ArticleActa crystallographica. Section D, Biological crystallography2012
Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement.
Article in Acta crystallographica. Section D, Biological crystallography, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
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- Molecular mechanism of Activin receptor inhibition by DLK1.Nature communications · 2025Article
- Article
- Dual factors required for cytochrome-P450-mediated hydrocarbon ring contraction in bacterial gibberellin phytohormone biosynthesis.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Yeast Ssd1 is a non-enzymatic member of the RNase II family with an alternative RNA recognition site.Nucleic acids research · 2022Article
- Structural insights into 3Fe-4S ferredoxins diversity inFrontiers in molecular biosciences · 2022Article
- Masitinib is a broad coronavirus 3CL inhibitor that blocks replication of SARS-CoV-2.Science (New York, N.Y.) · 2021Article
- Structural basis for preferential binding of human TCF4 to DNA containing 5-carboxylcytosine.Nucleic acids research · 2019Article
- Structure of Calcarisporiella thermophila Hsp104 Disaggregase that Antagonizes Diverse Proteotoxic Misfolding Events.Structure (London, England : 1993) · 2019Article
- Model validation: local diagnosis, correction and when to quit.Acta crystallographica. Section D, Structural biology · 2018Article
- Structure of a novel antibacterial toxin that exploits elongation factor Tu to cleave specific transfer RNAs.Nucleic acids research · 2017Article
- Crystal structures of TdsC, a dibenzothiophene monooxygenase from the thermophileThe Journal of biological chemistry · 2017Article
- Improving the efficiency of molecular replacement by utilizing a new iterative transform phasing algorithm.Acta crystallographica. Section A, Foundations and advances · 2016Article
- Multiple oligomeric structures of a bacterial small heat shock protein.Scientific reports · 2016Article
- Tools for Model Building and Optimization into Near-Atomic Resolution Electron Cryo-Microscopy Density Maps.Methods in enzymology · 2016Review
- Crystallographic study of a MATE transporter presents a difficult case in structure determination with low-resolution, anisotropic data and crystal twinning.Acta crystallographica. Section D, Biological crystallography · 2015Article
- Crystallization and X-ray diffraction studies of a complete bacterial fatty-acid synthase type I.Acta crystallographica. Section F, Structural biology communications · 2015Article
- Expression and crystallographic studies of the ligand-binding region of the human endocytic collagen receptor uPARAP.Acta crystallographica. Section F, Structural biology communications · 2015Article
- FEM: feature-enhanced map.Acta crystallographica. Section D, Biological crystallography · 2015Article
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7 authors.
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Abstract
An approach is presented for addressing the challenge of model rebuilding after molecular replacement in cases where the placed template is very different from the structure to be determined. The approach takes advantage of the observation that a template and target structure may have local structures that can be superimposed much more closely than can their complete structures. A density-guided procedure for deformation of a properly placed template is introduced. A shift in the coordinates of each residue in the structure is calculated based on optimizing the match of model density within a 6 Å radius of the center of that residue with a prime-and-switch electron-density map. The shifts are smoothed and applied to the atoms in each residue, leading to local deformation of the template that improves the match of map and model. The model is then refined to improve the geometry and the fit of model to the structure-factor data. A new map is then calculated and the process is repeated until convergence. The procedure can extend the routine applicability of automated molecular replacement, model building and refinement to search models with over 2 Å r.m.s.d. representing 65-100% of the structure.
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