International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

International Tables for Crystallography (2006). Vol. F. ch. 24.5, p. 676   | 1 | 2 |

Table 24.5.2.1 

H. M. Berman,a* J. Westbrook,a Z. Feng,a G. Gilliland,b T. N. Bhat,b H. Weissig,c I. N. Shindyalovc and P. E. Bourned

aDepartment of Chemistry, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854-8087, USA,bNational Institute of Standards and Technology, Biotechnology Division, 100 Bureau Drive, Gaithersburg, MD 20899, USA,cSan Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA, and dDepartment of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA
Correspondence e-mail:  berman@rcsb.rutgers.edu

Table 24.5.2.1| top | pdf |
Content of data in the PDB

(a) Content of all depositions (X-ray and NMR)

Source – specifications such as genus, species, strain, or variant of gene (cloned or synthetic); expression vector and host, or description of method of chemical synthesis
Sequence – full sequence of all macromolecular components
Chemical structure of cofactors and prosthetic groups
Names of all components in structure
Qualitative description of characteristics of structure
Literature citations for the structure submitted
Three-dimensional coordinates

(b) Additional items for X-ray structure determinations

Temperature factors and occupancies assigned to each atom
Crystallization conditions, including pH, temperature, solvents, salts, methods
Crystal data, including the unit-cell dimensions and space group
Presence of noncrystallographic symmetry
Data-collection information describing the methods used to collect the diffraction data including instrument, wavelength, temperature and processing programs
Data-collection statistics including data coverage, Rsym, data above 1, 2, 3σ levels and resolution limits
Refinement information including R factor, resolution limits, number of reflections, method of refinement, σ cutoff, geometry r.m.s.d.
Structure factors – h, k, l, Fobs, σ(Fobs)

(c) Additional items for NMR structure determinations

Model number for each coordinate set that is deposited and an indication if one should be designated as a representative, or an energy-minimized average model provided
Data-collection information describing the types of methods used, instrumentation, magnetic field strength, console, probe head, sample tube
Sample conditions, including solvent, macromolecule concentration ranges, concentration ranges of buffers, salts, antibacterial agents, other components, isotopic composition
Experimental conditions, including temperature, pH, pressure and oxidation state of structure determination and estimates of uncertainties in these values
Non-covalent heterogeneity of sample, including self-aggregation, partial isotope exchange, conformational heterogeneity resulting in slow chemical exchange
Chemical heterogeneity of the sample (e.g. evidence for deamidation or minor covalent species)
A list of NMR experiments used to determine the structure including those used to determine resonance assignments, NOE/ROE data, dynamical data, scalar coupling constants, and those used to infer hydrogen bonds and bound ligands. The relationship of these experiments to the constraint files are given explicitly
Constraint files used to derive the structure as described in task-force recommendations