Cowtan, Kevin orcid.org/0000-0002-0189-1437 and Agirre, Jon orcid.org/0000-0002-1086-0253 (2018) Macromolecular refinement by model morphing using non-atomic parameterizations. Acta crystallographica. Section D, Structural biology. ISSN 2059-7983
Abstract
Refinement is a critical step in the determination of a model which explains the crystallographic observations and thus best accounts for the missing phase components. The scattering density is usually described in terms of atomic parameters; however, in macromolecular crystallography the resolution of the data is generally insufficient to determine the values of these parameters for individual atoms. Stereochemical and geometric restraints are used to provide additional information, but produce interrelationships between parameters which slow convergence, resulting in longer refinement times. An alternative approach is proposed in which parameters are not attached to atoms, but to regions of the electron-density map. These parameters can move the density or change the local temperature factor to better explain the structure factors. Varying the size of the region which determines the parameters at a particular position in the map allows the method to be applied at different resolutions without the use of restraints. Potential applications include initial refinement of molecular-replacement models with domain motions, and potentially the use of electron density from other sources such as electron cryo-microscopy (cryo-EM) as the refinement model.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Keywords: | Computational methods,Low resolution,Refinement |
Dates: |
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Institution: | The University of York |
Academic Units: | The University of York The University of York > Faculty of Sciences (York) > Chemistry (York) |
Funding Information: | Funder Grant number SCIENCE AND TECHNOLOGY FACILITIES COUNCIL (STFC) PR130029 BBSRC (BIOTECHNOLOGY AND BIOLOGICAL SCIENCES RESEARCH COUNCIL) BB/L006383/1 BBSRC (BIOTECHNOLOGY AND BIOLOGICAL SCIENCES RESEARCH COUNCIL) BB/L006383/1 |
Depositing User: | Pure (York) |
Date Deposited: | 27 Sep 2017 14:15 |
Last Modified: | 30 Nov 2024 01:08 |
Published Version: | https://doi.org/10.1107/S205979831701350X |
Status: | Published |
Refereed: | Yes |
Identification Number: | 10.1107/S205979831701350X |
Related URLs: | |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:121766 |
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Description: Macromolecular refinement by model morphing using non-atomic parameterizations