : "abbreviation for \"yes\"" }, { "value" : "yes", "detail" : " polymer contains at least one different\n link" } ], "rcsb_description" : [ { "text" : "A flag to indicate whether the polymer contains at least\n one monomer-to-monomer link different from that implied by\n _entity_poly.type.", "context" : "dictionary" } ] }, "nstd_monomer" : { "type" : "string", "enum" : [ "n", "no", "y", "yes" ], "description" : "A flag to indicate whether the polymer contains at least\n one monomer that is not considered standard.", "rcsb_enum_annotated" : [ { "value" : "n", "detail" : "abbreviation for \"no\"" }, { "value" : "no", "detail" : "polymer contains no nonstandard monomers" }, { "value" : "y", "detail" : "abbreviation for \"yes\"" }, { "value" : "yes", "detail" : " polymer contains at least one nonstandard\n monomer" } ], "rcsb_description" : [ { "text" : "A flag to indicate whether the polymer contains at least\n one monomer that is not considered standard.", "context" : "dictionary" } ] }, "pdbx_seq_one_letter_code" : { "type" : "string", "examples" : [ "HHHH(MSE)AKQRSG or AUCGGAAU", "(MSE)SHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD" ], "description" : "Sequence of protein or nucleic acid polymer in standard one-letter\n codes of amino acids or nucleotides. Non-standard amino\n acids/nucleotides are represented by their Chemical\n Component Dictionary (CCD) codes in\n parenthesis. Deoxynucleotides are represented by the\n specially-assigned 2-letter CCD codes in parenthesis,\n with 'D' prefix added to their ribonucleotide\n counterparts. For hybrid polymer, each residue is\n represented by the code of its individual type. A\n cyclic polymer is represented in linear sequence from\n the chosen start to end.\n\nA for Alanine or Adenosine-5'-monophosphate\nC for Cysteine or Cytidine-5'-monophosphate\nD for Aspartic acid\nE for Glutamic acid\nF for Phenylalanine\nG for Glycine or Guanosine-5'-monophosphate\nH for Histidine\nI for Isoleucine or Inosinic Acid\nL for Leucine\nK for Lysine\nM for Methionine\nN for Asparagine or Unknown ribonucleotide\nO for Pyrrolysine\nP for Proline\nQ for Glutamine\nR for Arginine\nS for Serine\nT for Threonine\nU for Selenocysteine or Uridine-5'-monophosphate\nV for Valine\nW for Tryptophan\nY for Tyrosine\n(DA) for 2'-deoxyadenosine-5'-monophosphate\n(DC) for 2'-deoxycytidine-5'-monophosphate\n(DG) for 2'-deoxyguanosine-5'-monophosphate\n(DT) for Thymidine-5'-monophosphate\n(MSE) for Selenomethionine\n(SEP) for Phosphoserine\n(TPO) for Phosphothreonine\n(PTR) for Phosphotyrosine\n(PCA) for Pyroglutamic acid\n(UNK) for Unknown amino acid\n(ACE) for Acetylation cap\n(NH2) for Amidation cap", "rcsb_description" : [ { "text" : "Sequence of protein or nucleic acid polymer in standard one-letter\n codes of amino acids or nucleotides. Non-standard amino\n acids/nucleotides are represented by their Chemical\n Component Dictionary (CCD) codes in\n parenthesis. Deoxynucleotides are represented by the\n specially-assigned 2-letter CCD codes in parenthesis,\n with 'D' prefix added to their ribonucleotide\n counterparts. For hybrid polymer, each residue is\n represented by the code of its individual type. A\n cyclic polymer is represented in linear sequence from\n the chosen start to end.\n\nA for Alanine or Adenosine-5'-monophosphate\nC for Cysteine or Cytidine-5'-monophosphate\nD for Aspartic acid\nE for Glutamic acid\nF for Phenylalanine\nG for Glycine or Guanosine-5'-monophosphate\nH for Histidine\nI for Isoleucine or Inosinic Acid\nL for Leucine\nK for Lysine\nM for Methionine\nN for Asparagine or Unknown ribonucleotide\nO for Pyrrolysine\nP for Proline\nQ for Glutamine\nR for Arginine\nS for Serine\nT for Threonine\nU for Selenocysteine or Uridine-5'-monophosphate\nV for Valine\nW for Tryptophan\nY for Tyrosine\n(DA) for 2'-deoxyadenosine-5'-monophosphate\n(DC) for 2'-deoxycytidine-5'-monophosphate\n(DG) for 2'-deoxyguanosine-5'-monophosphate\n(DT) for Thymidine-5'-monophosphate\n(MSE) for Selenomethionine\n(SEP) for Phosphoserine\n(TPO) for Phosphothreonine\n(PTR) for Phosphotyrosine\n(PCA) for Pyroglutamic acid\n(UNK) for Unknown amino acid\n(ACE) for Acetylation cap\n(NH2) for Amidation cap", "context" : "dictionary" }, { "text" : "Chemical sequence expressed as string of one-letter amino acid codes. Modifications and non-standard amino acids should be input using the three letter code in parenthesis, e.g. (MSE)", "context" : "deposition" } ] }, "pdbx_seq_one_letter_code_can" : { "type" : "string", "examples" : [ "MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD" ], "description" : "Canonical sequence of protein or nucleic acid polymer in standard\n one-letter codes of amino acids or nucleotides,\n corresponding to the sequence in\n _entity_poly.pdbx_seq_one_letter_code. Non-standard\n amino acids/nucleotides are represented by the codes of\n their parents if parent is specified in\n _chem_comp.mon_nstd_parent_comp_id, or by letter 'X' if\n parent is not specified. Deoxynucleotides are\n represented by their canonical one-letter codes of A,\n C, G, or T.\n\n For modifications with several parent amino acids,\n\t all corresponding parent amino acid codes will be listed\n\t (ex. chromophores).", "rcsb_description" : [ { "text" : "Canonical sequence of protein or nucleic acid polymer in standard\n one-letter codes of amino acids or nucleotides,\n corresponding to the sequence in\n _entity_poly.pdbx_seq_one_letter_code. Non-standard\n amino acids/nucleotides are represented by the codes of\n their parents if parent is specified in\n _chem_comp.mon_nstd_parent_comp_id, or by letter 'X' if\n parent is not specified. Deoxynucleotides are\n represented by their canonical one-letter codes of A,\n C, G, or T.\n\n For modifications with several parent amino acids,\n\t all corresponding parent amino acid codes will be listed\n\t (ex. chromophores).", "context" : "dictionary" } ] }, "pdbx_sequence_evidence_code" : { "type" : "string", "enum" : [ "depositor provided", "derived from coordinates" ], "description" : "Evidence for the assignment of the polymer sequence.", "rcsb_description" : [ { "text" : "Evidence for the assignment of the polymer sequence.", "context" : "dictionary" } ] }, "pdbx_strand_id" : { "type" : "string", "examples" : [ "A,B", "A", "B", "A,B,C" ], "description" : "The PDB strand/chain id(s) corresponding to this polymer entity.", "rcsb_description" : [ { "text" : "The PDB strand/chain id(s) corresponding to this polymer entity.", "context" : "dictionary" } ] }, "pdbx_target_identifier" : { "type" : "string", "examples" : [ "JCSG-11211", "356560" ], "description" : "For Structural Genomics entries, the sequence's target identifier registered at the TargetTrack database.", "rcsb_description" : [ { "text" : "For Structural Genomics entries, the sequence's target identifier registered at the TargetTrack database.", "context" : "dictionary" } ] }, "rcsb_artifact_monomer_count" : { "type" : "integer", "description" : "Number of regions in the sample sequence identified as expression tags, linkers, or\n cloning artifacts.", "rcsb_description" : [ { "text" : "Number of regions in the sample sequence identified as expression tags, linkers, or\n cloning artifacts.", "context" : "dictionary" } ] }, "rcsb_conflict_count" : { "type" : "integer", "description" : "Number of monomer conflicts relative to the reference sequence.", "rcsb_description" : [ { "text" : "Number of monomer conflicts relative to the reference sequence.", "context" : "dictionary" } ] }, "rcsb_deletion_count" : { "type" : "integer", "description" : "Number of monomer deletions relative to the reference sequence.", "rcsb_description" : [ { "text" : "Number of monomer deletions relative to the reference sequence.", "context" : "dictionary" } ] }, "rcsb_entity_polymer_type" : { "type" : "string", "enum" : [ "DNA", "NA-hybrid", "Other", "Protein", "RNA" ], "description" : "A coarse-grained polymer entity type.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "DNA", "detail" : "polydeoxyribonucleotide" }, { "value" : "NA-hybrid", "detail" : "polydeoxyribonucleotide/polyribonucleotide hybrid" }, { "value" : "Other", "detail" : "polysaccharide(D), polysaccharide(L), cyclic-pseudo-peptide, peptide nucleic acid, or other" }, { "value" : "Protein", "detail" : "polypeptide(D) or polypeptide(L)" }, { "value" : "RNA", "detail" : "polyribonucleotide" } ], "rcsb_description" : [ { "text" : "A coarse-grained polymer entity type.", "context" : "dictionary" }, { "text" : "Polymer Entity Type", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Polymer Molecular Features", "priority_order" : 20 } ] }, "rcsb_insertion_count" : { "type" : "integer", "description" : "Number of monomer insertions relative to the reference sequence.", "rcsb_description" : [ { "text" : "Number of monomer insertions relative to the reference sequence.", "context" : "dictionary" } ] }, "rcsb_mutation_count" : { "type" : "integer", "description" : "Number of engineered mutations engineered in the sample sequence.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Number of engineered mutations engineered in the sample sequence.", "context" : "dictionary" }, { "text" : "Polymer Entity Mutation Count", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Polymer Molecular Features", "priority_order" : 30 } ], "rcsb_current_maximum_value" : 657.0, "rcsb_current_minimum_value" : 0.0 }, "rcsb_non_std_monomer_count" : { "type" : "integer", "description" : "Number of non-standard monomers in the sample sequence.", "rcsb_description" : [ { "text" : "Number of non-standard monomers in the sample sequence.", "context" : "dictionary" } ] }, "rcsb_non_std_monomers" : { "type" : "array", "items" : { "type" : "string", "description" : "Unique list of non-standard monomer chemical component identifiers in the sample sequence.", "rcsb_description" : [ { "text" : "Unique list of non-standard monomer chemical component identifiers in the sample sequence.", "context" : "dictionary" } ] }, "uniqueItems" : false }, "rcsb_prd_id" : { "type" : "string", "description" : "For polymer BIRD molecules the BIRD identifier for the entity.", "rcsb_description" : [ { "text" : "For polymer BIRD molecules the BIRD identifier for the entity.", "context" : "dictionary" } ] }, "rcsb_sample_sequence_length" : { "type" : "integer", "description" : "The monomer length of the sample sequence.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The monomer length of the sample sequence.", "context" : "dictionary" }, { "text" : "Polymer Entity Sequence Length", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Polymer Molecular Features", "priority_order" : 25 } ], "rcsb_current_maximum_value" : 43864.0, "rcsb_current_minimum_value" : 1.0 }, "type" : { "type" : "string", "enum" : [ "cyclic-pseudo-peptide", "other", "peptide nucleic acid", "polydeoxyribonucleotide", "polydeoxyribonucleotide/polyribonucleotide hybrid", "polypeptide(D)", "polypeptide(L)", "polyribonucleotide" ], "description" : "The type of the polymer.", "rcsb_description" : [ { "text" : "The type of the polymer.", "context" : "dictionary" } ] } }, "additionalProperties" : false }, "entity_src_gen" : { "type" : "array", "items" : { "type" : "object", "properties" : { "expression_system_id" : { "type" : "string", "description" : "A unique identifier for the expression system. This\n should be extracted from a local list of expression\n systems.", "rcsb_description" : [ { "text" : "A unique identifier for the expression system. This\n should be extracted from a local list of expression\n systems.", "context" : "dictionary" } ] }, "gene_src_common_name" : { "type" : "string", "examples" : [ "man", "yeast", "bacteria" ], "description" : "The common name of the natural organism from which the gene was\n obtained.", "rcsb_description" : [ { "text" : "The common name of the natural organism from which the gene was\n obtained.", "context" : "dictionary" } ] }, "gene_src_details" : { "type" : "string", "description" : "A description of special aspects of the natural organism from\n which the gene was obtained.", "rcsb_description" : [ { "text" : "A description of special aspects of the natural organism from\n which the gene was obtained.", "context" : "dictionary" } ] }, "gene_src_genus" : { "type" : "string", "examples" : [ "Homo", "Saccharomyces", "Escherichia" ], "description" : "The genus of the natural organism from which the gene was\n obtained.", "rcsb_description" : [ { "text" : "The genus of the natural organism from which the gene was\n obtained.", "context" : "dictionary" } ] }, "gene_src_species" : { "type" : "string", "examples" : [ "sapiens", "cerevisiae", "coli" ], "description" : "The species of the natural organism from which the gene was\n obtained.", "rcsb_description" : [ { "text" : "The species of the natural organism from which the gene was\n obtained.", "context" : "dictionary" } ] }, "gene_src_strain" : { "type" : "string", "examples" : [ "DH5a", "BMH 71-18" ], "description" : "The strain of the natural organism from which the gene was\n obtained, if relevant.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The strain of the natural organism from which the gene was\n obtained, if relevant.", "context" : "dictionary" }, { "text" : "Source Organism Strain", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Polymer Molecular Features", "priority_order" : 80 } ] }, "gene_src_tissue" : { "type" : "string", "examples" : [ "heart", "liver", "eye lens" ], "description" : "The tissue of the natural organism from which the gene was\n obtained.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The tissue of the natural organism from which the gene was\n obtained.", "context" : "dictionary" }, { "text" : "Gene Src Tissue (Entity Src Gen)", "context" : "brief" } ] }, "gene_src_tissue_fraction" : { "type" : "string", "examples" : [ "mitochondria", "nucleus", "membrane" ], "description" : "The subcellular fraction of the tissue of the natural organism\n from which the gene was obtained.", "rcsb_description" : [ { "text" : "The subcellular fraction of the tissue of the natural organism\n from which the gene was obtained.", "context" : "dictionary" } ] }, "host_org_common_name" : { "type" : "string", "examples" : [ "yeast", "bacteria" ], "description" : "The common name of the organism that served as host for the\n production of the entity. Where full details of the protein\n production are available it would be expected that this item\n be derived from _entity_src_gen_express.host_org_common_name\n or via _entity_src_gen_express.host_org_tax_id", "rcsb_description" : [ { "text" : "The common name of the organism that served as host for the\n production of the entity. Where full details of the protein\n production are available it would be expected that this item\n be derived from _entity_src_gen_express.host_org_common_name\n or via _entity_src_gen_express.host_org_tax_id", "context" : "dictionary" } ] }, "host_org_details" : { "type" : "string", "description" : "A description of special aspects of the organism that served as\n host for the production of the entity. Where full details of\n the protein production are available it would be expected that\n this item would derived from _entity_src_gen_express.host_org_details", "rcsb_description" : [ { "text" : "A description of special aspects of the organism that served as\n host for the production of the entity. Where full details of\n the protein production are available it would be expected that\n this item would derived from _entity_src_gen_express.host_org_details", "context" : "dictionary" } ] }, "host_org_genus" : { "type" : "string", "examples" : [ "Saccharomyces", "Escherichia" ], "description" : "The genus of the organism that served as host for the production\n of the entity.", "rcsb_description" : [ { "text" : "The genus of the organism that served as host for the production\n of the entity.", "context" : "dictionary" } ] }, "host_org_species" : { "type" : "string", "examples" : [ "cerevisiae", "coli" ], "description" : "The species of the organism that served as host for the\n production of the entity.", "rcsb_description" : [ { "text" : "The species of the organism that served as host for the\n production of the entity.", "context" : "dictionary" } ] }, "pdbx_alt_source_flag" : { "type" : "string", "enum" : [ "model", "sample" ], "description" : "This data item identifies cases in which an alternative source\n modeled.", "rcsb_description" : [ { "text" : "This data item identifies cases in which an alternative source\n modeled.", "context" : "dictionary" } ] }, "pdbx_beg_seq_num" : { "type" : "integer", "description" : "The beginning polymer sequence position for the polymer section corresponding\n to this source.