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Assessment of structural features in Cryo-EM density maps using SSE and side chain Z-scores.
- Source :
-
Journal of structural biology [J Struct Biol] 2018 Dec; Vol. 204 (3), pp. 564-571. Date of Electronic Publication: 2018 Aug 23. - Publication Year :
- 2018
-
Abstract
- We introduce a new method for assessing resolvability of structural features in density maps from Cryo-Electron Microscopy (Cryo-EM) using fitted or derived models. It calculates Z-scores for secondary structure elements (SSEs) and side chains. Z-scores capture how much larger the cross-correlation score (CCS) is for atoms in such features at their placed locations compared to the CCS at displaced positions. Z-scores are larger when the structural features are well-resolved, as confirmed by visual analysis. This method was applied to all 66 maps submitted to the 2015/2016 EMDB map challenge. For each map, the fitted model provided by the map committee was used in this assessment. The average Z-scores for each map and fitted model correlate moderately well with reported map resolutions (r <superscript>2</superscript> = 0.45 for SSE Z-scores and r <superscript>2</superscript> = 0.56 for side chain Z-scores). Rankings of the submitted maps based on average Z-scores seem to more closely agree with visual analysis. Z-scores can also be used to pinpoint which parts of a model are well-resolved in a map, and which parts of the model may need further fitting or refinement to make the model better match the density.<br /> (Copyright © 2018 Elsevier Inc. All rights reserved.)
Details
- Language :
- English
- ISSN :
- 1095-8657
- Volume :
- 204
- Issue :
- 3
- Database :
- MEDLINE
- Journal :
- Journal of structural biology
- Publication Type :
- Academic Journal
- Accession number :
- 30144506
- Full Text :
- https://doi.org/10.1016/j.jsb.2018.08.015