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REFMAC 5 for the refinement of macromolecular crystal structures
Open accessAbstract
This paper describes various components of the macromolecular crystallographic refinement program REFMAC5, which is distributed as part of the CCP4 suite. REFMAC5 utilizes different likelihood functions depending on the diffraction data employed (amplitudes or intensities), the presence of twinning and the availability of SAD/SIRAS experimental diffraction data. To ensure chemical and structural integrity of the refined model, REFMAC5 offers several classes of restraints and choices of model parameterization. Reliable models at resolutions at least as low as 4 Å can be achieved thanks to low-resolution refinement tools such as secondary-structure restraints, restraints to known homologous structures, automatic global and local NCS restraints, `jelly-body' restraints and the use of novel long-range restraints on atomic displacement parameters (ADPs) based on the Kullback-Leibler divergence. REFMAC5 additionally offers TLS parameterization and, when high-resolution data are available, fast refinement of anisotropic ADPs. Refinement in the presence of twinning is performed in a fully automated fashion. REFMAC5 is a flexible and highly optimized refinement package that is ideally suited for refinement across the entire resolution spectrum encountered in macromolecular crystallography.
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Phosphorylation of Cytochrome c Threonine 28 Regulates Electron Transport Chain Activity in Kidney
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Aster-dependent nonvesicular transport facilitates dietary cholesterol uptake
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Testosterone meets albumin – the molecular mechanism of sex hormone transport by serum albumins
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Increasing the efficiency of ligands for FK506-binding protein 51 by conformational control
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Structural characterization of the PPIase domain of FKBP51, a cochaperone of human Hsp90
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Structural Basis for Draxin-Modulated Axon Guidance and Fasciculation by Netrin-1 through DCC
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Quaternary dynamics of the SecA motor drive translocase catalysis.
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Structural basis for the recruitment of glycogen synthase by glycogenin
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The final step of 40S ribosomal subunit maturation is controlled by a dual key lock
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Structures of human constitutive nitric oxide synthases
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Autotaxin facilitates selective LPA receptor signaling
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Structure of the secretion domain of HxuA from Haemophilus influenzae
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De novo designed peptides for cellular delivery and subcellular localisation
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Selective Aster inhibitors distinguish vesicular and nonvesicular sterol transport mechanisms
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Khusnutdinova, A. N., Batyrova, K. A., Brown, G., Fedorchuk, T., Chai, Y. S., Skarina, T., Flick, R., Petit, A., Savchenko, A., Stogios, P., et al. (2023) · The FEBS Journal · doi:10.1111/febs.16903 · Cited by 40
Metadata
- Authors
- Murshudov, G. N., Skubák, P., Lebedev, A. A., Pannu, N. S., Steiner, R. A., Nicholls, R. A., Winn, M. D., Long, F., & Vagin, A. A.
- Venue
- Acta Crystallographica Section D Biological Crystallography
- Published
- 2011-03-18
- Volume
- 67
- Issue
- 4
- Pages
- 355-367
- ISSN
- 0907-4449 (ISSN-L)
- OpenAlex
- W2159211495
- Cited by
- 8,317
- References
- 4
- FWCI
- 235.33
- Type
- journal article
- Language
- en
- Open access
- hybrid
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.