{"doi":"10.1016/j.str.2022.08.004","title":"Assessing PDB macromolecular crystal structure confidence at the individual amino acid residue level","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.","journal":"Structure","year":2022,"id":240279,"datarank":1.4292090194761764,"base_score":3.8501476017100584,"endowment":3.8501476017100584,"self_citation_contribution":0.5775221402565088,"citation_network_contribution":0.8516868792196677,"self_endowment_contribution":0.5775221402565088,"citer_contribution":0.8516868792196677,"corpus_percentile":85.54962481627601,"corpus_rank":1869,"citation_count":46,"citer_count":35,"citers_with_citation_signal":23,"citers_with_endowment":23,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.8339,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":339379,"name":"Sebastian Bittrich","orcid":"0000-0003-3576-0387","position":1,"is_corresponding":false},{"id":867521,"name":"Sijian Wang","orcid":"0000-0002-7094-2816","position":2,"is_corresponding":false},{"id":23506,"name":"S.K. Burley","orcid":"0000-0002-2487-9713","position":3,"is_corresponding":false},{"id":623809,"name":"Chenghua Shao","orcid":"0000-0001-6817-7476","position":0,"is_corresponding":true}],"reference_count":48,"raw_metadata":null,"created_at":"2026-07-19T00:22:46.554789Z","pmid":"36049478","pmcid":"PMC9547844","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}