\n\n A reference to the sequence position in the entity_poly category.", "rcsb_description" : [ { "text" : "The beginning polymer sequence position for the polymer section corresponding\n to this source.\n\n A reference to the sequence position in the entity_poly category.", "context" : "dictionary" } ] }, "pdbx_description" : { "type" : "string", "description" : "Information on the source which is not given elsewhere.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Information on the source which is not given elsewhere.", "context" : "dictionary" }, { "text" : "Description (Entity Src Gen)", "context" : "brief" } ] }, "pdbx_end_seq_num" : { "type" : "integer", "description" : "The ending polymer sequence position for the polymer section corresponding\n to this source.\n\n A reference to the sequence position in the entity_poly category.", "rcsb_description" : [ { "text" : "The ending polymer sequence position for the polymer section corresponding\n to this source.\n\n A reference to the sequence position in the entity_poly category.", "context" : "dictionary" } ] }, "pdbx_gene_src_atcc" : { "type" : "string", "examples" : [ "6051" ], "description" : "American Type Culture Collection tissue culture number.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "American Type Culture Collection tissue culture number.", "context" : "dictionary" }, { "text" : "Gene Src Atcc (Entity Src Gen)", "context" : "brief" } ] }, "pdbx_gene_src_cell" : { "type" : "string", "examples" : [ "ENDOTHELIAL" ], "description" : "Cell type.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Cell type.", "context" : "dictionary" }, { "text" : "Gene Src Cell (Entity Src Gen)", "context" : "brief" } ] }, "pdbx_gene_src_cell_line" : { "type" : "string", "examples" : [ "HELA CELLS" ], "description" : "The specific line of cells.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The specific line of cells.", "context" : "dictionary" }, { "text" : "Gene Src Cell Line (Entity Src Gen)", "context" : "brief" } ] }, "pdbx_gene_src_cellular_location" : { "type" : "string", "examples" : [ "CYTOPLASM", "NUCLEUS" ], "description" : "Identifies the location inside (or outside) the cell.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Identifies the location inside (or outside) the cell.", "context" : "dictionary" }, { "text" : "Gene Src Cellular Location (Entity Src Gen)", "context" : "brief" } ] }, "pdbx_gene_src_fragment" : { "type" : "string", "examples" : [ "CYTOPLASM", "NUCLEUS" ], "description" : "A domain or fragment of the molecule.", "rcsb_description" : [ { "text" : "A domain or fragment of the molecule.", "context" : "dictionary" } ] }, "pdbx_gene_src_gene" : { "type" : "string", "description" : "Identifies the gene.", "rcsb_description" : [ { "text" : "Identifies the gene.", "context" : "dictionary" } ] }, "pdbx_gene_src_ncbi_taxonomy_id" : { "type" : "string", "description" : "NCBI Taxonomy identifier for the gene source organism.\n\n Reference:\n\n Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,\n Tatusova TA, Rapp BA (2000). Database resources of the National\n Center for Biotechnology Information. Nucleic Acids Res 2000 Jan\n 1;28(1):10-4\n\n Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,\n Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.", "rcsb_description" : [ { "text" : "NCBI Taxonomy identifier for the gene source organism.\n\n Reference:\n\n Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,\n Tatusova TA, Rapp BA (2000). Database resources of the National\n Center for Biotechnology Information. Nucleic Acids Res 2000 Jan\n 1;28(1):10-4\n\n Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,\n Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.", "context" : "dictionary" }, { "text" : "NCBI Taxonomy identifier for the gene source organism if known", "context" : "deposition" } ] }, "pdbx_gene_src_organ" : { "type" : "string", "examples" : [ "KIDNEY", "LIVER", "PANCREAS" ], "description" : "Organized group of tissues that carries on a specialized function.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Organized group of tissues that carries on a specialized function.", "context" : "dictionary" }, { "text" : "Gene Src Organ (Entity Src Gen)", "context" : "brief" } ] }, "pdbx_gene_src_organelle" : { "type" : "string", "examples" : [ "MITOCHONDRIA" ], "description" : "Organized structure within cell.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Organized structure within cell.", "context" : "dictionary" }, { "text" : "Gene Src Organelle (Entity Src Gen)", "context" : "brief" } ] }, "pdbx_gene_src_scientific_name" : { "type" : "string", "examples" : [ "Homo sapiens", "Saccharomyces Cerevisiae" ], "description" : "Scientific name of the organism.", "rcsb_description" : [ { "text" : "Scientific name of the organism.", "context" : "dictionary" } ] }, "pdbx_gene_src_variant" : { "type" : "string", "examples" : [ "DELTAH1DELTATRP" ], "description" : "Identifies the variant.", "rcsb_description" : [ { "text" : "Identifies the variant.", "context" : "dictionary" } ] }, "pdbx_host_org_atcc" : { "type" : "string", "description" : "Americal Tissue Culture Collection of the expression system. Where\n full details of the protein production are available it would\n be expected that this item would be derived from\n _entity_src_gen_express.host_org_culture_collection", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Americal Tissue Culture Collection of the expression system. Where\n full details of the protein production are available it would\n be expected that this item would be derived from\n _entity_src_gen_express.host_org_culture_collection", "context" : "dictionary" }, { "text" : "Host Org Atcc (Entity Src Gen)", "context" : "brief" } ] }, "pdbx_host_org_cell" : { "type" : "string", "examples" : [ "ENDOTHELIAL" ], "description" : "Cell type from which the gene is derived. Where\n entity.target_id is provided this should be derived from\n details of the target.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Cell type from which the gene is derived. Where\n entity.target_id is provided this should be derived from\n details of the target.", "context" : "dictionary" }, { "text" : "Host Org Cell (Entity Src Gen)", "context" : "brief" } ] }, "pdbx_host_org_cell_line" : { "type" : "string", "examples" : [ "HELA" ], "description" : "A specific line of cells used as the expression system. Where\n full details of the protein production are available it would\n be expected that this item would be derived from\n entity_src_gen_express.host_org_cell_line", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "A specific line of cells used as the expression system. Where\n full details of the protein production are available it would\n be expected that this item would be derived from\n entity_src_gen_express.host_org_cell_line", "context" : "dictionary" }, { "text" : "Host Org Cell Line (Entity Src Gen)", "context" : "brief" } ] }, "pdbx_host_org_cellular_location" : { "type" : "string", "examples" : [ "CYTOPLASM", "NUCLEUS" ], "description" : "Identifies the location inside (or outside) the cell which\n expressed the molecule.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Identifies the location inside (or outside) the cell which\n expressed the molecule.", "context" : "dictionary" }, { "text" : "Host Org Cellular Location (Entity Src Gen)", "context" : "brief" } ] }, "pdbx_host_org_culture_collection" : { "type" : "string", "description" : "Culture collection of the expression system. Where\n full details of the protein production are available it would\n be expected that this item would be derived somehwere, but\n exactly where is not clear.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Culture collection of the expression system. Where\n full details of the protein production are available it would\n be expected that this item would be derived somehwere, but\n exactly where is not clear.", "context" : "dictionary" }, { "text" : "Host Org Culture Collection (Entity Src Gen)", "context" : "brief" } ] }, "pdbx_host_org_gene" : { "type" : "string", "examples" : [ "HIV-1 POL", "GLNS7", "U1A (2-98, Y31H, Q36R)" ], "description" : "Specific gene which expressed the molecule.", "rcsb_description" : [ { "text" : "Specific gene which expressed the molecule.", "context" : "dictionary" } ] }, "pdbx_host_org_ncbi_taxonomy_id" : { "type" : "string", "description" : "NCBI Taxonomy identifier for the expression system organism.\n\n Reference:\n\n Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,\n Tatusova TA, Rapp BA (2000). Database resources of the National\n Center for Biotechnology Information. Nucleic Acids Res 2000 Jan\n 1;28(1):10-4\n\n Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,\n Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.", "rcsb_description" : [ { "text" : "NCBI Taxonomy identifier for the expression system organism.\n\n Reference:\n\n Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,\n Tatusova TA, Rapp BA (2000). Database resources of the National\n Center for Biotechnology Information. Nucleic Acids Res 2000 Jan\n 1;28(1):10-4\n\n Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,\n Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.", "context" : "dictionary" } ] }, "pdbx_host_org_organ" : { "type" : "string", "examples" : [ "KIDNEY" ], "description" : "Specific organ which expressed the molecule.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Specific organ which expressed the molecule.", "context" : "dictionary" }, { "text" : "Host Org Organ (Entity Src Gen)", "context" : "brief" } ] }, "pdbx_host_org_organelle" : { "type" : "string", "examples" : [ "MITOCHONDRIA" ], "description" : "Specific organelle which expressed the molecule.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Specific organelle which expressed the molecule.", "context" : "dictionary" }, { "text" : "Host Org Organelle (Entity Src Gen)", "context" : "brief" } ] }, "pdbx_host_org_scientific_name" : { "type" : "string", "examples" : [ "ESCHERICHIA COLI", "SACCHAROMYCES CEREVISIAE" ], "description" : "The scientific name of the organism that served as host for the\n production of the entity. Where full details of the protein\n production are available it would be expected that this item\n would be derived from _entity_src_gen_express.host_org_scientific_name\n or via _entity_src_gen_express.host_org_tax_id", "rcsb_description" : [ { "text" : "The scientific name of the organism that served as host for the\n production of the entity. Where full details of the protein\n production are available it would be expected that this item\n would be derived from _entity_src_gen_express.host_org_scientific_name\n or via _entity_src_gen_express.host_org_tax_id", "context" : "dictionary" } ] }, "pdbx_host_org_strain" : { "type" : "string", "examples" : [ "AR120" ], "description" : "The strain of the organism in which the entity was\nexpressed.", "rcsb_description" : [ { "text" : "The strain of the organism in which the entity was\nexpressed.", "context" : "dictionary" } ] }, "pdbx_host_org_tissue" : { "type" : "string", "examples" : [ "heart", "liver", "eye lens" ], "description" : "The specific tissue which expressed the molecule. Where full details\n of the protein production are available it would be expected that this\n item would be derived from _entity_src_gen_express.host_org_tissue", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The specific tissue which expressed the molecule. Where full details\n of the protein production are available it would be expected that this\n item would be derived from _entity_src_gen_express.host_org_tissue", "context" : "dictionary" }, { "text" : "Host Org Tissue (Entity Src Gen)", "context" : "brief" } ] }, "pdbx_host_org_tissue_fraction" : { "type" : "string", "examples" : [ "mitochondria", "nucleus", "membrane" ], "description" : "The fraction of the tissue which expressed the\nmolecule.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The fraction of the tissue which expressed the\nmolecule.", "context" : "dictionary" }, { "text" : "Host Org Tissue Fraction (Entity Src Gen)", "context" : "brief" } ] }, "pdbx_host_org_variant" : { "type" : "string", "examples" : [ "TRP-LAC", "LAMBDA DE3" ], "description" : "Variant of the organism used as the expression system. Where\n full details of the protein production are available it would\n be expected that this item be derived from\n entity_src_gen_express.host_org_variant or via\n _entity_src_gen_express.host_org_tax_id", "rcsb_description" : [ { "text" : "Variant of the organism used as the expression system. Where\n full details of the protein production are available it would\n be expected that this item be derived from\n entity_src_gen_express.host_org_variant or via\n _entity_src_gen_express.host_org_tax_id", "context" : "dictionary" } ] }, "pdbx_host_org_vector" : { "type" : "string", "examples" : [ "PBIT36", "PET15B", "PUC18" ], "description" : "Identifies the vector used. Where full details of the protein\n production are available it would be expected that this item\n would be derived from _entity_src_gen_clone.vector_name.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Identifies the vector used. Where full details of the protein\n production are available it would be expected that this item\n would be derived from _entity_src_gen_clone.vector_name.", "context" : "dictionary" }, { "text" : "Host Org Vector (Entity Src Gen)", "context" : "brief" } ] }, "pdbx_host_org_vector_type" : { "type" : "string", "examples" : [ "COSMID", "PLASMID" ], "description" : "Identifies the type of vector used (plasmid, virus, or cosmid).\n Where full details of the protein production are available it\n would be expected that this item would be derived from\n _entity_src_gen_express.vector_type.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Identifies the type of vector used (plasmid, virus, or cosmid).\n Where full details of the protein production are available it\n would be expected that this item would be derived from\n _entity_src_gen_express.vector_type.", "context" : "dictionary" }, { "text" : "Host Org Vector Type (Entity Src Gen)", "context" : "brief" } ] }, "pdbx_seq_type" : { "type" : "string", "enum" : [ "Biological sequence", "C-terminal tag", "Linker", "N-terminal tag" ], "description" : "This data item povides additional information about the sequence type.", "rcsb_description" : [ { "text" : "This data item povides additional information about the sequence type.", "context" : "dictionary" } ] }, "pdbx_src_id" : { "type" : "integer", "description" : "This data item is an ordinal identifier for entity_src_gen data records.", "rcsb_description" : [ { "text" : "This data item is an ordinal identifier for entity_src_gen data records.", "context" : "dictionary" } ] }, "plasmid_details" : { "type" : "string", "description" : "A description of special aspects of the plasmid that produced the\n entity in the host organism. Where full details of the protein\n production are available it would be expected that this item\n would be derived from _pdbx_construct.details of the construct\n pointed to from _entity_src_gen_express.plasmid_id.", "rcsb_description" : [ { "text" : "A description of special aspects of the plasmid that produced the\n entity in the host organism. Where full details of the protein\n production are available it would be expected that this item\n would be derived from _pdbx_construct.details of the construct\n pointed to from _entity_src_gen_express.plasmid_id.", "context" : "dictionary" } ] }, "plasmid_name" : { "type" : "string", "examples" : [ "pET3C", "pT123sab" ], "description" : "The name of the plasmid that produced the entity in the host\n organism. Where full details of the protein production are available\n it would be expected that this item would be derived from\n _pdbx_construct.name of the construct pointed to from\n _entity_src_gen_express.plasmid_id.