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With the improved density map after "focus" classification and refinement, we also compared our reconstructed F-subcomplex with the three crystal structures of clathrin AP1 (the F-subcomplex homologue) in different conformations as well as the structure of membrane-bound F-subcomplex in the "hyper-open" state (Dodonova et al., 2015) to fit into the focus-refined density map.
(C ) The part of the complex one would like to focus classification on (V2) is shown in red.
For example, one might want to focus classification on the part of the particle that is depicted in red in Figure 1A, and ignore any variations in the yellow part.
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The map quality of specific regions was dramatically improved by focused classification and refinement (Fig. S5 and Table S3).
Additional focused classification of Kir6.2 CTD with a soft mask but without alignment was used to separate 3D classes with different CTD conformations.
Here we review some of the latest ribosome structures, where cryo-EM allowed gaining unprecedented insights based on 3D structure sorting with focused classification and refinement methods helping to reach local resolution levels better than 3 Å.
In 2003, the IPC made an attempt to address "the overall objective to support and co-ordinate the ongoing development of accurate, reliable, consistent and credible sport focused classification systems and their implementation".
Areas of high variance can then be masked and used for focused classification to produce separate 3D density maps (87).
Because the reviewers do not see clear parallels with the focused classification method described by Penczek, Frank and Spahn, we have removed this comparison from the manuscript.
An additional focussed classification using a mask around the P-Site tRNA identified a final 27,415 particles that are unratcheted, bound to SRP, and contain improved density for the nascent chain.
As weak density for SRP in this population could be observed, a further focused classification was performed utilizing a mask around the observed extra-ribosomal density to identify 16% of this unratcheted population (27,627 particles) that contained SRP.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com