File:Observing-the-overall-rocking-motion-of-a-protein-in-a-crystal-ncomms9361-s3.ogv

English: Supplementary Movie 2 Illustration of rigid-body motion of ubiquitin (chain A) in cubic-PEG-ub crystals from MD simulation. The movie features a "typical" protein molecule in the sense of Figure 4. Specifically, the rocking correlation function is closest to the average rocking correlation functions, with minimum rms deviation between the two. The correlation functions classified as outliers (green curves in Figure 4) have been excluded from consideration. To generate the frames, a rigid protein structure (1UBQ) has been superimposed onto the instantaneous coordinates of the selected ubiquitin molecule in the MD trajectory (via Cα atoms in the secondary structure). The sequence of the frames, therefore, represents instantaneous orientations of the rigid-body ubiquitin molecule; the internal dynamics and translational motions have been removed. The movie covers the entire length of each trajectory, which is 1 us, and are sampled at 1 ns interval. The perspective used in this movie is identical to the one in the other two movies (obtained via the appropriate crystal symmetry transformations).