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Figure 7
Conformational ensemble of the Amber-refined structure obtained from the D-model with PDB code 1dt4. Eight protein molecules in the simulated UC are superimposed via the Cα atoms of the secondary-structure regions. The individual structures are colored according to the deviation from the mean coordinates. Only those side chains where the deviation reaches 2.5 Å are visualized in the plot. Additionally, those side chains that sample different rotameric states (according to Lovell et al., 2000BB60) are labeled in the plot. As expected, the refined S-model displays a somewhat greater amount of conformational heterogeneity compared with the refined D-model (results not shown).

IUCrJ
Volume 9| Part 1| January 2022| Pages 114-133
ISSN: 2052-2525
https://doi.org/10.1107/S2052252521011891