It is also evident from the MD simulations that the average structures are similar to that of corresponding X-ray structures.
The structure from the simulation with the lowest RMSD compared to the averaged structure was considered as the centroid structure of that simulation since the average structures are not actual structures from the simulation.
The torsion angles of the deoxyriboses of the average structure were compared with experimental data of the 5′-GpC-3′ cross-link.
With regard to deoxyribose pseudorotation, the sugar puckers in the average structure were either C1′- exo, C2′- endo, C3′- exo, or O4′- endo. Figure 3A,B displays the base stacking at the cross-linked base pairs.
Average bond distances for both the local structure and the incommensurate average structure were estimated by fitting Gaussian functions to the observed partial pair distribution functions, g ij (r), which represents distribution of bond distances for every pair of atom types, as described in eq 4 (Supporting Information section S1).
For structural comparisons, averaged structures were determined from the snapshots of each MD.
Likewise, for the greenbug AChE complex, the distance between the Cys289 sulfur atom and the AMTS17 thiol sulfur atom was used to generate the MMDS-refined 3D model, and the distances calculated from the initial structure and the four time-average structures were 6.5, 3.8, 7.5, 5.5, and 8.9 Å, respectively.
For the 13 simulations of the human complex, the distances of the Ser203 hydroxyl oxygen atom to the AMTS13 thiol sulfur atom calculated from the initial structure and the 13 time-average structures were 4.1, 6.2, 6.4, 9.6, 18.9, 8.5, 5.8, 13.5, 8.7, 8.9, 10.4, 11.0, 4.7, and 8.1 Å, respectively, indicating good sampling achieved by the 10-ns-long MMDSs.
