Data Deposition and Annotation

The wwPDB has created a 2014 calendar
that illustrates how X-ray crystallography
enables our understanding of biology at
the atomic level.

In the first quarter of 2014, 2419 experimentally-determined structure coordinate entries were deposited to the archive.

85.4% were deposited with a release status of hold until publication; 11.0% were released as soon as annotation of the entry was complete; and 3.6% were held until a particular date. 92.3% of these entries were determined by X-ray crystallographic methods; 6.1% were determined by NMR methods.

During the same period, 2346 structures and 147 EMDB maps were released in the PDB.

For structures with HPUB status, entries will be released as part of the weekly update upon confirmation the corresponding article has been published.

The wwPDB receives publication dates and citation information directly from a few journals (see wwPDB's Information for Journals). For most articles, however, the wwPDB searches PubMed and scans the literature for publication information. Citations emailed to deposit@wwpdb.org are also greatly appreciated.

There is a one-year limit on the length of a hold period, including HPUBs. If the citation for a structure is not published within the one-year period, depositors will be given the option to either release or withdraw the deposition.

The wwPDB partners have launched a new deposition system for structures determined using X-ray crystallography at deposit.wwpdb.org.

This system was developed to allow the wwPDB partners to meet the evolving needs of the scientific community over the next decade, including support for very large systems, complex chemistry, and joint use of multiple experimental methods. It will replace all current deposition and annotation systems in use at the wwPDB deposition centers, and will lead to improved efficiency and consistency.

New and enhanced features of the deposition system include:

• the generation of X-ray validation reports (following the recommendations of the wwPDB X-ray Validation Task Force)
• improved capture and review of ligand information
• the ability to replace coordinate and/or experimental data files pre- and post-submission
• improved communication process between depositors and wwPDB curators
• ability to preview and download the PDBx/mmCIF entry file prior to submission

Depositors will have the option to use the new system or one of the legacy deposition tools (ADIT, AutoDep) for most of 2014. After the transition to the new system, the legacy tools will be available for a limited period of time to complete any unfinished deposition sessions.

Up-to-date information about the new system is available at wwpdb.org. Two new videos demonstrate how to review and submit ligands in this new system: How to review and confirm suggested matches to a ligand and How to provide mandatory chemical information.

Visit wwPDB.org to learn more about:

• Announcement: Standardization of Amino Acid Nomenclature
• Download the wwPDB calendar for IYCr:2014
• Archiving Structures Derived from SAS Data
• X-ray Validation Reports for Archived PDB Structures