Assessment Of Structural Features Research Articles

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

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 (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.

Liquid‐ and solid‐state (CP‐MAS) multinuclear magnetic resonance study of some 2,5‐dihydro‐1,2,5‐oxoniastannaboratoles—carboncarbon coupling constants, 1J(13C13C), in organometallic‐substituted alkenes

AbstractDerivatives of 2,5‐dihydro‐1,2,5‐oxoniastannaboratoles were studied by multinuclear magnetic resonance both in the liquid (11B, 13C, 29Si, 119Sn NMR) and solid state (13C, 29Si, 119Sn CP/MAS NMR). Together with the results of the x‐ray analysis of the 4,5,5‐triethyl‐2,5‐dihydro‐1,2,2‐trimethyl‐3‐phenyl‐1,2,5‐oxoniastannaboratole‐tetrahydrofuran adduct (1‐THF) (space group P21/c) the NMR data [chemical shifts and coupling constants J(119SnE) (E = 13C, 29Si, 119Sn)] allowed the assessment of structural features in solution and in the solid state (e.g. the weakened coordinative Sn‐O interactions in 1‐THF in solution). The 1J(13C13C) values in 4,5,5‐triethyl‐2,5‐dihydro‐1,2,2‐trimethyl‐3‐trimethylsilyl‐ and ‐3‐trimethylstannyl‐1,2,5‐oxoniastannaboratole and in some non‐cyclic alkenes bearing organometallic substituents were measured using INEPT experiments based on 3J(13C1H) long‐range coupling constants. In the presence of one boryl‐ and two stannyl groups the magnitude of 1J(13C13C) values is reduced to ca. 30 Hz. A positive sign for 2J(119Sn117Sn) in 2‐diethylboryl‐1,1‐bis(trimethylstannyl)but‐1‐ene was determined by 2D 13C1H and 2D 119Sn‐H heteronuclear shift correlations. Scalar 13C11B and 119Sn‐11B coupling has been observed for the first time in 119Sn CP‐MAS NMR spectra.