ArticleStructure (London, England : 1993)2012
Improving the accuracy of macromolecular structure refinement at 7 Å resolution.
Article in Structure (London, England : 1993), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Structural Impact of Ex Vivo Resistance Mutations on HIV-1 Integrase Polymers Induced by Allosteric Inhibitors.Journal of molecular biology · 2025Article
- Structural mechanism of DNA recognition by the p204 HIN domain.Nucleic acids research · 2021Article
- Closing the Gap for Electronic Short-Circuiting: Photosystem I Mixed Monolayers Enable Improved Anisotropic Electron Flow in Biophotovoltaic Devices.Angewandte Chemie (International ed. in English) · 2021Article
- Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance.Chemical reviews · 2019Article
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- Structural Basis for Inhibitor-Induced Aggregation of HIV Integrase.PLoS biology · 2016Article
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- Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps.eLife · 2016Article
- Structural evidence for Nap1-dependent H2A-H2B deposition and nucleosome assembly.The EMBO journal · 2016Article
- Dissecting the Molecular Mechanism of Nucleotide-Dependent Activation of the KtrAB K+ Transporter.PLoS biology · 2016Article
- New method to compute Rcomplete enables maximum likelihood refinement for small datasets.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Integrative, dynamic structural biology at atomic resolution--it's about time.Nature methods · 2015Review
- The RUBISCO to Photosystem II Ratio Limits the Maximum Photosynthetic Rate in Picocyanobacteria.Life (Basel, Switzerland) · 2015Article
- xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures.Acta crystallographica. Section D, Biological crystallography · 2014Article
- Deformable elastic network refinement for low-resolution macromolecular crystallography.Acta crystallographica. Section D, Biological crystallography · 2014Article
- X-ray crystal structure of the passenger domain of plasmid encoded toxin(Pet), an autotransporter enterotoxin from enteroaggregative Escherichia coli (EAEC).Biochemical and biophysical research communications · 2014Article
- Building a pseudo-atomic model of the anaphase-promoting complex.Acta crystallographica. Section D, Biological crystallography · 2013Article
- Molecular replacement then and now.Acta crystallographica. Section D, Biological crystallography · 2013Review
- An autoinhibited structure of α-catenin and its implications for vinculin recruitment to adherens junctions.The Journal of biological chemistry · 2013Article
- Structural basis for recruitment and activation of the AP-1 clathrin adaptor complex by Arf1.Cell · 2013Article
Corrections and comments
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6 authors.
Funding
Abstract
In X-ray crystallography, molecular replacement and subsequent refinement is challenging at low resolution. We compared refinement methods using synchrotron diffraction data of photosystem I at 7.4 Å resolution, starting from different initial models with increasing deviations from the known high-resolution structure. Standard refinement spoiled the initial models, moving them further away from the true structure and leading to high R(free)-values. In contrast, DEN refinement improved even the most distant starting model as judged by R(free), atomic root-mean-square differences to the true structure, significance of features not included in the initial model, and connectivity of electron density. The best protocol was DEN refinement with initial segmented rigid-body refinement. For the most distant initial model, the fraction of atoms within 2 Å of the true structure improved from 24% to 60%. We also found a significant correlation between R(free) values and the accuracy of the model, suggesting that R(free) is useful even at low resolution.
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