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, pp. 675-676   | 1 | 2 |

Section 24.5.2.1. Content of the data collected by the PDB

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

24.5.2.1. Content of the data collected by the PDB

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All the data collected from depositors by the PDB are considered primary data. Primary data contain, in addition to the coordinates, general information required for all deposited structures and information specific to the method of structure determination. Table 24.5.2.1[link] contains the general information that the PDB collects for all structures as well as the additional information collected for those structures determined by X-ray methods. The additional items listed for the NMR structures are derived from the International Union of Pure and Applied Chemistry recommendations (Markley et al., 1998[link]) and will be implemented in the near future.

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

The information content of data submitted by the depositor is likely to change as new methods for data collection, structure determination and refinement evolve and advance. In addition, the ways in which these data are captured is likely to change as the software for structure determination and refinement produce the necessary data items as part of their output. The data-input system for the PDB, ADIT, has been designed so as to incorporate these likely changes easily.

References

First citationMarkley, J. L., Bax, A., Arata, Y., Hilbers, C. W., Kaptein, R., Sykes, B. D., Wright, P. E. & Wüthrich, K. (1998). Recommendations for the presentation of NMR structures of proteins and nucleic acids. IUPAC–IUBMB–IUPAB Inter-Union Task Group on the standardization of data bases of protein and nucleic acid structures determined by NMR spectroscopy. J. Biomol. Nucl. Magn. Reson. 12, 1–23.Google Scholar








































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