International Tables for Crystallography (2006). Vol. G. ch. 3.6, pp. 144-198
https://doi.org/10.1107/97809553602060000738 |
Chapter 3.6. Classification and use of macromolecular data
Chapter index
ADIT A3.6.2.4
ambient conditions
mmCIF 3.6.5.2
ATOM_SITE 3.6.3, 3.6.6.1.5, 3.6.7.1, 3.6.7.1, 3.6.7.1.1, 3.6.7.1.1, 3.6.7.1.1, 3.6.7.1.1, 3.6.7.1.1, 3.6.7.1.1, 3.6.7.1.1, 3.6.7.1.1, 3.6.7.1.2, 3.6.7.1.4, 3.6.7.2.2, 3.6.7.3, 3.6.7.3.1, 3.6.7.3.2, 3.6.7.5.1, 3.6.7.5.2, 3.6.7.5.3, A3.6.2.1
_atom_site.auth_seq_id 3.6.7.1.1
_atom_site.B_iso_or_equiv 3.6.7.1.1
_atom_site.disorder_assembly 3.6.7.1.4
_atom_site.disorder_group 3.6.7.1.4
_atom_site.group_PDB 3.6.7.1.1
_atom_site.label_atom_id 3.6.7.1.1
_atom_site.label_entity_id 3.6.7.1.1
_atom_site.label_seq_id 3.6.7.1.1
_atom_site.type_symbol 3.6.7.1.1
_atom_site_anisotrop.id 3.6.7.1.1
ATOM_SITES_ALT 3.6.3, 3.6.7.1, 3.6.7.1, 3.6.7.1.1, 3.6.7.1.4, 3.6.7.1.4, 3.6.7.1.4, 3.6.7.1.4, 3.6.7.2
_atom_sites_alt.id 3.6.7.1.1
_atom_sites_footnote.id 3.6.7.1.1
atom sites
alternative conformations 3.6.7.1.4
isotropic displacement parameters 3.6.7.1.1
mmCIF 3.6.7.1
occupancy 3.6.3
positional coordinates 3.6.7.1.1
biological function 3.6.3
BioMagResBank A3.6.2.3.1
bond type 3.6.7.2.2
bond valence 3.6.7.7
Cambridge Structural Database 3.6.7.2.2
category group
mmCIF 3.6.4
CHEM_COMP 3.6.3, 3.6.3, 3.6.7, 3.6.7, 3.6.7.1.1, 3.6.7.2, 3.6.7.2, 3.6.7.2, 3.6.7.2.1, 3.6.7.2.2, 3.6.7.2.2, 3.6.7.2.2, 3.6.7.2.2, 3.6.7.2.2, 3.6.7.2.3, 3.6.7.2.3, 3.6.7.3.2, 3.6.7.3.2
_chem_comp.id 3.6.7.1.1
_chem_comp.one_letter_code 3.6.7.2.2
_chem_comp.three_letter_code 3.6.7.2.2
_chem_comp_atom.atom_id 3.6.7.1.1
CHEM_LINK 3.6.7, 3.6.7, 3.6.7.2, 3.6.7.2, 3.6.7.2, 3.6.7.2, 3.6.7.2.1, 3.6.7.2.3, 3.6.7.2.3, 3.6.7.2.3, 3.6.7.2.3, 3.6.7.2.3, 3.6.7.2.3, 3.6.7.2.3, 3.6.7.2.3, 3.6.7.2.3, 3.6.7.5.3
_chem_link.id 3.6.7.2.3
_chemical.entry_id 3.6.7.2.1
chemical components (mmCIF) 3.6.7.2.2
chemical entity
mmCIF 3.6.7.2.2
chemical species, handling in mmCIF 3.6.7.2
CIFTr A3.6.2.4
computer programs
ADIT A3.6.2.4
CIFTr A3.6.2.4
PDB_EXTRACT A3.6.2.4
PROTIN/PROLSQ 3.6.6.2.3
RESTRAIN 3.6.6.2.3
connectivity
structural interactions (mmCIF) 3.6.7.5.3
coreCIF
embedded in mmCIF dictionary 3.6.1
crambin (mmCIF example structure) 3.6.3
Cruickshank diffraction-component precision index 3.6.6.2.1
cryo-electron microscopy A3.6.2.3, A3.6.2.3.2
database
entries 3.6.7.5.6
