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. 2020 Dec;26(12):1755–1766. doi: 10.1261/rna.071100.119

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© 2020 Chang et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society

This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

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FIGURE 1. — HNMMC refinement of a deformed tRNA. (A) The DOF of a tRNA. Each helical stem (red, blue, green, and yellow) of a tRNA is defined as a natural move (indicated in each box), which can translate and rotate independently, with each red dot as a center of rotation and translation. Two flexible unpaired loops are colored gray. (B) The starting tRNA model with 8.72-Å C4′ RMSD to the target structure fitted in the target map. (C) The refined model with the lowest total energy (E_total) has a C4′ RMSD of 1.37 Å to the target structure. Each helical stem of the tRNA model is colored red, blue, green, and yellow, respectively, based on the DOF defined in A. The transparent density is Gaussian-blurred from the target structure to 5-Å resolution.