ArticleActa crystallographica. Section D, Structural biology2024
Utilizing anomalous signals for element identification in macromolecular crystallography.
Article in Acta crystallographica. Section D, Structural biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- The Untangle Challenge for accurate ensemble models.bioRxiv : the preprint server for biology · 2026Article
- Cat_Wiz: a stereochemistry-guided toolkit for locating, diagnosing, and annotating Mg2+ ions in RNA structures.Nucleic acids research · 2026Article
- Nickel binding to c-Src SH3 domain facilitates crystallization.bioRxiv : the preprint server for biology · 2025Article
- De Novo Hydration of Cryo-EM Reconstructions through Molecular Dynamics Simulations of the Excess Chemical Potential.bioRxiv : the preprint server for biology · 2025Article
- Principles of ion binding to RNA inferred from the analysis of a 1.55 Å resolution bacterial ribosome structure - Part I: Mg2.Nucleic acids research · 2025Article
- Nickel Binding to the c-Src SH3 Domain Facilitates Crystallization.Protein and peptide letters · 2025Article
- How Do Gepotidacin and Zoliflodacin Stabilize DNA Cleavage Complexes with Bacterial Type IIA Topoisomerases? 1. Experimental Definition of Metal Binding Sites.International journal of molecular sciences · 2024Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
AlphaFold2 has revolutionized structural biology by offering unparalleled accuracy in predicting protein structures. Traditional methods for determining protein structures, such as X-ray crystallography and cryo-electron microscopy, are often time-consuming and resource-intensive. AlphaFold2 provides models that are valuable for molecular replacement, aiding in model building and docking into electron density or potential maps. However, despite its capabilities, models from AlphaFold2 do not consistently match the accuracy of experimentally determined structures, need to be validated experimentally and currently miss some crucial information, such as post-translational modifications, ligands and bound ions. In this paper, the advantages are explored of collecting X-ray anomalous data to identify chemical elements, such as metal ions, which are key to understanding certain structures and functions of proteins. This is achieved through methods such as calculating anomalous difference Fourier maps or refining the imaginary component of the anomalous scattering factor f''. Anomalous data can serve as a valuable complement to the information provided by AlphaFold2 models and this is particularly significant in elucidating the roles of metal ions.
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