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New wwPDB X-ray structure validation reports support depositors, journal editors and referees

The wwPDB partners are pleased to announce that new, considerably more informative X-ray structure validation reports are now being provided to depositors as part of the structure annotation process. The reports can be used by depositors to assess the quality of their structures, and by journal editors and referees as a useful tool in the manuscript-review process.

The new reports implement recommendations of a large group of community experts on validation [1,2]. They were originally scheduled to be introduced as part of the new wwPDB Deposition & Annotation system, which will come online in 2014. However, initial feedback on the reports has been very positive and therefore the reports are provided for all new X-ray crystal structures deposited PDBe, PDBj, and RCSB PDB as of August 1, 2013.

"Validation 'at the gate' is crucial to improving the quality and consistency of the structural archive," said Gerard Kleywegt, Head of PDBe. "The new wwPDB validation reports for X-ray crystal structures draw on a wealth of community experience in the validation of models, experimental data and the fit of the model to these data. The new style reports are a huge improvement compared to the reports previously provided by the wwPDB partners. Initial feedback from depositors, annotation staff and users alike has been very positive and this has in fact motivated us to start delivering the reports much earlier than we had planned. We strongly encourage journal editors and referees to request these reports from depositors as part of the manuscript submission and review process."

Provision of wwPDB validation reports is already required by the International Union of Crystallography (IUCr) journals as part of their submission process, and the wwPDB partners hope that the launch of the new improved reports will encourage other journals to follow suit.

The new X-ray validation reports have been prepared according to the recommendations of the wwPDB X-ray Validation Task Force [1,2], first convened in April 2008. The validation pipeline uses tried and tested software, including MolProbity, Xtriage, Mogul, EDS and various CCP4 programs. The reports include the results of geometry checks, structure factor validation, and ligand validation. They summarise the quality of the structure and highlight specific concerns by considering the coordinates of the model, the diffraction data and the fit between the two. Easily interpretable summary information that compares the quality of a model with that of other models in the archive is also provided to further support depositors, journal editors and referees.

The reports will be sent to depositors of X-ray crystal structures upon completion of the curation process by wwPDB annotation staff. Later this year, a standalone web service will be released which can be used to generate validation reports prior to deposition. Please note that the reports and the online documentation are still undergoing active development. This means that there may be a few cases where a report cannot be generated (we endeavour to fix such cases as soon as we can), and that the content and layout of the reports is subject to change. However, the wwPDB partners feel that the benefits of providing the new reports vastly outweigh these issues. Early in 2014, validation reports for all X-ray crystal structures already in the PDB archive will be made publicly available as PDF files, together with XML files that contain exhaustive validation information for each entry (e.g., complete lists of outliers for every criterion). Validation pipelines for structures determined by NMR spectroscopy [3] or 3D cryo-electron microscopy [4] are under development and will be introduced at a later stage.

Further information, including sample X-ray validation reports, is provided. We welcome your feedback on the new validation reports. If you would like to send us your comments or questions, then please contact

[1] Read RJ, Adams PD, Arendall WB, III, Brunger AT, Emsley P, Joosten RP, Kleywegt GJ, Krissinel EB, Lutteke T, Otwinowski Z, Perrakis A, Richardson JS, Sheffler WH, Smith JL, Tickle IJ, Vriend G, Zwart PH. (2011) A new generation of crystallographic validation tools for the Protein Data Bank. Structure 19: 1395-1412. doi: 10.1016/j.str.2011.08.006

[2] Gore S., Velankar S. and Kleywegt G.J. Implementing an X-ray validation pipeline for the Protein Data Bank 2012, Acta Cryst., D68, 478-483. doi: 10.1107/S0907444911050359

[3] Montelione GT, Nilges M, Bax A, Güntert P, Herrmann T, Richardson JS, Schwieters C, Vranken WF, Vuister GW, Wishart DS, Berman HM, Kleywegt GJ, Markley JL. (in press) Recommendations of the wwPDB NMR Structure Validation Task Force. Structure.

[4] Henderson R, Sali A, Baker ML, Carragher B, Devkota B, Downing KH, Egelman EH, Feng Z, Frank J, Grigorieff N, Jiang W, Ludtke SJ, Medalia O, Penczek PA, Rosenthal PB, Rossmann MG, Schmid MF, Schroder GF, Steven AC, Stokes DL, Westbrook JD, Wriggers W, Yang H, Young J, Berman HM, Chiu W, Kleywegt GJ, Lawson CL. (2012) Outcome of the first electron microscopy validation task force meeting. Structure 20: 205-214. doi: 10.1016/j.str.2011.08.006

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2013-08-05 (last edited: more than 1 year ago)2014-01-17
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