Newsletter | Fall 2015 ⋅ Number 67

Data Deposition and Annotation

In the third quarter of 2015, 2979 experimentally-determined structure coordinate entries were deposited to the archive. During the same period, 2776 structures and 220 EMDB maps were released in the PDB.

A total of 8386 entries have been deposited in 2015.

Of the structures deposited during this year, 86.0% were deposited with a release status of hold until publication; 9.1% were released as soon as annotation of the entry was complete; and 4.9% were held until a particular date. 92.9% of these entries were determined by X-ray crystallographic methods; 4.9% were determined by NMR methods.

ADIT was retired on July 19, 2015 for structures determined using X-ray crystallography. Any in-progress ADIT X-ray deposition sessions need to be completed before that time.

wwPDB launched the Deposition Tool for structures determined using X-ray crystallography in 2014 as part of a new Deposition and Annotation System. Using this system, more than 10,100 structures have been deposited and annotated, and more than 5,300 structures released in the archive.

Features of the new system include use of the PDBx/mmCIF data format, which produces more uniform data; the ability to replace data files pre- and post-deposition; enhanced communication; improved annotation; and geometric and experimental data checking based on recommendations from expert task forces. Detailed information and video tutorials are available.

ADIT will continue to accept depositions from other experimental methods. Deposition tools for NMR and 3DEM are being developed by the wwPDB. Questions and comments should be sent to

The wwPDB established a wwPDB Hybrid Methods Task Force composed of experts in the various experimental fields that are contributing to these hybrid studies, experts in hybrid modeling, and experts in archiving. The white paper from the first meeting has been published:

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop
Structure 23: 1156–1167; doi: 10.1016/j.str.2015.05.013