Worldwide Protein Data Bank validation information: usage and trends

Abstract

Realising the importance of assessing the quality of the biomolecular structures deposited in the Protein Data Bank (PDB), the Worldwide Protein Data Bank (wwPDB) partners established Validation Task Forces to obtain advice on the methods and standards to be used to validate structures determined by X-ray crystallography, nuclear magnetic resonance spectroscopy and three-dimensional electron cryo-microscopy. The resulting wwPDB validation pipeline is an integral part of the wwPDB OneDep deposition, biocuration and validation system. The wwPDB Validation Service webserver (https://validate.wwpdb.org) can be used to perform checks prior to deposition. Here, it is shown how validation metrics can be combined to produce an overall score that allows the ranking of macromolecular structures and domains in search results. The ValTrends^DB database provides users with a convenient way to access and analyse validation information and other properties of X-ray crystal structures in the PDB, including investigating trends in and correlations between different structure properties and validation metrics.

Keywords: PDB; Protein Data Bank; X-ray crystallography; quality control; three-dimensional macromolecular structure; validation.

Figure 1

Slider plots for PDB entries 2de2 (a) and 2de4 (b).

Figure 2

The use of combined validation metrics in the PDBe search facility to rank the available structures of human cellular retinoic acid-binding protein type 2.

Figure 3

ValTrends^DB plots showing how the overall validation metrics for protein geometry, as reported in wwPDB VRs, have improved with time. (a) Percentage Ramachandran outliers as assessed by MolProbity (Chen et al., 2010 ▸). (b) Percentage side-chain rotamer outliers as assessed by MolProbity. (c) MolProbity all-atom clashscore. Only structures determined by X-ray crystallography were included in the analysis. In each case the box plot shows the inter-quartile range. The red dot marks the weighted arithmetic mean as explained in Appendix A .

Figure 4

ValTrends^DB plot showing how the percentage RSRZ electron-density-fit outliers metric (Kleywegt et al., 2004 ▸) varies with deposition date.