data collection
mmCIF data items 3.6.5.2
DDL1 (Dictionary Definition Language)
_type_conditions 3.6.4
DDL2 (Dictionary Definition Language)
_item_aliases.alias_name 3.6.1
diffraction experiment, overview 3.6.5.2
DIFFRN 3.6.5, 3.6.5.2, 3.6.5.2, 3.6.5.2, 3.6.5.2, 3.6.5.2, 3.6.5.2, 3.6.5.2, 3.6.5.2, 3.6.5.2, 3.6.5.2, 3.6.6.1.6
_diffrn.id 3.6.5.2
DIFFRN_SCALE_GROUP 3.6.5.2
disorder 3.6.6.2.2
ENTITY 3.6.3, 3.6.7, 3.6.7.1.1, 3.6.7.3, 3.6.7.3, 3.6.7.3, 3.6.7.3, 3.6.7.3, 3.6.7.3, 3.6.7.3.1, 3.6.7.3.1, 3.6.7.3.1, 3.6.7.3.2, 3.6.7.5.1
_entity.details 3.6.7.3.1
_entity_link.link_id 3.6.7.2.3
_entity_poly.nstd_chirality 3.6.7.3.2
_entity_poly.nstd_linkage 3.6.7.3.2
_entity_poly.nstd_monomer 3.6.7.3.2
_entity_poly.type_details 3.6.7.3.2
_entity_poly_seq.num 3.6.7.1.1
European Bioinformatics Institute A3.6.2
experimental measurements
mmCIF data items 3.6.5
_exptl_crystal_grow.details 3.6.5.3.2
_exptl_crystal_grow.method 3.6.5.3.2
_exptl_crystal_grow.method_ref 3.6.5.3.2
_exptl_crystal_grow.pH 3.6.5.3.2
_exptl_crystal_grow_comp.sol_id 3.6.5.3.2
external reference file
standard chemical data for monomers 3.6.7.2.2
genetically manipulated source of biological macromolecules 3.6.7.3.1
intensity measurements 3.6.5.2
excluded from refinement 3.6.6.2.1
units (mmCIF) 3.6.6.3.1
used in refinement 3.6.6.3
International Structural Genomics Organization A3.6.2
intramolecular geometry 3.6.7.2.3
IUCr A3.6.2
keywords 3.6.7.5.8
metadata 3.6.9
mmCIF
atom properties 3.6.7
chemistry 3.6.7
classification and use 3.6.1
data collection 3.6.5.2
design considerations 3.6.2
experimental measurements 3.6.5
history 3.6.1
list of categories A3.6.1.1
relation to PDB format 3.6.8.3.2
structure analysis 3.6.6
use in PDB data management A3.6.2
molecular chemistry, differences between coreCIF and mmCIF 3.6.7.2.1
monomer components of biological macromolecules 3.6.7.2.2
natural tissue, source of biological macromolecules 3.6.7.3.1
NMRStar A3.6.2.3.1
NMR structures 3.6.7.1.4, A3.6.2.3.1
PDB_EXTRACT A3.6.2.4
phasing 3.6.6.1
isomorphous replacement 3.6.6.1.3
MAD 3.6.6.1.4
MIR 3.6.6.1.5
molecular averaging 3.6.6.1.2
_phasing_set.id 3.6.6.1.6
_phasing_set_refln.set_id 3.6.6.1.6
Protein Data Bank Japan A3.6.2
Protein Expression Purification and Crystallization database (PEPCdb) A3.6.2.3.3
protein production A3.6.2.3.3
PROTIN/PROLSQ 3.6.6.2.3
publishing
data items (mmCIF) 3.6.8
redundancy 3.6.6.2.1
