Finding High-Quality Metal Ion-Centric Regions Across the Worldwide Protein Data Bank.

ABSTRACT: As the number of macromolecular structures in the worldwide Protein Data Bank (wwPDB) continues to grow rapidly, more attention is being paid to the quality of its data, especially for use in aggregated structural and dynamics analyses. In this study, we systematically analyzed 3.5 Å regions around all metal ions across all PDB entries with supporting electron density maps available from the PDB in Europe. All resulting metal ion-centric regions were evaluated with respect to four quality-control criteria involving electron density resolution, atom occupancy, symmetry atom exclusion, and regional electron density discrepancy. The resulting list of metal binding sites passing all four criteria possess high regional structural quality and should be beneficial to a wide variety of downstream

SUBMITTER: Yao S 

PROVIDER: S-EPMC6751499 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature