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Overview and applications of map and model validation tools in the CCP-EM software suite.
Joseph, Agnel Praveen; Malhotra, Sony; Burnley, Tom; Winn, Martyn D.
  • Joseph AP; Scientific Computing Department, Science and Technology Facilities Council, Didcot OX11 0FA, UK. agnel-praveen.joseph@stfc.ac.uk.
  • Malhotra S; Scientific Computing Department, Science and Technology Facilities Council, Didcot OX11 0FA, UK. agnel-praveen.joseph@stfc.ac.uk.
  • Burnley T; Scientific Computing Department, Science and Technology Facilities Council, Didcot OX11 0FA, UK. agnel-praveen.joseph@stfc.ac.uk.
  • Winn MD; Scientific Computing Department, Science and Technology Facilities Council, Didcot OX11 0FA, UK. agnel-praveen.joseph@stfc.ac.uk.
Faraday Discuss ; 240(0): 196-209, 2022 Nov 08.
Article in English | MEDLINE | ID: covidwho-1972674
ABSTRACT
Cryogenic electron microscopy (cryo-EM) has recently been established as a powerful technique for solving macromolecular structures. Although the best resolutions achievable are improving, a significant majority of data are still resolved at resolutions worse than 3 Å, where it is non-trivial to build or fit atomic models. The map reconstructions and atomic models derived from the maps are also prone to errors accumulated through the different stages of data processing. Here, we highlight the need to evaluate both model geometry and fit to data at different resolutions. Assessment of cryo-EM structures from SARS-CoV-2 highlights a bias towards optimising the model geometry to agree with the most common conformations, compared to the agreement with data. We present the CoVal web service which provides multiple validation metrics to reflect the quality of atomic models derived from cryo-EM data of structures from SARS-CoV-2. We demonstrate that further refinement can lead to improvement of the agreement with data without the loss of geometric quality. We also discuss the recent CCP-EM developments aimed at addressing some of the current shortcomings.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Experimental Studies / Prognostic study Limits: Humans Language: English Journal: Faraday Discuss Journal subject: Chemistry Year: 2022 Document Type: Article Affiliation country: D2fd00103a

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Experimental Studies / Prognostic study Limits: Humans Language: English Journal: Faraday Discuss Journal subject: Chemistry Year: 2022 Document Type: Article Affiliation country: D2fd00103a