REFINE 3.6.6, 3.6.6.2, 3.6.6.2, 3.6.6.2, 3.6.6.2.1, 3.6.6.2.1, 3.6.6.2.1, 3.6.6.2.1, 3.6.6.2.2, 3.6.6.2.3
_refine.correlation_coeff_Fo_to_Fc 3.6.6.2.1
_refine.details 3.6.6.2.1
_refine.entry_id 3.6.6.2.1
_refine.ls_percent_reflns_obs 3.6.6.2.1
_refine.overall_SU_B 3.6.6.2.1
_refine.overall_SU_ML 3.6.6.2.1
_refine.overall_SU_R_Cruickshank_DPI 3.6.6.2.1
_refine.overall_SU_R_free 3.6.6.2.1
_refine_b_iso.class 3.6.6.2.4
_refine_ls_restr_ncs.ncs_model_details 3.6.6.2.3
_refine_occupancy.class 3.6.6.2.4
Research Collaboratory for Structural Bioinformatics A3.6.2
resolution limits 3.6.6.1.5
RESTRAIN 3.6.6.2.3
secondary structure (protein) 3.6.7.5.2
sequence alignment 3.6.7.5.6
_software.citation_id 3.6.8.2
_software.contact_author 3.6.8.2
_software.contact_author_email 3.6.8.2
_software.date 3.6.8.2
_software.location 3.6.8.2
_software.name 3.6.8.2
SPINE A3.6.2.3.3
STRUCT 3.6.3, 3.6.7, 3.6.7.1.1, 3.6.7.3, 3.6.7.3.1, 3.6.7.4, 3.6.7.5, 3.6.7.5, 3.6.7.5, 3.6.7.5.1, 3.6.7.5.1, 3.6.7.5.1, 3.6.7.5.1
_struct.entry_id 3.6.7.5.1
_struct_biol.details 3.6.7.5.1
_struct_conf.details 3.6.7.5.2
_struct_conf_type.criteria 3.6.7.5.2
_struct_conf_type.id 3.6.7.5.2
_struct_conf_type.reference 3.6.7.5.2
STRUCT_CONN 3.6.3, 3.6.7.2.3, 3.6.7.5, 3.6.7.5.3, 3.6.7.5.3, 3.6.7.5.3, 3.6.7.5.3, 3.6.7.5.3, 3.6.7.5.3, 3.6.7.5.3, 3.6.7.5.3, 3.6.7.5.3
_struct_conn.conn_type_id 3.6.7.5.3
_struct_conn.details 3.6.7.5.3
_struct_conn_type.criteria 3.6.7.5.3
_struct_conn_type.id 3.6.7.5.3
_struct_conn_type.reference 3.6.7.5.3
_struct_ref.biol_id 3.6.7.5.6
_struct_ref.entity_id 3.6.7.5.6
_struct_ref.id 3.6.7.5.6
_struct_ref.seq_align 3.6.7.5.6
_struct_ref.seq_dif 3.6.7.5.6
STRUCT_SHEET_* 3.6.7.5.2
_struct_sheet_range.symmetry 3.6.7.5.7
structural genomics A3.6.2.2
structural model
mmCIF data items 3.6.7
Structural Proteomics in Europe A3.6.2.3.3
structure analysis
mmCIF 3.6.6
symmetry
mmcif 3.6.7.6
systematic absences 3.6.6.3.1
unit cell
parameters and measurement conditions 3.6.5.1
visualization 3.6.3
web sites
PDB deposition: http://deposit.pdb.org/ A3.6.2.3.3
PDB mmCIF site: http://mmcif.pdb.org/ A3.6.2, A3.6.2.3.2
PDB Protein Expression Purification and Crystallization Database: http://pepcdb.pdb.org/ A3.6.2.3.3
PDB software tools: http://sw-tools.pdb.org/ A3.6.2.4
Structural Proteomics in Europe: http://www.spineurope.org/ A3.6.2.3.3
Wilson B factor 3.6.6.3.2
Worldwide PDB A3.6.2