Fig. 2: Results obtained by LocBFactor and LocOccupancy for the Saccharomyces cerevisiae pre-catalytic B complex spliceosome sample.
From: Local computational methods to improve the interpretability and analysis of cryo-EM maps
A Central slice along Z axis of the obtained unsharpened map using EMPIAR 10180 single particles. Coloured squares mark parts of the map corresponding to clear spliceosome densities (green and red), flexible and low-resolution spliceosomal regions (yellow and blue) and background (magenta). B Guinier plots at map points indicated in the coloured squares using a resolution range of [15–4.28] Å. Solid lines represent SNR-weighted values of the logarithm of structure factor amplitudes, while discontinued lines show the fitted lines. C Spliceosome map coloured with the obtained occupancy map by LocOccupancy. The occupancy ranges from 0 (red colour) to 1 (blue colour), indicating no macromolecular density and full occupancy, respectively. D Spliceosome map coloured with the B-factor map to be used for sharpening (slope of the local Guinier plot multiplied by 4) obtained by LocBFactor using a resolution range of [15–4.28] Å. The local B-factor values in the figure range approximately between −800 and −200 Å2. In this figure, noise B-factors (B-factors obtained from amplitudes below the noise level for the used resolution range) are filtered out and appear with black colour. E Local resolution map obtained by Resmap approach. The local resolution ranges between 4 (blue colour) and 15 Å (red colour). F Spliceosome map coloured with the obtained A map (local values of the logarithm of structure factor amplitudes at 15 Å). The values range between −11.0 (magenta colour) and −9.0 (cyan colour) approximately. G Spliceosome map coloured with the B-factor map (B-map) obtained by LocBFactor using a resolution range of [20–15] Å. The B-factor values range between −1100 (magenta colour) and −300 (cyan colour) approximately. H Guinier plots at map points indicated in the coloured squares using a resolution range of [20–15] Å. Solid lines represent SNR-weighted values of the logarithm of structure factor amplitudes, while discontinued lines show the fitted lines. I Spliceosome map coloured with the obtained A map (local values of the logarithm of structure factor amplitudes at 20 Å). The values range between −10.5 (magenta colour) and −6.5 (cyan colour) approximately.
