Assessment of Structural Features in Cryo-EM Density Maps using SSE and Side Chain Z-Scores

Publication date: Available online 23 August 2018Source: Journal of Structural BiologyAuthor(s): Grigore Pintilie, Wah ChiuAbstractWe introduce a new method for assessing resolvability of structural features in density maps from Cryo-Electron Microscopy (Cryo-EM) using a fitted model. It calculates Z-scores for secondary structure elements (SSEs) and side chains. Z-scores capture how much larger the cross-correlations score (CCS) is for atoms in such features at their placed location 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 (r2=0.45 for SSE Z-scores and r2=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.
Source: Journal of Structural Biology - Category: Biology Source Type: research
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