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The name of the plasmid that produced the entity in the host\n organism. Where full details of the protein production are available\n it would be expected that this item would be derived from\n _pdbx_construct.name of the construct pointed to from\n _entity_src_gen_express.plasmid_id.", "context" : "dictionary" }, { "text" : "Plasmid Name (Entity Src Gen)", "context" : "brief" } ] } }, "additionalProperties" : false, "required" : [ "pdbx_src_id" ] }, "minItems" : 1, "uniqueItems" : true }, "entity_src_nat" : { "type" : "array", "items" : { "type" : "object", "properties" : { "common_name" : { "type" : "string", "examples" : [ "man", "yeast", "bacteria" ], "description" : "The common name of the organism from which the entity\n was isolated.", "rcsb_description" : [ { "text" : "The common name of the organism from which the entity\n was isolated.", "context" : "dictionary" } ] }, "details" : { "type" : "string", "description" : "A description of special aspects of the organism from which the\n entity was isolated.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "A description of special aspects of the organism from which the\n entity was isolated.", "context" : "dictionary" }, { "text" : "Details (Entity Src Nat)", "context" : "brief" } ] }, "genus" : { "type" : "string", "examples" : [ "Homo", "Saccharomyces", "Escherichia" ], "description" : "The genus of the organism from which the entity was isolated.", "rcsb_description" : [ { "text" : "The genus of the organism from which the entity was isolated.", "context" : "dictionary" } ] }, "pdbx_alt_source_flag" : { "type" : "string", "enum" : [ "model", "sample" ], "description" : "This data item identifies cases in which an alternative source\n modeled.", "rcsb_description" : [ { "text" : "This data item identifies cases in which an alternative source\n modeled.", "context" : "dictionary" } ] }, "pdbx_atcc" : { "type" : "string", "examples" : [ "6051" ], "description" : "Americal Tissue Culture Collection number.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Americal Tissue Culture Collection number.", "context" : "dictionary" }, { "text" : "Atcc (Entity Src Nat)", "context" : "brief" } ] }, "pdbx_beg_seq_num" : { "type" : "integer", "description" : "The beginning polymer sequence position for the polymer section corresponding\n to this source.\n\n A reference to the sequence position in the entity_poly category.", "rcsb_description" : [ { "text" : "The beginning polymer sequence position for the polymer section corresponding\n to this source.\n\n A reference to the sequence position in the entity_poly category.", "context" : "dictionary" } ] }, "pdbx_cell" : { "type" : "string", "examples" : [ "BHK-21" ], "description" : "A particular cell type.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "A particular cell type.", "context" : "dictionary" }, { "text" : "Cell (Entity Src Nat)", "context" : "brief" } ] }, "pdbx_cell_line" : { "type" : "string", "examples" : [ "HELA" ], "description" : "The specific line of cells.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The specific line of cells.", "context" : "dictionary" }, { "text" : "Cell Line (Entity Src Nat)", "context" : "brief" } ] }, "pdbx_cellular_location" : { "type" : "string", "description" : "Identifies the location inside (or outside) the cell.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Identifies the location inside (or outside) the cell.", "context" : "dictionary" }, { "text" : "Cellular Location (Entity Src Nat)", "context" : "brief" } ] }, "pdbx_end_seq_num" : { "type" : "integer", "description" : "The ending polymer sequence position for the polymer section corresponding\n to this source.\n\n A reference to the sequence position in the entity_poly category.", "rcsb_description" : [ { "text" : "The ending polymer sequence position for the polymer section corresponding\n to this source.\n\n A reference to the sequence position in the entity_poly category.", "context" : "dictionary" } ] }, "pdbx_fragment" : { "type" : "string", "description" : "A domain or fragment of the molecule.", "rcsb_description" : [ { "text" : "A domain or fragment of the molecule.", "context" : "dictionary" } ] }, "pdbx_ncbi_taxonomy_id" : { "type" : "string", "description" : "NCBI Taxonomy identifier for the source organism.\n\n Reference:\n\n Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,\n Tatusova TA, Rapp BA (2000). Database resources of the National\n Center for Biotechnology Information. Nucleic Acids Res 2000 Jan\n 1;28(1):10-4\n\n Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,\n Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.", "rcsb_description" : [ { "text" : "NCBI Taxonomy identifier for the source organism.\n\n Reference:\n\n Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,\n Tatusova TA, Rapp BA (2000). Database resources of the National\n Center for Biotechnology Information. Nucleic Acids Res 2000 Jan\n 1;28(1):10-4\n\n Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,\n Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.", "context" : "dictionary" }, { "text" : "NCBI Taxonomy identifier for the source organism if known", "context" : "deposition" } ] }, "pdbx_organ" : { "type" : "string", "examples" : [ "KIDNEY" ], "description" : "Organized group of tissues that carries on a specialized function.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Organized group of tissues that carries on a specialized function.", "context" : "dictionary" }, { "text" : "Organ (Entity Src Nat)", "context" : "brief" } ] }, "pdbx_organelle" : { "type" : "string", "examples" : [ "MITOCHONDRIA" ], "description" : "Organized structure within cell.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Organized structure within cell.", "context" : "dictionary" }, { "text" : "Organelle (Entity Src Nat)", "context" : "brief" } ] }, "pdbx_organism_scientific" : { "type" : "string", "examples" : [ "Bos taurus", "BOS TAURUS", "SUS SCROFA", "ASPERGILLUS ORYZAE" ], "description" : "Scientific name of the organism of the natural source.", "rcsb_description" : [ { "text" : "Scientific name of the organism of the natural source.", "context" : "dictionary" } ] }, "pdbx_plasmid_details" : { "type" : "string", "examples" : [ "PLC28 DERIVATIVE" ], "description" : "Details about the plasmid.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Details about the plasmid.", "context" : "dictionary" }, { "text" : "Plasmid Details (Entity Src Nat)", "context" : "brief" } ] }, "pdbx_plasmid_name" : { "type" : "string", "examples" : [ "pB322" ], "description" : "The plasmid containing the gene.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The plasmid containing the gene.", "context" : "dictionary" }, { "text" : "Plasmid Name (Entity Src Nat)", "context" : "brief" } ] }, "pdbx_secretion" : { "type" : "string", "examples" : [ "saliva", "urine", "venom" ], "description" : "Identifies the secretion from which the molecule was isolated.", "rcsb_description" : [ { "text" : "Identifies the secretion from which the molecule was isolated.", "context" : "dictionary" } ] }, "pdbx_src_id" : { "type" : "integer", "description" : "This data item is an ordinal identifier for entity_src_nat data records.", "rcsb_description" : [ { "text" : "This data item is an ordinal identifier for entity_src_nat data records.", "context" : "dictionary" } ] }, "pdbx_variant" : { "type" : "string", "description" : "Identifies the variant.", "rcsb_description" : [ { "text" : "Identifies the variant.", "context" : "dictionary" } ] }, "species" : { "type" : "string", "examples" : [ "sapiens", "cerevisiae", "coli" ], "description" : "The species of the organism from which the entity was isolated.", "rcsb_description" : [ { "text" : "The species of the organism from which the entity was isolated.", "context" : "dictionary" } ] }, "strain" : { "type" : "string", "examples" : [ "DH5a", "BMH 71-18" ], "description" : "The strain of the organism from which the entity was isolated.", "rcsb_description" : [ { "text" : "The strain of the organism from which the entity was isolated.", "context" : "dictionary" } ] }, "tissue" : { "type" : "string", "examples" : [ "heart", "liver", "eye lens" ], "description" : "The tissue of the organism from which the entity was isolated.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The tissue of the organism from which the entity was isolated.", "context" : "dictionary" }, { "text" : "Tissue (Entity Src Nat)", "context" : "brief" } ] }, "tissue_fraction" : { "type" : "string", "examples" : [ "mitochondria", "nucleus", "membrane" ], "description" : "The subcellular fraction of the tissue of the organism from\n which the entity was isolated.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The subcellular fraction of the tissue of the organism from\n which the entity was isolated.", "context" : "dictionary" }, { "text" : "Tissue Fraction (Entity Src Nat)", "context" : "brief" } ] } }, "additionalProperties" : false, "required" : [ "pdbx_src_id" ] }, "minItems" : 1, "uniqueItems" : true }, "pdbx_entity_src_syn" : { "type" : "array", "items" : { "type" : "object", "properties" : { "details" : { "type" : "string", "examples" : [ "This sequence occurs naturally in humans." ], "description" : "A description of special aspects of the source for the\n synthetic entity.", "rcsb_description" : [ { "text" : "A description of special aspects of the source for the\n synthetic entity.", "context" : "dictionary" } ] }, "ncbi_taxonomy_id" : { "type" : "string", "description" : "NCBI Taxonomy identifier of the organism from which the sequence of\n the synthetic entity was derived.\n\n Reference:\n\n Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,\n Tatusova TA, Rapp BA (2000). Database resources of the National\n Center for Biotechnology Information. Nucleic Acids Res 2000 Jan\n 1;28(1):10-4\n\n Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,\n Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.", "rcsb_description" : [ { "text" : "NCBI Taxonomy identifier of the organism from which the sequence of\n the synthetic entity was derived.\n\n Reference:\n\n Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,\n Tatusova TA, Rapp BA (2000). Database resources of the National\n Center for Biotechnology Information. Nucleic Acids Res 2000 Jan\n 1;28(1):10-4\n\n Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,\n Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.", "context" : "dictionary" }, { "text" : "NCBI Taxonomy identifier of the organism from which the sequence of the synthetic entity was derived", "context" : "deposition" } ] }, "organism_common_name" : { "type" : "string", "examples" : [ "house mouse" ], "description" : "The common name of the organism from which the sequence of\n the synthetic entity was derived.", "rcsb_description" : [ { "text" : "The common name of the organism from which the sequence of\n the synthetic entity was derived.", "context" : "dictionary" } ] }, "organism_scientific" : { "type" : "string", "examples" : [ "synthetic construct", "Mus musculus" ], "description" : "The scientific name of the organism from which the sequence of\n the synthetic entity was derived.", "rcsb_description" : [ { "text" : "The scientific name of the organism from which the sequence of\n the synthetic entity was derived.", "context" : "dictionary" } ] }, "pdbx_alt_source_flag" : { "type" : "string", "enum" : [ "model", "sample" ], "description" : "This data item identifies cases in which an alternative source\n modeled.", "rcsb_description" : [ { "text" : "This data item identifies cases in which an alternative source\n modeled.", "context" : "dictionary" } ] }, "pdbx_beg_seq_num" : { "type" : "integer", "description" : "The beginning polymer sequence position for the polymer section corresponding\n to this source.\n\n A reference to the sequence position in the entity_poly category.", "rcsb_description" : [ { "text" : "The beginning polymer sequence position for the polymer section corresponding\n to this source.\n\n A reference to the sequence position in the entity_poly category.", "context" : "dictionary" } ] }, "pdbx_end_seq_num" : { "type" : "integer", "description" : "The ending polymer sequence position for the polymer section corresponding\n to this source.\n\n A reference to the sequence position in the entity_poly category.", "rcsb_description" : [ { "text" : "The ending polymer sequence position for the polymer section corresponding\n to this source.\n\n A reference to the sequence position in the entity_poly category.", "context" : "dictionary" } ] }, "pdbx_src_id" : { "type" : "integer", "description" : "This data item is an ordinal identifier for pdbx_entity_src_syn data records.", "rcsb_description" : [ { "text" : "This data item is an ordinal identifier for pdbx_entity_src_syn data records.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "pdbx_src_id" ] }, "minItems" : 1, "uniqueItems" : true }, "rcsb_cluster_flexibility" : { "type" : "object", "properties" : { "avg_rmsd" : { "type" : "number", "description" : "Average RMSD refer to average pairwise RMSD (Root Mean Square Deviation of C-alpha atoms) between structures in the cluster (95% sequence identity) where a given entity belongs.", "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "Average RMSD refer to average pairwise RMSD (Root Mean Square Deviation of C-alpha atoms) between structures in the cluster (95% sequence identity) where a given entity belongs.", "context" : "dictionary" } ] }, "label" : { "type" : "string", "description" : "Structural flexibility in the cluster (95% sequence identity) where a given entity belongs.", "rcsb_description" : [ { "text" : "Structural flexibility in the cluster (95% sequence identity) where a given entity belongs.", "context" : "dictionary" } ] }, "link" : { "type" : "string", "description" : "Link to the associated PDBFlex database entry.", "rcsb_description" : [ { "text" : "Link to the associated PDBFlex database entry.", "context" : "dictionary" } ] }, "max_rmsd" : { "type" : "number", "description" : "Maximal RMSD refer to maximal pairwise RMSD (Root Mean Square Deviation of C-alpha atoms) between structures in the cluster (95% sequence identity) where a given entity belongs.", "rcsb_units" : "angstroms", "rcsb_description" : [ { "text" : "Maximal RMSD refer to maximal pairwise RMSD (Root Mean Square Deviation of C-alpha atoms) between structures in the cluster (95% sequence identity) where a given entity belongs.", "context" : "dictionary" } ] }, "provenance_code" : { "type" : "string", "enum" : [ "PDBFlex" ], "description" : "Provenance code indicating the origin of the flexibility data.", "rcsb_description" : [ { "text" : "Provenance code indicating the origin of the flexibility data.", "context" : "dictionary" } ] } }, "additionalProperties" : false }, "rcsb_cluster_membership" : { "type" : "array", "items" : { "type" : "object", "properties" : { "cluster_id" : { "type" : "integer", "description" : "Identifier for a cluster at the specified level of sequence identity within the cluster data set.", "rcsb_description" : [ { "text" : "Identifier for a cluster at the specified level of sequence identity within the cluster data set.", "context" : "dictionary" } ] }, "identity" : { "type" : "integer", "description" : "Sequence identity expressed as an integer percent value.", "rcsb_description" : [ { "text" : "Sequence identity expressed as an integer percent value.