Work

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

Year: 2022

Type: article

Abstract: 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.

Source: Structure

DOI: 10.1016/j.str.2022.08.004

Authors: Chenghua Shao, Sebastian Bittrich, Sijian Wang, Stephen K. Burley

Institutions: Rutgers, The State University of New Jersey, San Diego Supercomputer Center, University of California San Diego, Rutgers Cancer Institute

Language: English

Topic: Enzyme Structure and Function

Subfield: Structural Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: hybrid

Estimated APC paid: $8,900