Assessing PDB macromolecular crystal structure confidence at the individual amino acid residue level.

Chenghua Shao, Sebastian Bittrich, Sijian Wang, Stephen K Burley

Structure (London, England : 1993) 2022 Oct 06

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Approximately 87% of the more than 190,000 atomic-level three-dimensional (3D) biostructures in the PDB were determined using macromolecular crystallography (MX). Agreement between 3D atomic coordinates and experimental data for >100 million individual amino acid residues occurring within ∼150,000 PDB MX structures was analyzed in detail. The real-space correlation coefficient (RSCC) calculated using the 3D atomic coordinates for each residue and experimental-data-derived electron density enables outlier detection of unreliable atomic coordinates (particularly important for poorly resolved side-chain atoms) and ready evaluation of local structure quality by PDB users. For human protein MX structures in PDB, comparisons of the per-residue RSCC metric with AlphaFold2-computed structure model confidence (pLDDT-predicted local distance difference test) document (1) that RSCC values and pLDDT scores are correlated (median correlation coefficient ∼0.41), and (2) that experimentally determined MX structures (3.5 Å resolution or better) are more reliable than AlphaFold2-computed structure models and should be used preferentially whenever possible. Copyright © 2022 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Citation

Chenghua Shao, Sebastian Bittrich, Sijian Wang, Stephen K Burley. Assessing PDB macromolecular crystal structure confidence at the individual amino acid residue level. Structure (London, England : 1993). 2022 Oct 06;30(10):1385-1394.e3