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "cluster_id", "identity" ] }, "minItems" : 1, "uniqueItems" : true, "rcsb_nested_indexing" : true }, "rcsb_entity_host_organism" : { "type" : "array", "items" : { "type" : "object", "properties" : { "beg_seq_num" : { "type" : "integer", "description" : "The beginning polymer sequence position for the polymer section corresponding\n to this host organism.\n\n A reference to the sequence position in the entity_poly category.", "rcsb_description" : [ { "text" : "The beginning polymer sequence position for the polymer section corresponding\n to this host organism.\n\n A reference to the sequence position in the entity_poly category.", "context" : "dictionary" } ] }, "common_name" : { "type" : "string", "description" : "The common name of the host organism", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The common name of the host organism", "context" : "dictionary" }, { "text" : "Common Name (Entity Host Organism)", "context" : "brief" } ] }, "end_seq_num" : { "type" : "integer", "description" : "The ending polymer sequence position for the polymer section corresponding\n to this host organism.\n\n A reference to the sequence position in the entity_poly category.", "rcsb_description" : [ { "text" : "The ending polymer sequence position for the polymer section corresponding\n to this host organism.\n\n A reference to the sequence position in the entity_poly category.", "context" : "dictionary" } ] }, "ncbi_common_names" : { "type" : "array", "items" : { "type" : "string", "description" : "Common names associated with this taxonomy code obtained from NCBI Taxonomy Database.\n\n These names correspond to the taxonomy identifier assigned by the PDB depositor.\n\nReferences:\n\nSayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V,\nChurch DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY,\nHelmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR,\nMiller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E,\nSherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G,\nTatusova TA, Wagner L, Yaschenko E, Ye J (2009). Database resources\nof the National Center for Biotechnology Information. Nucleic Acids\nRes. 2009 Jan;37(Database issue):D5-15. Epub 2008 Oct 21.\n\nBenson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009).\nGenBank. Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31.\nEpub 2008 Oct 21.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Common names associated with this taxonomy code obtained from NCBI Taxonomy Database.\n\n These names correspond to the taxonomy identifier assigned by the PDB depositor.\n\nReferences:\n\nSayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V,\nChurch DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY,\nHelmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR,\nMiller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E,\nSherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G,\nTatusova TA, Wagner L, Yaschenko E, Ye J (2009). Database resources\nof the National Center for Biotechnology Information. Nucleic Acids\nRes. 2009 Jan;37(Database issue):D5-15. Epub 2008 Oct 21.\n\nBenson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009).\nGenBank. Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31.\nEpub 2008 Oct 21.", "context" : "dictionary" }, { "text" : "Common Name of Expression Organism", "context" : "brief" } ] }, "uniqueItems" : false }, "ncbi_parent_scientific_name" : { "type" : "string", "description" : "The parent scientific name in the NCBI taxonomy hierarchy (depth=1) associated with this taxonomy code.\n\nReferences:\n\nSayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V,\nChurch DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY,\nHelmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR,\nMiller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E,\nSherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G,\nTatusova TA, Wagner L, Yaschenko E, Ye J (2009). Database resources\nof the National Center for Biotechnology Information. Nucleic Acids\nRes. 2009 Jan;37(Database issue):D5-15. Epub 2008 Oct 21.\n\nBenson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009).\nGenBank. Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31.\nEpub 2008 Oct 21.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The parent scientific name in the NCBI taxonomy hierarchy (depth=1) associated with this taxonomy code.\n\nReferences:\n\nSayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V,\nChurch DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY,\nHelmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR,\nMiller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E,\nSherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G,\nTatusova TA, Wagner L, Yaschenko E, Ye J (2009). Database resources\nof the National Center for Biotechnology Information. Nucleic Acids\nRes. 2009 Jan;37(Database issue):D5-15. Epub 2008 Oct 21.\n\nBenson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009).\nGenBank. Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31.\nEpub 2008 Oct 21.", "context" : "dictionary" }, { "text" : "Ncbi Parent Scientific Name (Entity Host Organism)", "context" : "brief" } ] }, "ncbi_scientific_name" : { "type" : "string", "description" : "The scientific name associated with this taxonomy code aggregated by the NCBI Taxonomy Database.\n\n This name corresponds to the taxonomy identifier assigned by the PDB depositor.\n\n\nReferences:\n\nSayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V,\nChurch DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY,\nHelmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR,\nMiller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E,\nSherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G,\nTatusova TA, Wagner L, Yaschenko E, Ye J (2009). Database resources\nof the National Center for Biotechnology Information. Nucleic Acids\nRes. 2009 Jan;37(Database issue):D5-15. Epub 2008 Oct 21.\n\nBenson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009).\nGenBank. Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31.\nEpub 2008 Oct 21.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The scientific name associated with this taxonomy code aggregated by the NCBI Taxonomy Database.\n\n This name corresponds to the taxonomy identifier assigned by the PDB depositor.\n\n\nReferences:\n\nSayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V,\nChurch DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY,\nHelmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR,\nMiller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E,\nSherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G,\nTatusova TA, Wagner L, Yaschenko E, Ye J (2009). Database resources\nof the National Center for Biotechnology Information. Nucleic Acids\nRes. 2009 Jan;37(Database issue):D5-15. Epub 2008 Oct 21.\n\nBenson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009).\nGenBank. Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31.\nEpub 2008 Oct 21.", "context" : "dictionary" }, { "text" : "Expression Organism", "context" : "brief" } ] }, "ncbi_taxonomy_id" : { "type" : "integer", "description" : "NCBI Taxonomy identifier for the host organism.\n\n\n Reference:\n\n Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,\n Tatusova TA, Rapp BA (2000). Database resources of the National\n Center for Biotechnology Information. Nucleic Acids Res 2000 Jan\n 1;28(1):10-4\n\n Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,\n Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.", "rcsb_description" : [ { "text" : "NCBI Taxonomy identifier for the host organism.\n\n\n Reference:\n\n Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,\n Tatusova TA, Rapp BA (2000). Database resources of the National\n Center for Biotechnology Information. Nucleic Acids Res 2000 Jan\n 1;28(1):10-4\n\n Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,\n Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.", "context" : "dictionary" } ] }, "pdbx_src_id" : { "type" : "integer", "description" : "An identifier for an entity segment.", "rcsb_description" : [ { "text" : "An identifier for an entity segment.", "context" : "dictionary" } ] }, "provenance_source" : { "type" : "string", "enum" : [ "PDB Primary Data", "Primary Data" ], "description" : "A code indicating the provenance of the host organism.", "rcsb_description" : [ { "text" : "A code indicating the provenance of the host organism.", "context" : "dictionary" } ] }, "scientific_name" : { "type" : "string", "description" : "The scientific name of the host organism", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The scientific name of the host organism", "context" : "dictionary" }, { "text" : "Scientific Name (Entity Host Organism)", "context" : "brief" } ] }, "taxonomy_lineage" : { "type" : "array", "items" : { "type" : "object", "properties" : { "depth" : { "type" : "integer", "description" : "Members of the NCBI Taxonomy lineage as parent taxonomy lineage depth (1-N)", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Members of the NCBI Taxonomy lineage as parent taxonomy lineage depth (1-N)", "context" : "dictionary" }, { "text" : "Depth (Taxonomy Lineage)", "context" : "brief" } ], "rcsb_current_maximum_value" : 40.0, "rcsb_current_minimum_value" : 1.0 }, "id" : { "type" : "string", "examples" : [ "469008", "10469" ], "description" : "Members of the NCBI Taxonomy lineage as parent taxonomy idcodes.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Members of the NCBI Taxonomy lineage as parent taxonomy idcodes.", "context" : "dictionary" }, { "text" : "Expression System Organism Taxonomy ID", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Polymer Molecular Features", "priority_order" : 105 } ] }, "name" : { "type" : "string", "examples" : [ "Escherichia coli BL21(DE3)", "Baculovirus" ], "description" : "Members of the NCBI Taxonomy lineage as parent taxonomy names.", "rcsb_search_context" : [ "exact-match", "full-text", "suggest" ], "rcsb_full_text_priority" : 20, "rcsb_description" : [ { "text" : "Members of the NCBI Taxonomy lineage as parent taxonomy names.", "context" : "dictionary" }, { "text" : "Expression System Organism Taxonomy Name", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Polymer Molecular Features", "priority_order" : 100 } ] } }, "additionalProperties" : false }, "uniqueItems" : false } }, "additionalProperties" : false, "required" : [ "pdbx_src_id" ] }, "minItems" : 1, "uniqueItems" : true }, "rcsb_entity_source_organism" : { "type" : "array", "items" : { "type" : "object", "properties" : { "beg_seq_num" : { "type" : "integer", "description" : "The beginning polymer sequence position for the polymer section corresponding\n to this source.\n\n A reference to the sequence position in the entity_poly category.", "rcsb_description" : [ { "text" : "The beginning polymer sequence position for the polymer section corresponding\n to this source.\n\n A reference to the sequence position in the entity_poly category.", "context" : "dictionary" } ] }, "common_name" : { "type" : "string", "description" : "The common name for the source organism assigned by the PDB depositor.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The common name for the source organism assigned by the PDB depositor.", "context" : "dictionary" }, { "text" : "Common Name (Entity Source Organism)", "context" : "brief" } ] }, "end_seq_num" : { "type" : "integer", "description" : "The ending polymer sequence position for the polymer section corresponding\n to this source.\n\n A reference to the sequence position in the entity_poly category.", "rcsb_description" : [ { "text" : "The ending polymer sequence position for the polymer section corresponding\n to this source.\n\n A reference to the sequence position in the entity_poly category.", "context" : "dictionary" } ] }, "ncbi_common_names" : { "type" : "array", "items" : { "type" : "string", "examples" : [ "human", "mouse", "pig" ], "description" : "Common names associated with this taxonomy code aggregated by the NCBI Taxonomy Database.\n\n These name correspond to the taxonomy identifier assigned by the PDB depositor.\n\nReferences:\n\nSayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V,\nChurch DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY,\nHelmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR,\nMiller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E,\nSherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G,\nTatusova TA, Wagner L, Yaschenko E, Ye J (2009). Database resources\nof the National Center for Biotechnology Information. Nucleic Acids\nRes. 2009 Jan;37(Database issue):D5-15. Epub 2008 Oct 21.\n\nBenson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009).\nGenBank. Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31.\nEpub 2008 Oct 21.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Common names associated with this taxonomy code aggregated by the NCBI Taxonomy Database.\n\n These name correspond to the taxonomy identifier assigned by the PDB depositor.\n\nReferences:\n\nSayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V,\nChurch DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY,\nHelmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR,\nMiller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E,\nSherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G,\nTatusova TA, Wagner L, Yaschenko E, Ye J (2009). Database resources\nof the National Center for Biotechnology Information. Nucleic Acids\nRes. 2009 Jan;37(Database issue):D5-15. Epub 2008 Oct 21.\n\nBenson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009).\nGenBank. Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31.\nEpub 2008 Oct 21.", "context" : "dictionary" }, { "text" : "Common Name of the Source Organism", "context" : "brief" } ] }, "uniqueItems" : false }, "ncbi_parent_scientific_name" : { "type" : "string", "examples" : [ "Archaea", "Bacteria", "Eukaryota", "Adnaviria", "Bicaudaviridae", "Clavaviridae", "Duplodnaviria" ], "description" : "A parent scientific name in the NCBI taxonomy hierarchy of the source organism assigned by the PDB depositor.\n For cellular organism this corresponds to a superkingdom (e.g., Archaea, Bacteria, Eukaryota). For viruses this\n corresponds to a clade (e.g. Adnaviria, Bicaudaviridae, Clavaviridae). For other and unclassified entries this\n corresponds to the first level of any taxonomic rank below the root level.\n\nReferences:\n\nSayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V,\nChurch DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY,\nHelmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR,\nMiller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E,\nSherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G,\nTatusova TA, Wagner L, Yaschenko E, Ye J (2009). Database resources\nof the National Center for Biotechnology Information. Nucleic Acids\nRes. 2009 Jan;37(Database issue):D5-15. Epub 2008 Oct 21.\n\nBenson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009).\nGenBank. Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31.\nEpub 2008 Oct 21.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "A parent scientific name in the NCBI taxonomy hierarchy of the source organism assigned by the PDB depositor.