Newsletter | Fall 2016 ⋅ Number 71
To enable better annotation and tracking, the wwPDB partners encourage depositors to provide ORCID identifiers and information on relevant grants funding their research when depositing PDB data. ORCID identifiers are unique to each researcher; usage will help avoid ambiguity in attributing the correct authorship of PDB, BMRB, and EMDB entries. In order to register an ORCID, please visit http://orcid.org. Provision of funding agency and grant information will enable better impact tracking and statistics.
In the third quarter of 2016, 2717 experimentally-determined structure coordinate entries were deposited to the archive. 85.9% were deposited with a release status of hold until publication; 8.9% were released as soon as annotation of the entry was complete; and 5.2% were held until a particular date. 91.7% of these entries were determined by X-ray crystallographic methods; 4.3% were determined by NMR methods. During the same period, 3025 structures and 260 EMDB maps were released in
the PDB. The new wwPDB Validation Server at https://validate.wwpdb.org now generates preliminary validation reports for structures solved by NMR and 3D Electron Microscopy, in addition to X-ray crystallography. wwPDB strongly encourages the use of the Validation Server at any time during the structure determination process, but particularly when preparing structures for deposition to the wwPDB. Validation Server reports provide identical information to the ones generated at deposition. Structural models may be assessed independently or together with experimental data (crystallographic structure factors or NMR chemical shifts) for validation of model/data correspondence. Deposition of atomic models determined by 3D Electron cryo-Microscopy (3DEM) to the PDB now requires prior or simultaneous deposition of the associated 3DEM volume maps to EMDB. Maps and models can be deposited at a member site of the Worldwide Protein Data Bank (wwpdb.org) using the joint PDB, EMDB and BMRB deposition tool made available by RCSB PDB (http://deposit.wwpdb.org), PDBe (https://deposit-pdbe.wwpdb.org), and PDBj (http://deposit-pdbj.wwpdb.org). Data can be released following the authors' release instructions, once they have been processed and approved. wwPDB and EMDB policies both allow for a maximum hold period of one year for model and associated map depositions. Note that for joint PDB/EMDB depositions, the hold period will be the same for the map(s) and the model(s). This policy change aligns the deposition requirements for 3DEM models with those for structures determined by other techniques, for which deposition of experimental data has been mandatory since 2008. The policy change was developed on the basis of input from the PDB and EMDB user communities and has been unanimously endorsed by the wwPDB Advisory Committee.Deposition Statistics
wwPDB Validation Server Upgrade
Map Volume Deposition to EMDB Mandatory for PDB Depositions of 3DEM models
