RCSB PDB Newsletter

Data Deposition and Annotation

Deposition Statistics

From July 1-September 30, 2012, 2583 experimentally-determined structures were deposited to the PDB archive, and then processed and annotated by wwPDB teams.

Of the structures deposited in 2012 so far, 81% were deposited with a release status of hold until publication; 15% were released as soon as annotation of the entry was complete; and 4% were held until a particular date. 93% of these entries were determined by X-ray crystallographic methods; 6% were determined by NMR methods.

During the same time period, 2167 structures were released and made publicly available in the PDB.

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Prepare Data for Deposition with pdb_extract and SF-Tool

Tools are available to help prepare data files for deposition with ADIT. Using these resources can help minimize errors, validate data, and save time during the deposition process.

pdb_extract extracts key details from the output files produced by many X-ray crystallographic and NMR applications. The program merges these data into mmCIF data files that can be used with ADIT for validation and deposition.

pdb_extract features include support for:

Data from hybrid method experiments
NCS and TLS ranges in BUSTER and REFMAC
Improved mtz-to-mmCIF conversion
Quality assessment of X-ray data

Depositors can upload files into the pdb_extract webserver or download the latest workstation version at pdb-extract.rcsb.org.

SF-Tool

SF-Tool is a streamlined, web-based tool for validating X-ray, neutron, and hybrid experimental data. Visit sf-tool.rcsb.org to:

Validate model coordinates against structure factor data
Easily convert structure factor files between different formats (mmCIF, MTZ, CNS/CNX, XPLOR, SHELX, TNT, HKL2000, SCALEPACK, D*Trek, SAINT, and more)
Check for and validate twinned or detwinned data

The latest release of SF-Tool includes support for neutron and hybrid experiments; incorporates checks from REFMAC,¹ PHENIX,² and SFCHECK;³ and converts multiple data sets into a single mmCIF file.

wwPDB News:

Special Symposium on PDB: Basis for Life Science and Drug Development

A special PDB symposium will be held on Saturday, October 13, 2012 at Hearton Hall in Osaka, Japan. The meeting is free and open to the public.

Presentations will include:

wwPDB and its Impacts on Science and Society, Haruki Nakamura, Osaka University
Impact of the Protein Data Bank on Drug Discovery, Stephen Kevin Burley, University of California at San Diego
Molecular Nanomachines in Living Organisms-Exquisite Structural Design Far Beyond State-of-the-Art Nanotechnology, Keiichi Namba, Osaka University

The symposium is organized by the wwPDB Foundation, and is sponsored by the National Bioscience Database Center-Japan Science and Technology Agency; Institute for Protein Research, Osaka University; Graduate School of Frontier Biosciences, Osaka University; The Biophysical Society of Japan; Protein Science Society of Japan; and the Osaka Pharmaceutical Manufacturers Association.

For more information, see wwpdb.org.

Science as an open enterprise

The wwPDB's management of the PDB archive was highlighted as a major international data initiative with well-defined protocols for the selection and incorporation of new data and access to them in a report from The Royal Society on openness in scientific data. The full report, entitled Science as an open enterprise, is online at royalsociety.org.

G. N. Murshudov, A. A. Vagin, E. J. Dodson. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D53: 240-255.
P. D. Adams, R. W. Grosse-Kunstleve, L.-W. Hung, T. R. Ioerger, A. j. McCoy, N. W. Moriarty, R. J. Read, J. C. Sacchettini, N. K. Sauter, T. C. Terwilliger. (2002) PHENIX: building new software for automated crystallographic structure determination. Acta Crystallographica D58: 1948-1954.
A. A. Vaguine, J. Richelle, S. J. Wodak. (1999) SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Crystallogr D Biol Crystallogr 55: 191-205.