\n For cellular organism this corresponds to a superkingdom (e.g., Archaea, Bacteria, Eukaryota). For viruses this\n corresponds to a clade (e.g. Adnaviria, Bicaudaviridae, Clavaviridae). For other and unclassified entries this\n corresponds to the first level of any taxonomic rank below the root level.\n\nReferences:\n\nSayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V,\nChurch DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY,\nHelmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR,\nMiller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E,\nSherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G,\nTatusova TA, Wagner L, Yaschenko E, Ye J (2009). Database resources\nof the National Center for Biotechnology Information. Nucleic Acids\nRes. 2009 Jan;37(Database issue):D5-15. Epub 2008 Oct 21.\n\nBenson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009).\nGenBank. Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31.\nEpub 2008 Oct 21.", "context" : "dictionary" }, { "text" : "Parent Scientific Name (typically superkingdom or clade)", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Polymer Molecular Features", "priority_order" : 70 } ] }, "ncbi_scientific_name" : { "type" : "string", "description" : "The scientific name associated with this taxonomy code aggregated by the NCBI Taxonomy Database.\n\n This name corresponds to the taxonomy identifier assigned by the PDB depositor.\n\n\nReferences:\n\nSayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V,\nChurch DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY,\nHelmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR,\nMiller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E,\nSherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G,\nTatusova TA, Wagner L, Yaschenko E, Ye J (2009). Database resources\nof the National Center for Biotechnology Information. Nucleic Acids\nRes. 2009 Jan;37(Database issue):D5-15. Epub 2008 Oct 21.\n\nBenson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009).\nGenBank. Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31.\nEpub 2008 Oct 21.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The scientific name associated with this taxonomy code aggregated by the NCBI Taxonomy Database.\n\n This name corresponds to the taxonomy identifier assigned by the PDB depositor.\n\n\nReferences:\n\nSayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V,\nChurch DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY,\nHelmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR,\nMiller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E,\nSherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G,\nTatusova TA, Wagner L, Yaschenko E, Ye J (2009). Database resources\nof the National Center for Biotechnology Information. Nucleic Acids\nRes. 2009 Jan;37(Database issue):D5-15. Epub 2008 Oct 21.\n\nBenson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009).\nGenBank. Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31.\nEpub 2008 Oct 21.", "context" : "dictionary" }, { "text" : "Scientific Name of the Source Organism", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Polymer Molecular Features", "priority_order" : 65 } ] }, "ncbi_taxonomy_id" : { "type" : "integer", "description" : "NCBI Taxonomy identifier for the gene source organism assigned by the PDB depositor.\n\n Reference:\n\n Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,\n Tatusova TA, Rapp BA (2000). Database resources of the National\n Center for Biotechnology Information. Nucleic Acids Res 2000 Jan\n 1;28(1):10-4\n\n Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,\n Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.", "rcsb_description" : [ { "text" : "NCBI Taxonomy identifier for the gene source organism assigned by the PDB depositor.\n\n Reference:\n\n Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,\n Tatusova TA, Rapp BA (2000). Database resources of the National\n Center for Biotechnology Information. Nucleic Acids Res 2000 Jan\n 1;28(1):10-4\n\n Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,\n Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.", "context" : "dictionary" } ] }, "pdbx_src_id" : { "type" : "integer", "description" : "An identifier for the entity segment.", "rcsb_description" : [ { "text" : "An identifier for the entity segment.", "context" : "dictionary" } ] }, "provenance_source" : { "type" : "string", "enum" : [ "NCBI", "PDB Primary Data", "Primary Data", "UniProt" ], "description" : "Reference to the provenance of the source organism details for the entity. \n Primary data indicates information obtained from the same source as the structural model.\n UniProt and NCBI are provided as alternate sources of provenance for organism details.", "rcsb_description" : [ { "text" : "Reference to the provenance of the source organism details for the entity. \n Primary data indicates information obtained from the same source as the structural model.\n UniProt and NCBI are provided as alternate sources of provenance for organism details.", "context" : "dictionary" } ] }, "scientific_name" : { "type" : "string", "description" : "The scientific name of the source organism assigned by the PDB depositor.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The scientific name of the source organism assigned by the PDB depositor.", "context" : "dictionary" }, { "text" : "Scientific Name (Entity Source Organism)", "context" : "brief" } ] }, "source_type" : { "type" : "string", "enum" : [ "genetically engineered", "natural", "synthetic" ], "description" : "The source type for the entity", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The source type for the entity", "context" : "dictionary" }, { "text" : "Source Organism Type", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Polymer Molecular Features", "priority_order" : 75 } ] }, "taxonomy_lineage" : { "type" : "array", "items" : { "type" : "object", "properties" : { "depth" : { "type" : "integer", "description" : "Members of the NCBI Taxonomy lineage as parent taxonomy lineage depth (1-N)", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Members of the NCBI Taxonomy lineage as parent taxonomy lineage depth (1-N)", "context" : "dictionary" }, { "text" : "Depth (Taxonomy Lineage)", "context" : "brief" } ], "rcsb_current_maximum_value" : 41.0, "rcsb_current_minimum_value" : 1.0 }, "id" : { "type" : "string", "examples" : [ "9606", "10090" ], "description" : "Members of the NCBI Taxonomy lineage as parent taxonomy idcodes.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Members of the NCBI Taxonomy lineage as parent taxonomy idcodes.", "context" : "dictionary" }, { "text" : "Source Organism Taxonomy ID (Full Lineage)", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Polymer Molecular Features", "priority_order" : 60 } ] }, "name" : { "type" : "string", "examples" : [ "Homo sapiens", "Mus musculus" ], "description" : "Memebers of the NCBI Taxonomy lineage as parent taxonomy names.", "rcsb_search_context" : [ "exact-match", "full-text", "suggest" ], "rcsb_full_text_priority" : 20, "rcsb_description" : [ { "text" : "Memebers of the NCBI Taxonomy lineage as parent taxonomy names.", "context" : "dictionary" }, { "text" : "Source Organism Taxonomy Name (Full Lineage)", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Polymer Molecular Features", "priority_order" : 55 } ] } }, "additionalProperties" : false }, "uniqueItems" : false }, "rcsb_gene_name" : { "type" : "array", "items" : { "type" : "object", "properties" : { "provenance_source" : { "type" : "string", "enum" : [ "NCBI", "PDB Primary Data", "Primary Data", "UniProt" ], "description" : "A code indicating the provenance of the source organism details for the entity", "rcsb_description" : [ { "text" : "A code indicating the provenance of the source organism details for the entity", "context" : "dictionary" } ] }, "value" : { "type" : "string", "examples" : [ "lacA", "hemH" ], "description" : "Gene name.", "rcsb_search_context" : [ "exact-match", "suggest" ], "rcsb_full_text_priority" : 20, "rcsb_description" : [ { "text" : "Gene name.", "context" : "dictionary" }, { "text" : "Gene Name", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Polymer Molecular Features", "priority_order" : 50 } ] } }, "additionalProperties" : false }, "uniqueItems" : false } }, "additionalProperties" : false, "required" : [ "pdbx_src_id" ] }, "minItems" : 1, "uniqueItems" : true }, "rcsb_genomic_lineage" : { "type" : "array", "items" : { "type" : "object", "properties" : { "depth" : { "type" : "integer", "description" : "Classification hierarchy depth.", "rcsb_description" : [ { "text" : "Classification hierarchy depth.", "context" : "dictionary" } ] }, "id" : { "type" : "string", "examples" : [ "9606", "568815441", "414325" ], "description" : "Automatically assigned ID that uniquely identifies taxonomy, chromosome or gene in the Genome Location Browser.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Automatically assigned ID that uniquely identifies taxonomy, chromosome or gene in the Genome Location Browser.", "context" : "dictionary" }, { "text" : "Chromosomal Locus (Browser ID)", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Polymer Molecular Features", "priority_order" : 160 } ] }, "name" : { "type" : "string", "examples" : [ "Homo sapiens", "8", "defensin beta 103A" ], "description" : "A human-readable term name.", "rcsb_description" : [ { "text" : "A human-readable term name.", "context" : "dictionary" } ] } }, "additionalProperties" : false }, "minItems" : 1, "uniqueItems" : true }, "rcsb_membrane_lineage" : { "type" : "array", "items" : { "type" : "object", "properties" : { "depth" : { "type" : "integer", "description" : "Hierarchy depth.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Hierarchy depth.", "context" : "dictionary" }, { "text" : "Depth (Membrane Lineage)", "context" : "brief" } ], "rcsb_current_maximum_value" : 2.0, "rcsb_current_minimum_value" : 0.0 }, "id" : { "type" : "string", "examples" : [ "MONOTOPIC MEMBRANE PROTEINS.Oxidases.Monoamine Oxidase A" ], "description" : "Automatically assigned ID for membrane classification term in the Membrane Protein Browser.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Automatically assigned ID for membrane classification term in the Membrane Protein Browser.", "context" : "dictionary" }, { "text" : "Id (Membrane Lineage)", "context" : "brief" } ] }, "name" : { "type" : "string", "description" : "Membrane protein classification term.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Membrane protein classification term.", "context" : "dictionary" }, { "text" : "Name (Membrane Lineage)", "context" : "brief" } ] } }, "additionalProperties" : false }, "minItems" : 1, "uniqueItems" : true, "rcsb_nested_indexing" : true }, "rcsb_polymer_entity" : { "type" : "object", "properties" : { "details" : { "type" : "string", "description" : "A description of special aspects of the entity.", "rcsb_description" : [ { "text" : "A description of special aspects of the entity.", "context" : "dictionary" } ] }, "formula_weight" : { "type" : "number", "examples" : [ 40.0, 105.0 ], "description" : "Formula mass (KDa) of the entity.", "rcsb_search_context" : [ "default-match" ], "rcsb_units" : "kilodaltons", "rcsb_description" : [ { "text" : "Formula mass (KDa) of the entity.", "context" : "dictionary" }, { "text" : "Polymer Entity Molecular Weight", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Polymer Molecular Features", "priority_order" : 35 } ], "rcsb_current_maximum_value" : 13596.138, "rcsb_current_minimum_value" : 0.075 }, "pdbx_description" : { "type" : "string", "examples" : [ "Green fluorescent protein", "23S ribosomal RNA", "NAD-dependent protein deacylase sirtuin-5, mitochondrial" ], "description" : "A description of the polymer entity.", "rcsb_search_context" : [ "exact-match", "full-text", "suggest" ], "rcsb_full_text_priority" : 20, "rcsb_description" : [ { "text" : "A description of the polymer entity.", "context" : "dictionary" }, { "text" : "Polymer Entity Description", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Polymer Molecular Features", "priority_order" : 5 } ] }, "pdbx_ec" : { "type" : "string", "examples" : [ "2.7.7.7" ], "description" : "Enzyme Commission (EC) number(s)", "rcsb_description" : [ { "text" : "Enzyme Commission (EC) number(s)", "context" : "dictionary" } ] }, "pdbx_fragment" : { "type" : "string", "examples" : [ "KLENOW FRAGMENT", "REPLICASE OPERATOR HAIRPIN", "C-TERMINAL DOMAIN" ], "description" : "Polymer entity fragment description(s).", "rcsb_description" : [ { "text" : "Polymer entity fragment description(s).", "context" : "dictionary" } ] }, "pdbx_mutation" : { "type" : "string", "examples" : [ "Y31H", "DEL(298-323)" ], "description" : "Details about any polymer entity mutation(s).", "rcsb_description" : [ { "text" : "Details about any polymer entity mutation(s).", "context" : "dictionary" } ] }, "pdbx_number_of_molecules" : { "type" : "integer", "description" : "The number of molecules of the entity in the entry.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of molecules of the entity in the entry.", "context" : "dictionary" }, { "text" : "Number Of Molecules (Polymer Entity)", "context" : "brief" } ], "rcsb_current_maximum_value" : 1356.0, "rcsb_current_minimum_value" : 1.0 }, "rcsb_multiple_source_flag" : { "type" : "string", "enum" : [ "N", "Y" ], "description" : "A code indicating the entity has multiple biological sources.", "rcsb_description" : [ { "text" : "A code indicating the entity has multiple biological sources.", "context" : "dictionary" } ] }, "rcsb_source_part_count" : { "type" : "integer", "description" : "The number of biological sources for the polymer entity. Multiple source contributions\n may come from the same organism (taxonomy).", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of biological sources for the polymer entity. Multiple source contributions\n may come from the same organism (taxonomy).", "context" : "dictionary" }, { "text" : "Polymer Entity Source Count", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Polymer Molecular Features", "priority_order" : 85 } ], "rcsb_current_maximum_value" : 21.0, "rcsb_current_minimum_value" : 0.0 }, "rcsb_source_taxonomy_count" : { "type" : "integer", "description" : "The number of distinct source taxonomies for the polymer entity. Commonly used to identify chimeric polymers.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The number of distinct source taxonomies for the polymer entity. Commonly used to identify chimeric polymers.", "context" : "dictionary" }, { "text" : "Polymer Entity Distinct Taxonomy Count", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Polymer Molecular Features", "priority_order" : 90 } ], "rcsb_current_maximum_value" : 5.0, "rcsb_current_minimum_value" : 0.0 }, "src_method" : { "type" : "string", "enum" : [ "man", "nat", "syn" ], "description" : "The method by which the sample for the polymer entity was produced.\n Entities isolated directly from natural sources (tissues, soil\n samples etc.) are expected to have further information in the\n ENTITY_SRC_NAT category. Entities isolated from genetically\n manipulated sources are expected to have further information in\n the ENTITY_SRC_GEN category.", "rcsb_enum_annotated" : [ { "value" : "man", "detail" : " entity isolated from a genetically\n manipulated source" }, { "value" : "nat", "detail" : " entity isolated from a natural source" }, { "value" : "syn", "detail" : " entity obtained synthetically" } ], "rcsb_description" : [ { "text" : "The method by which the sample for the polymer entity was produced.\n Entities isolated directly from natural sources (tissues, soil\n samples etc.) are expected to have further information in the\n ENTITY_SRC_NAT category. Entities isolated from genetically\n manipulated sources are expected to have further information in\n the ENTITY_SRC_GEN category.", "context" : "dictionary" }, { "text" : "The method by which the sample for the polymer entity was produced", "context" : "deposition" } ] }, "rcsb_ec_lineage" : { "type" : "array", "items" : { "type" : "object", "properties" : { "depth" : { "type" : "integer", "description" : "Members of the enzyme classification lineage as parent classification hierarchy depth (1-N).", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Members of the enzyme classification lineage as parent classification hierarchy depth (1-N).", "context" : "dictionary" }, { "text" : "Depth (Ec Lineage)", "context" : "brief" } ], "rcsb_current_maximum_value" : 4.0, "rcsb_current_minimum_value" : 1.0 }, "id" : { "type" : "string", "examples" : [ "2", "2.7.1.153" ], "description" : "Members of the enzyme classification lineage as parent classification codes.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Members of the enzyme classification lineage as parent classification codes.", "context" : "dictionary" }, { "text" : "Enzyme Classification Number", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Polymer Molecular Features", "priority_order" : 110 } ] }, "name" : { "type" : "string", "examples" : [ "Transferases", "phosphatidylinositol-4,5-bisphosphate 3-kinase" ], "description" : "Members of the enzyme classification lineage as parent classification names.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Members of the enzyme classification lineage as parent classification names.", "context" : "dictionary" }, { "text" : "Enzyme Classification Name", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Polymer Molecular Features", "priority_order" : 115 } ] } }, "additionalProperties" : false }, "uniqueItems" : false, "rcsb_nested_indexing" : true }, "rcsb_macromolecular_names_combined" : { "type" : "array", "items" : { "type" : "object", "properties" : { "name" : { "type" : "string", "examples" : [ "Lysozyme C", "Plasmid recombination enzyme", "Pyruvate carboxylase" ], "description" : "Combined list of macromolecular names.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Combined list of macromolecular names.", "context" : "dictionary" }, { "text" : "Macromolecule Name", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Polymer Molecular Features", "priority_order" : 10 } ] }, "provenance_code" : { "type" : "string", "description" : "Combined list of macromolecular names associated provenance code.\n\n ECO (https://github.com/evidenceontology/evidenceontology)", "rcsb_description" : [ { "text" : "Combined list of macromolecular names associated provenance code.\n\n ECO (https://github.com/evidenceontology/evidenceontology)", "context" : "dictionary" } ] }, "provenance_source" : { "type" : "string", "enum" : [ "PDB Preferred Name", "PDB Synonym" ], "description" : "Combined list of macromolecular names associated name source.", "rcsb_description" : [ { "text" : "Combined list of macromolecular names associated name source.", "context" : "dictionary" } ] } }, "additionalProperties" : false }, "uniqueItems" : false }, "rcsb_enzyme_class_combined" : { "type" : "array", "items" : { "type" : "object", "properties" : { "depth" : { "type" : "integer", "description" : "The enzyme classification hierarchy depth (1-N).", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The enzyme classification hierarchy depth (1-N).", "context" : "dictionary" }, { "text" : "Depth (Enzyme Class Combined)", "context" : "brief" } ], "rcsb_current_maximum_value" : 4.0, "rcsb_current_minimum_value" : 1.0 }, "ec" : { "type" : "string", "description" : "Combined list of enzyme class assignments.", "rcsb_search_context" : [ "exact-match", "full-text" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Combined list of enzyme class assignments.", "context" : "dictionary" }, { "text" : "Ec (Enzyme Class Combined)", "context" : "brief" } ] }, "provenance_source" : { "type" : "string", "enum" : [ "PDB Primary Data", "UniProt" ], "description" : "Combined list of enzyme class associated provenance sources.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Combined list of enzyme class associated provenance sources.", "context" : "dictionary" }, { "text" : "Provenance Source (Enzyme Class Combined)", "context" : "brief" } ] } }, "additionalProperties" : false }, "uniqueItems" : false, "rcsb_nested_indexing" : true }, "rcsb_polymer_name_combined" : { "type" : "object", "properties" : { "names" : { "type" : "array", "items" : { "type" : "string", "description" : "Protein name annotated by the UniProtKB or macromolecular name assigned by the PDB.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Protein name annotated by the UniProtKB or macromolecular name assigned by the PDB.", "context" : "dictionary" }, { "text" : "Polymer Entity Name Combined", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Polymer Molecular Features", "priority_order" : 15 } ] }, "uniqueItems" : true, "minItems" : 1 }, "provenance_source" : { "type" : "string", "enum" : [ "PDB Description", "PDB Preferred Name", "UniProt Name" ], "description" : "Provenance source for the combined protein names.", "rcsb_enum_annotated" : [ { "value" : "PDB Description", "detail" : "PDB Description", "name" : "A description of the entity (_entity.pdbx_description)" }, { "value" : "PDB Preferred Name", "detail" : "PDB Preferred Name", "name" : "A description of special aspects of the entity 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entity sequence in PDB entry" }, { "value" : "UniProt", "detail" : "The reference polymer sequence in UniProt entry" } ], "rcsb_description" : [ { "text" : "Code residue coordinate system for the assigned feature.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "enum" : [ "CARD_MODEL", "IMGT_ANTIBODY_DESCRIPTION", "IMGT_ANTIBODY_DOMAIN_NAME", "IMGT_ANTIBODY_GENE_ALLELE_NAME", "IMGT_ANTIBODY_ORGANISM_NAME", "IMGT_ANTIBODY_PROTEIN_NAME", "IMGT_ANTIBODY_RECEPTOR_DESCRIPTION", "IMGT_ANTIBODY_RECEPTOR_TYPE", "Pfam", "SABDAB_ANTIBODY_ANTIGEN_NAME", "SABDAB_ANTIBODY_NAME", "SABDAB_ANTIBODY_TARGET", "artifact", "disorder", "disorder_binding", "hydropathy", "modified_monomer", "mutation" ], "examples" : [ "mutation", "artifact" ], "description" : "A type or category of the feature.", "rcsb_enum_annotated" : [ { "value" : "CARD_MODEL", "detail" : "Comprehensive Antibiotic Resistance Database Detection Model", "name" : "CARD AMR Detection Model" }, { "value" : "IMGT_ANTIBODY_DESCRIPTION", "detail" : "International Immunogenetic Information System (IMGT) antibody description", "name" : "IMGT Antibody Description" }, { "value" : "IMGT_ANTIBODY_DOMAIN_NAME", "detail" : "International Immunogenetic Information System (IMGT) domain name", "name" : "IMGT Antibody Domain Name" }, { "value" : "IMGT_ANTIBODY_GENE_ALLELE_NAME", "detail" : "International Immunogenetic Information System (IMGT) gene and allele name", "name" : "IMGT Antibody Gene and Allele Name" }, { "value" : "IMGT_ANTIBODY_ORGANISM_NAME", "detail" : "International Immunogenetic Information System (IMGT) organism name", "name" : "IMGT Antibody Organism Name" }, { "value" : "IMGT_ANTIBODY_PROTEIN_NAME", "detail" : "International Immunogenetic Information System (IMGT) protein name", "name" : "IMGT Antibody Protein Name" }, { "value" : "IMGT_ANTIBODY_RECEPTOR_DESCRIPTION", "detail" : "International Immunogenetic Information System (IMGT) receptor description", "name" : "IMGT Antibody Receptor Description" }, { "value" : "IMGT_ANTIBODY_RECEPTOR_TYPE", "detail" : "International Immunogenetic Information System (IMGT) receptor type", "name" : "IMGT Antibody Receptor Type" }, { "value" : "Pfam", "detail" : "Pfam Protein Family", "name" : "Pfam Protein Family" }, { "value" : "SABDAB_ANTIBODY_ANTIGEN_NAME", "detail" : "Structural Antibody Database (SAbDab) antibody antigen name", "name" : "SAbDab Antibody Antigen Name" }, { "value" : "SABDAB_ANTIBODY_NAME", "detail" : "Therapeutic Structural Antibody Database (Thera-SAbDab) antibody name", "name" : "SAbDab Antibody Name" }, { "value" : "SABDAB_ANTIBODY_TARGET", "detail" : "Therapeutic Structural Antibody Database (Thera-SAbDab) antigen targeted by the antibody", "name" : "SAbDab Antibody Target" }, { "value" : "artifact", "detail" : "Cloning artifact, expression tag, linker", "name" : "Cloning artifact, expression tag, linker" }, { "value" : "disorder", "detail" : "Per-residue intrinsic disorder probability", "name" : "Predicted disorder" }, { "value" : "disorder_binding", "detail" : "Per-residue disorder-to-binding propensity score", "name" : "Predicted binding disorder" }, { "value" : "hydropathy", "detail" : "Per-residue hydropathy score", "name" : "Hydropathy score" }, { "value" : "modified_monomer", "detail" : "Modified chemical component", "name" : "Modified chemical component" }, { "value" : "mutation", "detail" : "Engineered mutations and chemical modifications", "name" : "Engineered mutations and chemical modifications" } ], "rcsb_description" : [ { "text" : "A type or category of the feature.", "context" : "dictionary" }, { "text" : "Feature Type", "context" : "brief" } ] }, "feature_positions" : { "type" : "array", "items" : { "type" : "object", "properties" : { "beg_comp_id" : { "type" : "string", "examples" : [ "TRP", "VAL" ], "description" : "An identifier for the leading monomer corresponding to the feature assignment.", "rcsb_description" : [ { "text" : "An identifier for the leading monomer corresponding to the feature assignment.", "context" : "dictionary" } ] }, "beg_seq_id" : { "type" : "integer", "description" : "An identifier for the monomer at which this segment of the feature begins.", "rcsb_description" : [ { "text" : "An identifier for the monomer at which this segment of the feature begins.", "context" : "dictionary" } ] }, "end_seq_id" : { "type" : "integer", "description" : "An identifier for the monomer at which this segment of the feature ends.", "rcsb_description" : [ { "text" : "An identifier for the monomer at which this segment of the feature ends.", "context" : "dictionary" } ] }, "value" : { "type" : "number", "examples" : [ 5.0, 0.25 ], "description" : "The value for the feature over this monomer segment.", "rcsb_description" : [ { "text" : "The value for the feature over this monomer segment.", "context" : "dictionary" } ] }, "values" : { "type" : "array", "items" : { "type" : "number", "examples" : [ 5.0, 0.25 ], "description" : "The value(s) for the feature over this monomer segment.", "rcsb_description" : [ { "text" : "The value(s) for the feature over this monomer segment.", "context" : "dictionary" } ] }, "uniqueItems" : false } }, "additionalProperties" : false, "required" : [ "beg_seq_id" ] }, "uniqueItems" : false }, "additional_properties" : { "type" : "array", "items" : { "type" : "object", "properties" : { "name" : { "type" : "string", "enum" : [ "CARD_MODEL_DESCRIPTION", "CARD_MODEL_ORGANISM", "PARENT_COMP_ID" ], "examples" : [ "PARENT_COMP_ID" ], "description" : "The additional property name.", "rcsb_enum_annotated" : [ { "value" : "CARD_MODEL_DESCRIPTION", "detail" : "CARD Model Description" }, { "value" : "CARD_MODEL_ORGANISM", "detail" : "CARD Model Organism" }, { "value" : "PARENT_COMP_ID", "detail" : "Parent Chemical Component Reference Dictionary Identifier" } ], "rcsb_description" : [ { "text" : "The additional property name.", "context" : "dictionary" } ] }, "values" : { "type" : "array", "items" : { "anyOf" : [ { "type" : "string" }, { "type" : "integer" }, { "type" : "number" } ], "examples" : [ "globin-like", "2.54", "300" ], "description" : "The value(s) of the additional property.", "rcsb_description" : [ { "text" : "The value(s) of the additional property.", "context" : "dictionary" } ] }, "uniqueItems" : false } }, "additionalProperties" : false }, "uniqueItems" : false } }, "additionalProperties" : false, "required" : [ "type" ] }, "minItems" : 1, "uniqueItems" : true }, "rcsb_polymer_entity_feature_summary" : { "type" : "array", "items" : { "type" : "object", "properties" : { "count" : { "type" : "integer", "description" : "The feature count.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The feature count.", "context" : "dictionary" }, { "text" : "Count Per Polymer Entity", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Polymer Molecular Features", "priority_order" : 140 } ] }, "coverage" : { "type" : "number", "examples" : [ 0.012, 0.00132 ], "description" : "The fractional feature coverage relative to the full entity sequence.\n For instance, the fraction of features such as mutations, artifacts or modified monomers\n relative to the length of the entity sequence.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The fractional feature coverage relative to the full entity sequence.\n For instance, the fraction of features such as mutations, artifacts or modified monomers\n relative to the length of the entity sequence.", "context" : "dictionary" }, { "text" : "Coverage Fraction Per Polymer Entity", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Polymer Molecular Features", "priority_order" : 145 } ] }, "maximum_length" : { "type" : "integer", "description" : "The maximum feature length.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The maximum feature length.", "context" : "dictionary" }, { "text" : "Maximum Length (Polymer Entity Feature Summary)", "context" : "brief" } ], "rcsb_current_maximum_value" : 1001.0, "rcsb_current_minimum_value" : 1.0 }, "maximum_value" : { "type" : "number", "examples" : [ 1.012, 0.813 ], "description" : "The maximum feature value.", "rcsb_description" : [ { "text" : "The maximum feature value.", "context" : "dictionary" } ] }, "minimum_length" : { "type" : "integer", "description" : "The minimum feature length.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The minimum feature length.", "context" : "dictionary" }, { "text" : "Minimum Length (Polymer Entity Feature Summary)", "context" : "brief" } ], "rcsb_current_maximum_value" : 1001.0, "rcsb_current_minimum_value" : 1.0 }, "minimum_value" : { "type" : "number", "examples" : [ 0.012, 0.00132 ], "description" : "The minimum feature value.", "rcsb_description" : [ { "text" : "The minimum feature value.", "context" : "dictionary" } ] }, "type" : { "type" : "string", "enum" : [ "CARD_MODEL", "IMGT_ANTIBODY_DESCRIPTION", "IMGT_ANTIBODY_DOMAIN_NAME", "IMGT_ANTIBODY_GENE_ALLELE_NAME", "IMGT_ANTIBODY_ORGANISM_NAME", "IMGT_ANTIBODY_PROTEIN_NAME", "IMGT_ANTIBODY_RECEPTOR_DESCRIPTION", "IMGT_ANTIBODY_RECEPTOR_TYPE", "Pfam", "SABDAB_ANTIBODY_ANTIGEN_NAME", "SABDAB_ANTIBODY_NAME", "SABDAB_ANTIBODY_TARGET", "artifact", "modified_monomer", "mutation" ], "examples" : [ "mutation", "artifact" ], "description" : "Type or category of the feature.