Back to Search Start Over

Assessment of structural features in Cryo-EM density maps using SSE and side chain Z-scores.

Authors :
Pintilie G
Chiu W
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