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Figure 2
The side-chain dynamics of residue Arg73 in time representation and ensemble representation. First column: comparison of the experimental crystal structure (gray) and the recovered structures solved using the simulated diffraction data obtained from the MD trajectories at 298 K (red) and 250 K (orange). Residue 73 in the recovered structures is highlighted in cyan. Second column: electron density of residues 71–73 in the recovered structures (red for 298 K, orange for 250 K) and in our experimental structure (gray). Third column: the temporal `bundles' containing 125 lysozyme molecules extracted from the uniformly spaced MD frames at 298 and 250 K (the frames sample the final two-thirds of the trajectory from 100 to 300 ns). Fourth column: the ensemble (spatial) `bundles' containing 125 lysozyme molecules extracted from the last MD frame at 298 and 250 K. Note that for the trajectories that have not fully converged the thus-defined spatial bundles should be broader than the corresponding temporal bundles.

IUCrJ
Volume 10| Part 1| January 2023| Pages 16-26
ISSN: 2052-2525
https://doi.org/10.1107/S2052252522011198