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "CARD_MODEL", "detail" : "Comprehensive Antibiotic Resistance Database Detection Model", "name" : "CARD AMR Detection Model" }, { "value" : "IMGT_ANTIBODY_DESCRIPTION", "detail" : "International Immunogenetic Information System (IMGT) antibody description", "name" : "IMGT Antibody Description" }, { "value" : "IMGT_ANTIBODY_DOMAIN_NAME", "detail" : "International Immunogenetic Information System (IMGT) domain name", "name" : "IMGT Antibody Domain Name" }, { "value" : "IMGT_ANTIBODY_GENE_ALLELE_NAME", "detail" : "International Immunogenetic Information System (IMGT) gene and allele name", "name" : "IMGT Antibody Gene and Allele Name" }, { "value" : "IMGT_ANTIBODY_ORGANISM_NAME", "detail" : "International Immunogenetic Information System (IMGT) organism name", "name" : "IMGT Antibody Organism Name" }, { "value" : "IMGT_ANTIBODY_PROTEIN_NAME", "detail" : "International Immunogenetic Information System (IMGT) protein name", "name" : "IMGT Antibody Protein Name" }, { "value" : "IMGT_ANTIBODY_RECEPTOR_DESCRIPTION", "detail" : "International Immunogenetic Information System (IMGT) receptor description", "name" : "IMGT Antibody Receptor Description" }, { "value" : "IMGT_ANTIBODY_RECEPTOR_TYPE", "detail" : "International Immunogenetic Information System (IMGT) receptor type", "name" : "IMGT Antibody Receptor Type" }, { "value" : "Pfam", "detail" : "Pfam Protein Family", "name" : "Pfam Protein Family" }, { "value" : "SABDAB_ANTIBODY_ANTIGEN_NAME", "detail" : "Structural Antibody Database (SAbDab) antibody antigen name", "name" : "SAbDab Antibody Antigen Name" }, { "value" : "SABDAB_ANTIBODY_NAME", "detail" : "Therapeutic Structural Antibody Database (Thera-SAbDab) antibody name", "name" : "SAbDab Antibody Name" }, { "value" : "SABDAB_ANTIBODY_TARGET", "detail" : "Therapeutic Structural Antibody Database (Thera-SAbDab) antigen targeted by the antibody", "name" : "SAbDab Antibody Target" }, { "value" : "artifact", "detail" : "Cloning artifact, expression tag, linker", "name" : "Cloning artifact, expression tag, linker" }, { "value" : "modified_monomer", "detail" : "Modified chemical component", "name" : "Modified chemical component" }, { "value" : "mutation", "detail" : "Engineered mutations and chemical modifications", "name" : "Engineered mutations and chemical modifications" } ], "rcsb_description" : [ { "text" : "Type or category of the feature.", "context" : "dictionary" }, { "text" : "Type (Polymer Entity Feature Summary)", "context" : "brief" } ] } }, "additionalProperties" : false }, "minItems" : 1, "uniqueItems" : true, "rcsb_nested_indexing" : true, "rcsb_nested_indexing_context" : [ { "category_name" : "feature_summary", "category_path" : "rcsb_polymer_entity_feature_summary.type", "context_attributes" : [ { "context_value" : "artifact", "attributes" : [ { "examples" : [ 1, 10 ], "path" : "rcsb_polymer_entity_feature_summary.count", "rcsb_current_minimum_value" : 1.0, "rcsb_current_maximum_value" : 22.0 }, { "examples" : [ 0.02, 0.12 ], "path" : "rcsb_polymer_entity_feature_summary.coverage", "rcsb_current_minimum_value" : 3.0E-4, "rcsb_current_maximum_value" : 0.97279 } ] }, { "context_value" : "modified_monomer", "attributes" : [ { "examples" : [ 2, 5 ], "path" : "rcsb_polymer_entity_feature_summary.count", "rcsb_current_minimum_value" : 1.0, "rcsb_current_maximum_value" : 4128.0 }, { "examples" : [ 0.01, 0.05 ], "path" : "rcsb_polymer_entity_feature_summary.coverage", "rcsb_current_minimum_value" : 3.0E-4, "rcsb_current_maximum_value" : 1.0 } ] } ] } ] }, "rcsb_polymer_entity_group_membership" : { "type" : "array", "items" : { "type" : "object", "properties" : { "aggregation_method" : { "type" : "string", "enum" : [ "matching_uniprot_accession", "sequence_identity" ], "description" : "Method used to establish group membership", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Method used to establish group membership", "context" : "dictionary" }, { "text" : "Aggregation Method (Polymer Entity Group Membership)", "context" : "brief" } ] }, "group_id" : { "type" : "string", "examples" : [ "1_100", "P00003" ], "description" : "A unique identifier for a group of entities", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "A unique identifier for a group of entities", "context" : "dictionary" }, { "text" : "Polymer Entity Group ID(s)", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "ID(s) and Keywords", "priority_order" : 65 } ] }, "similarity_cutoff" : { "type" : "number", "description" : "Degree of similarity expressed as a floating-point number", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "Degree of similarity expressed as a floating-point number", "context" : "dictionary" }, { "text" : "Similarity Cutoff (Polymer Entity Group Membership)", "context" : "brief" } ], "rcsb_current_maximum_value" : 100.0, "rcsb_current_minimum_value" : 30.0 }, "aligned_regions" : { "type" : "array", "items" : { "type" : "object", "properties" : { "entity_beg_seq_id" : { "type" : "integer", "description" : "An identifier for the monomer in the entity sequence at which this segment of the alignment begins.", "rcsb_description" : [ { "text" : "An identifier for the monomer in the entity sequence at which this segment of the alignment begins.", "context" : "dictionary" } ] }, "length" : { "type" : "integer", "description" : "The length of this segment of the alignment.", "rcsb_description" : [ { "text" : "The length of this segment of the alignment.", "context" : "dictionary" } ] }, "ref_beg_seq_id" : { "type" : "integer", "description" : "An identifier for the monomer in the reference sequence at which this segment of the alignment begins.", "rcsb_description" : [ { "text" : "An identifier for the monomer in the reference sequence at which this segment of the alignment begins.", "context" : "dictionary" } ] } }, "additionalProperties" : false }, "uniqueItems" : false } }, "additionalProperties" : false, "required" : [ "aggregation_method", "group_id" ] }, "minItems" : 1, "uniqueItems" : true, "rcsb_nested_indexing" : true }, "rcsb_polymer_entity_keywords" : { "type" : "object", "properties" : { "text" : { "type" : "string", "description" : "Keywords describing this polymer entity.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "Keywords describing this polymer entity.", "context" : "dictionary" }, { "text" : "Text (Polymer Entity Keywords)", "context" : "brief" } ] } }, "additionalProperties" : false }, "rcsb_polymer_entity_name_com" : { "type" : "array", "items" : { "type" : "object", "properties" : { "name" : { "type" : "string", "examples" : [ "HIV protease monomer", "hemoglobin alpha chain" ], "description" : "A common name for the polymer entity.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "A common name for the polymer entity.", "context" : "dictionary" }, { "text" : "Name (Polymer Entity Name Com)", "context" : "brief" } ] } }, "additionalProperties" : false, "required" : [ "name" ] }, "minItems" : 1, "uniqueItems" : true }, "rcsb_polymer_entity_name_sys" : { "type" : "array", "items" : { "type" : "object", "properties" : { "name" : { "type" : "string", "description" : "The systematic name for the polymer entity.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The systematic name for the polymer entity.", "context" : "dictionary" }, { "text" : "Name (Polymer Entity Name Sys)", "context" : "brief" } ] }, "system" : { "type" : "string", "examples" : [ "Chemical Abstracts conventions" ], "description" : "The system used to generate the systematic name of the polymer entity.", "rcsb_description" : [ { "text" : "The system used to generate the systematic name of the polymer entity.", "context" : "dictionary" } ] } }, "additionalProperties" : false, "required" : [ "name" ] }, "minItems" : 1, "uniqueItems" : true }, "rcsb_related_target_references" : { "type" : "array", "items" : { "type" : "object", "properties" : { "related_resource_name" : { "type" : "string", "enum" : [ "ChEMBL", "DrugBank", "Pharos" ], "examples" : [ "DrugBank", "ChEMBL", "Pharos" ], "description" : "The related target data resource name.", "rcsb_enum_annotated" : [ { "value" : "ChEMBL", "detail" : "ChEMBL, manually curated database of bioactive molecules with drug-like properties", "name" : "ChEMBL" }, { "value" : "DrugBank", "detail" : "DrugBank, database containing information on drugs and drug targets", "name" : "DrugBank" }, { "value" : "Pharos", "detail" : "User interface to the Knowledge Management Center (KMC) for the Illuminating the Druggable Genome (IDG)", "name" : "Pharos" } ], "rcsb_description" : [ { "text" : "The related target data resource name.", "context" : "dictionary" } ] }, "related_resource_version" : { "type" : "string", "examples" : [ "6.11.0" ], "description" : "The version of the target data resource.", "rcsb_description" : [ { "text" : "The version of the target data resource.", "context" : "dictionary" } ] }, "related_target_id" : { "type" : "string", "description" : "An identifier for the target sequence in the related data resource.", "rcsb_description" : [ { "text" : "An identifier for the target sequence in the related data resource.", "context" : "dictionary" } ] }, "target_taxonomy_id" : { "type" : "integer", "description" : "NCBI Taxonomy identifier for the target organism.\n\n Reference:\n\n Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,\n Tatusova TA, Rapp BA (2000). Database resources of the National\n Center for Biotechnology Information. Nucleic Acids Res 2000 Jan\n 1;28(1):10-4\n\n Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,\n Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.", "rcsb_description" : [ { "text" : "NCBI Taxonomy identifier for the target organism.\n\n Reference:\n\n Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD,\n Tatusova TA, Rapp BA (2000). Database resources of the National\n Center for Biotechnology Information. Nucleic Acids Res 2000 Jan\n 1;28(1):10-4\n\n Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA,\n Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.", "context" : "dictionary" } ] }, "aligned_target" : { "type" : "array", "items" : { "type" : "object", "properties" : { "entity_beg_seq_id" : { "type" : "integer", "description" : "The position of the monomer in the entity sequence at which the alignment begins.", "rcsb_description" : [ { "text" : "The position of the monomer in the entity sequence at which the alignment begins.", "context" : "dictionary" } ] }, "length" : { "type" : "integer", "description" : "The length of the alignment.", "rcsb_description" : [ { "text" : "The length of the alignment.", "context" : "dictionary" } ] }, "target_beg_seq_id" : { "type" : "integer", "description" : "The position of the monomer in the target sequence at which the alignment begins.", "rcsb_description" : [ { "text" : "The position of the monomer in the target sequence at which the alignment begins.", "context" : "dictionary" } ] } }, "additionalProperties" : false }, "uniqueItems" : false } }, "additionalProperties" : false }, "minItems" : 1, "uniqueItems" : true }, "rcsb_target_cofactors" : { "type" : "array", "items" : { "type" : "object", "properties" : { "binding_assay_value" : { "type" : "number", "examples" : [ 6.82 ], "description" : "The value measured or determined by the assay.", "rcsb_description" : [ { "text" : "The value measured or determined by the assay.", "context" : "dictionary" } ] }, "binding_assay_value_type" : { "type" : "string", "enum" : [ "pAC50", "pEC50", "pIC50", "pKd", "pKi" ], "examples" : [ "pIC50", "pEC50" ], "description" : "The type of measurement or value determined by the assay.", "rcsb_enum_annotated" : [ { "value" : "pAC50", "detail" : "half maximal activity concentration ", "name" : "pAC50", "units" : "-log(M)" }, { "value" : "pEC50", "detail" : "half maximal effective concentration", "name" : "pEC50", "units" : "-log(M)" }, { "value" : "pIC50", "detail" : "half maximal inhibitory concentration ", "name" : "pIC50", "units" : "-log(M)" }, { "value" : "pKd", "detail" : "binding dissociation constant", "name" : "pKd", "units" : "-log(M)" }, { "value" : "pKi", "detail" : "binding inhibitory constant", "name" : "pKi", "units" : "-log(M)" } ], "rcsb_description" : [ { "text" : "The type of measurement or value determined by the assay.", "context" : "dictionary" } ] }, "cofactor_InChIKey" : { "type" : "string", "examples" : [ "BNOCDEBUFVJMQI-REOHCLBHSA-N" ], "description" : "Standard IUPAC International Chemical Identifier (InChI) descriptor key\n for the cofactor.\n\n InChI, the IUPAC International Chemical Identifier,\n by Stephen R Heller, Alan McNaught, Igor Pletnev, Stephen Stein and Dmitrii Tchekhovskoi,\n Journal of Cheminformatics, 2015, 7:23", "rcsb_description" : [ { "text" : "Standard IUPAC International Chemical Identifier (InChI) descriptor key\n for the cofactor.\n\n InChI, the IUPAC International Chemical Identifier,\n by Stephen R Heller, Alan McNaught, Igor Pletnev, Stephen Stein and Dmitrii Tchekhovskoi,\n Journal of Cheminformatics, 2015, 7:23", "context" : "dictionary" } ] }, "cofactor_SMILES" : { "type" : "string", "examples" : [ "OC(=O)[CH](CF)O[P](O)(O)=O" ], "description" : "Simplified molecular-input line-entry system (SMILES) descriptor for the cofactor.\n\n Weininger D (February 1988). \"SMILES, a chemical language and information system. 1.\n Introduction to methodology and encoding rules\". Journal of Chemical Information and Modeling. 28 (1): 31-6.\n\n Weininger D, Weininger A, Weininger JL (May 1989).\n \"SMILES. 2. Algorithm for generation of unique SMILES notation\",\n Journal of Chemical Information and Modeling. 29 (2): 97-101.", "rcsb_description" : [ { "text" : "Simplified molecular-input line-entry system (SMILES) descriptor for the cofactor.\n\n Weininger D (February 1988). \"SMILES, a chemical language and information system. 1.\n Introduction to methodology and encoding rules\". Journal of Chemical Information and Modeling. 28 (1): 31-6.\n\n Weininger D, Weininger A, Weininger JL (May 1989).\n \"SMILES. 2. Algorithm for generation of unique SMILES notation\",\n Journal of Chemical Information and Modeling. 29 (2): 97-101.", "context" : "dictionary" } ] }, "cofactor_chem_comp_id" : { "type" : "string", "examples" : [ "0Z3", "CD9" ], "description" : "The chemical component definition identifier for the cofactor.", "rcsb_description" : [ { "text" : "The chemical component definition identifier for the cofactor.", "context" : "dictionary" } ] }, "cofactor_description" : { "type" : "string", "examples" : [ "A synthetic naphthoquinone without the isoprenoid side chain and biological activity,\n but can be converted to active vitamin K2, menaquinone, after alkylation in vivo." ], "description" : "The cofactor description.", "rcsb_description" : [ { "text" : "The cofactor description.", "context" : "dictionary" } ] }, "cofactor_name" : { "type" : "string", "examples" : [ "Menadione" ], "description" : "The cofactor name.", "rcsb_description" : [ { "text" : "The cofactor name.", "context" : "dictionary" } ] }, "cofactor_prd_id" : { "type" : "string", "examples" : [ "PRD_000010" ], "description" : "The BIRD definition identifier for the cofactor.", "rcsb_description" : [ { "text" : "The BIRD definition identifier for the cofactor.", "context" : "dictionary" } ] }, "cofactor_resource_id" : { "type" : "string", "examples" : [ "CHEMBL1987", "DB00170" ], "description" : "Identifier for the cofactor assigned by the resource.", "rcsb_description" : [ { "text" : "Identifier for the cofactor assigned by the resource.", "context" : "dictionary" } ] }, "mechanism_of_action" : { "type" : "string", "examples" : [ "Menadione (vitamin K3) is involved as a cofactor in the posttranslational gamma-carboxylation of glutamic acid residues of certain proteins i\nn the body. These proteins include the vitamin K-dependent coagulation factors II (prothrombin), VII (proconvertin), IX (Christmas factor), X (Stuart factor), protein\nC, protein S, protein Zv and a growth-arrest-specific factor (Gas6)." ], "description" : "Mechanism of action describes the biochemical interaction through which the\n cofactor produces a pharmacological effect.", "rcsb_description" : [ { "text" : "Mechanism of action describes the biochemical interaction through which the\n cofactor produces a pharmacological effect.", "context" : "dictionary" } ] }, "neighbor_flag" : { "type" : "string", "enum" : [ "N", "Y" ], "examples" : [ "Y", "N" ], "description" : "A flag to indicate the cofactor is a structural neighbor of this\n entity.", "rcsb_enum_annotated" : [ { "value" : "N", "detail" : "No", "name" : "N" }, { "value" : "Y", "detail" : "Yes", "name" : "Y" } ], "rcsb_description" : [ { "text" : "A flag to indicate the cofactor is a structural neighbor of this\n entity.", "context" : "dictionary" } ] }, "patent_nos" : { "type" : "array", "items" : { "type" : "string", "examples" : [ "US9346839" ], "description" : "Patent numbers reporting the pharmacology or activity data.", "rcsb_description" : [ { "text" : "Patent numbers reporting the pharmacology or activity data.", "context" : "dictionary" } ] }, "uniqueItems" : false }, "pubmed_ids" : { "type" : "array", "items" : { "type" : "integer", "description" : "PubMed identifiers for literature supporting the pharmacology or activity data.", "rcsb_description" : [ { "text" : "PubMed identifiers for literature supporting the pharmacology or activity data.", "context" : "dictionary" } ] }, "uniqueItems" : false }, "resource_name" : { "type" : "string", "enum" : [ "ChEMBL", "DrugBank", "Pharos" ], "examples" : [ "DrugBank", "ChEMBL", "Pharos" ], "description" : "Resource providing target and cofactor data.", "rcsb_enum_annotated" : [ { "value" : "ChEMBL", "detail" : "ChEMBL, manually curated database of bioactive molecules with drug-like properties", "name" : "ChEMBL" }, { "value" : "DrugBank", "detail" : "DrugBank, database containing information on drugs and drug targets", "name" : "DrugBank" }, { "value" : "Pharos", "detail" : "User interface to the Knowledge Management Center (KMC) for the Illuminating the Druggable Genome (IDG)", "name" : "Pharos" } ], "rcsb_description" : [ { "text" : "Resource providing target and cofactor data.", "context" : "dictionary" } ] }, "resource_version" : { "type" : "string", "examples" : [ "V4_0_2" ], "description" : "Version of the information distributed by the data resource.", "rcsb_description" : [ { "text" : "Version of the information distributed by the data resource.", "context" : "dictionary" } ] }, "target_resource_id" : { "type" : "string", "examples" : [ "P00734", "CHEMBL2242" ], "description" : "Identifier for the target assigned by the resource.", "rcsb_description" : [ { "text" : "Identifier for the target assigned by the resource.", "context" : "dictionary" } ] } }, "additionalProperties" : false }, "minItems" : 1, "uniqueItems" : true }, "rcsb_membrane_lineage_provenance_code" : { "type" : "string", "enum" : [ "Homology", "Mpstruc" ], "description" : "Mpstruc keyword denotes original annotation, Homology keyword denotes annotation inferred by homology.", "rcsb_description" : [ { "text" : "Mpstruc keyword denotes original annotation, Homology keyword denotes annotation inferred by homology.", "context" : "dictionary" } ] }, "drugbank_container_identifiers" : { "type" : "object", "properties" : { "drugbank_id" : { "type" : "string", "description" : "The DrugBank accession code", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The DrugBank accession code", "context" : "dictionary" }, { "text" : "Drugbank Id (Drugbank Container Identifiers)", "context" : "brief" } ] } }, "additionalProperties" : false, "required" : [ "drugbank_id" ] }, "drugbank_info" : { "type" : "object", "properties" : { "affected_organisms" : { "type" : "array", "items" : { "type" : "string", "examples" : [ "Humans and other mammals" ], "description" : "The DrugBank drug affected organisms.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The DrugBank drug affected organisms.", "context" : "dictionary" }, { "text" : "Affected Organisms (Drugbank Info)", "context" : "brief" } ] }, "uniqueItems" : false }, "atc_codes" : { "type" : "array", "items" : { "type" : "string", "examples" : [ "A11HA04" ], "description" : "The Anatomical Therapeutic Chemical Classification System (ATC) codes.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The Anatomical Therapeutic Chemical Classification System (ATC) codes.", "context" : "dictionary" }, { "text" : "Atc Codes (Drugbank Info)", "context" : "brief" } ] }, "uniqueItems" : false }, "brand_names" : { "type" : "array", "items" : { "type" : "string", "examples" : [ "Atriphos; Striadyne" ], "description" : "DrugBank drug brand names.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "DrugBank drug brand names.", "context" : "dictionary" }, { "text" : "Drug Brand Name", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Chemical Components", "priority_order" : 35 } ] }, "uniqueItems" : false }, "cas_number" : { "type" : "string", "examples" : [ "56-65-5" ], "description" : "The DrugBank assigned Chemical Abstracts Service identifier.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The DrugBank assigned Chemical Abstracts Service identifier.", "context" : "dictionary" }, { "text" : "Cas Number (Drugbank Info)", "context" : "brief" } ] }, "description" : { "type" : "string", "description" : "The DrugBank drug description.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The DrugBank drug description.", "context" : "dictionary" }, { "text" : "Description (Drugbank Info)", "context" : "brief" } ] }, "drug_categories" : { "type" : "array", "items" : { "type" : "string", "examples" : [ "Adenine Nucleotides;Carbohydrates;Dietary Supplements" ], "description" : "The DrugBank drug categories.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The DrugBank drug categories.", "context" : "dictionary" }, { "text" : "Drug Categories (Drugbank Info)", "context" : "brief" } ] }, "uniqueItems" : false }, "drug_groups" : { "type" : "array", "items" : { "type" : "string", "enum" : [ "approved", "experimental", "illicit", "investigational", "nutraceutical", "vet_approved", "withdrawn" ], "examples" : [ "approved", "nutraceutical" ], "description" : "The DrugBank drug groups determine their drug development status.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_enum_annotated" : [ { "value" : "approved", "detail" : "A drug that has been approved in at least one jurisdiction, at some point in time", "name" : "Approved" }, { "value" : "experimental", "detail" : "A compound that has been shown experimentally to bind specific proteins in mammals, bacteria, viruses, fungi, or parasites", "name" : "Experimental" }, { "value" : "illicit", "detail" : "A drug that is scheduled in at least one jurisdiction, at some point in time", "name" : "Illicit" }, { "value" : "investigational", "detail" : "A drug that is in some phase of the drug approval process in at least one jurisdiction", "name" : "Investigational" }, { "value" : "nutraceutical", "detail" : "A drug that is a pharmaceutical-grade and standardized nutrient (with confirmed or unconfirmed health benefits)", "name" : "Nutraceutical" }, { "value" : "vet_approved", "detail" : "A drug that has been approved in at least one jurisdiction, at some point in time for the treatment of animals", "name" : "Vet Approved" }, { "value" : "withdrawn", "detail" : "A previously approved drug that has been withdrawn from the market in at least one jurisdiction, at some point in time", "name" : "Withdrawn" } ], "rcsb_description" : [ { "text" : "The DrugBank drug groups determine their drug development status.", "context" : "dictionary" }, { "text" : "Drug Groups", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Chemical Components", "priority_order" : 40 } ] }, "minItems" : 1, "uniqueItems" : true }, "drugbank_id" : { "type" : "string", "description" : "The DrugBank accession code", "rcsb_description" : [ { "text" : "The DrugBank accession code", "context" : "dictionary" } ] }, "indication" : { "type" : "string", "examples" : [ "For nutritional supplementation, also for treating dietary shortage or imbalance" ], "description" : "The DrugBank drug indication.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The DrugBank drug indication.", "context" : "dictionary" }, { "text" : "Indication (Drugbank Info)", "context" : "brief" } ] }, "mechanism_of_action" : { "type" : "string", "examples" : [ "ATP is able to store and transport chemical energy within cells." ], "description" : "The DrugBank drug mechanism of actions.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The DrugBank drug mechanism of actions.", "context" : "dictionary" }, { "text" : "Mechanism Of Action (Drugbank Info)", "context" : "brief" } ] }, "name" : { "type" : "string", "description" : "The DrugBank drug name.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The DrugBank drug name.", "context" : "dictionary" }, { "text" : "Name (Drugbank Info)", "context" : "brief" } ] }, "pharmacology" : { "type" : "string", "examples" : [ "Adenosine triphosphate (ATP) is the nucleotide known in biochemistry as the \"molecular currency\" of intracellular energy transfer; that is, ATP is able to store and transport chemical energy within cells. ATP also plays an important role in the synthesis of nucleic acids. The total quantity of ATP in the human body is about 0.1 mole. The energy used by human cells requires the hydrolysis of 200 to 300 moles of ATP daily. This means that each ATP molecule is recycled 2000 to 3000 times during a single day. ATP cannot be stored, hence its consumption must closely follow its synthesis." ], "description" : "The DrugBank drug pharmacology.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The DrugBank drug pharmacology.", "context" : "dictionary" }, { "text" : "Pharmacology (Drugbank Info)", "context" : "brief" } ] }, "synonyms" : { "type" : "array", "items" : { "type" : "string", "examples" : [ "Adenosine-5'-triphosphate; ATP" ], "description" : "DrugBank drug name synonyms.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "DrugBank drug name synonyms.", "context" : "dictionary" }, { "text" : "Synonyms (Drugbank Info)", "context" : "brief" } ] }, "uniqueItems" : false }, "drug_products" : { "type" : "array", "items" : { "type" : "object", "properties" : { "approved" : { "type" : "string", "enum" : [ "N", "Y" ], "description" : "Indicates whether this drug has been approved by the regulating government.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "Indicates whether this drug has been approved by the regulating government.", "context" : "dictionary" }, { "text" : "Drug Is Approved", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Chemical Components", "priority_order" : 45 } ] }, "country" : { "type" : "string", "enum" : [ "Canada", "EU", "US" ], "examples" : [ "Canada" ], "description" : "The country where this commercially available drug has been approved.", "rcsb_search_context" : [ "exact-match" ], "rcsb_full_text_priority" : 10, "rcsb_description" : [ { "text" : "The country where this commercially available drug has been approved.", "context" : "dictionary" }, { "text" : "Drug Market Availability", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Chemical Components", "priority_order" : 60 } ] }, "ended_marketing_on" : { "type" : "string", "format" : "date", "examples" : [ "2003-07-30" ], "description" : "The ending date for market approval.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The ending date for market approval.", "context" : "dictionary" }, { "text" : "Drug Marketing End", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Chemical Components", "priority_order" : 55 } ], "rcsb_current_maximum_value" : 2.5430112E12, "rcsb_current_minimum_value" : -1.0729152E12 }, "name" : { "type" : "string", "examples" : [ "Hivid Tab 0.375mg" ], "description" : "The proprietary name(s) provided by the manufacturer for any commercially available products containing this drug.", "rcsb_description" : [ { "text" : "The proprietary name(s) provided by the manufacturer for any commercially available products containing this drug.", "context" : "dictionary" } ] }, "source" : { "type" : "string", "enum" : [ "DPD", "EMA", "FDA NDC" ], "examples" : [ "DPD" ], "description" : "Source of this product information. For example, a value of DPD indicates this information was retrieved from the Canadian Drug Product Database.", "rcsb_enum_annotated" : [ { "value" : "DPD", "detail" : "Canadian Drug Product Database" }, { "value" : "EMA", "detail" : "European Medcines Agency" }, { "value" : "FDA NDC", "detail" : "United States Food and Drug Administration National Drug Code" } ], "rcsb_description" : [ { "text" : "Source of this product information. For example, a value of DPD indicates this information was retrieved from the Canadian Drug Product Database.", "context" : "dictionary" } ] }, "started_marketing_on" : { "type" : "string", "format" : "date", "examples" : [ "1992-12-31" ], "description" : "The starting date for market approval.", "rcsb_search_context" : [ "default-match" ], "rcsb_description" : [ { "text" : "The starting date for market approval.", "context" : "dictionary" }, { "text" : "Drug Marketing Start", "context" : "brief" } ], "rcsb_search_group" : [ { "group_name" : "Chemical Components", "priority_order" : 50 } ], "rcsb_current_maximum_value" : 3.3766848E12, "rcsb_current_minimum_value" : -2.8401408E12 } }, "additionalProperties" : false }, "uniqueItems" : true, "minItems" : 1, "rcsb_nested_indexing" : true } }, "additionalProperties" : false, "required" : [ "drugbank_id" ] }, "drugbank_target" : { "type" : "array", "items" : { "type" : "object", "properties" : { "interaction_type" : { "type" : "string", "description" : "The type of target interaction.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The type of target interaction.", "context" : "dictionary" }, { "text" : "Interaction Type (Drugbank Target)", "context" : "brief" } ] }, "name" : { "type" : "string", "description" : "The target name.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The target name.", "context" : "dictionary" }, { "text" : "Name (Drugbank Target)", "context" : "brief" } ] }, "ordinal" : { "type" : "integer", "description" : "The value of _drugbank_target.ordinal distinguishes\n related examples for each chemical component.", "rcsb_description" : [ { "text" : "The value of _drugbank_target.ordinal distinguishes\n related examples for each chemical component.", "context" : "dictionary" } ] }, "organism_common_name" : { "type" : "string", "description" : "The organism common name.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The organism common name.", "context" : "dictionary" }, { "text" : "Organism Common Name (Drugbank Target)", "context" : "brief" } ] }, "reference_database_accession_code" : { "type" : "string", "examples" : [ "Q9HD40" ], "description" : "The reference identifier code for the target interaction reference.", "rcsb_description" : [ { "text" : "The reference identifier code for the target interaction reference.", "context" : "dictionary" } ] }, "reference_database_name" : { "type" : "string", "enum" : [ "UniProt" ], "examples" : [ "UniProt" ], "description" : "The reference database name for the target interaction.", "rcsb_description" : [ { "text" : "The reference database name for the target interaction.", "context" : "dictionary" } ] }, "seq_one_letter_code" : { "type" : "string", "examples" : [ "MAKQRSG..." ], "description" : "Target sequence expressed as string of one-letter amino acid codes.", "rcsb_description" : [ { "text" : "Target sequence expressed as string of one-letter amino acid codes.", "context" : "dictionary" } ] }, "target_actions" : { "type" : "array", "items" : { "type" : "string", "description" : "The actions of the target interaction.", "rcsb_search_context" : [ "full-text" ], "rcsb_full_text_priority" : 1, "rcsb_description" : [ { "text" : "The actions of the target interaction.", "context" : "dictionary" }, { "text" : "Target Actions (Drugbank Target)", "context" : "brief" } ] }, "uniqueItems" : false } }, "additionalProperties" : false, "required" : [ "ordinal" ] }, "minItems" : 1, "uniqueItems" : true } }, "additionalProperties" : false, "required" : [ "rcsb_nonpolymer_entity_container_identifiers", "rcsb_id", "rcsb_assembly_container_identifiers", "rcsb_uniprot_container_identifiers", "rcsb_branched_entity_container_identifiers", "rcsb_entry_container_identifiers", "rcsb_entry_info", "rcsb_pubmed_container_identifiers", "rcsb_polymer_entity_container_identifiers" ], "$id" : "https://github.com/rcsb/py-rcsb_exdb_assets/tree/master/json_schema_definitions/json-min-db-dw-col-core_drugbank.json", "$schema" : "http://json-schema.org/draft-04/schema#", "title" : "Text Service Metadata", "description" : "", "$comment" : "Schema version: 1.56.1" }