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Figure 1
MD–MX procedure to revise macromolecular crystal structures. In this procedure, an initial crystal structure S (top left) is used to prepare an MD simulation model, using ensemble refinement to generate a set of diverse conformations (the ensemble-refinement model, E; top center). Snapshots from the MD simulation (top right) are used to generate simulated data and MD ensemble visualizations (bottom right; protein density in purple and water density in cyan). The initial structure is refined against the simulated data, leading to a revised protein structure, Mprot, and a new water network, Mall (bottom center; densities on bottom right). The revised structure is refined against the experimental data to produce the initial MD-revised structure Ri, and manual improvements are made guided by the MD density and snapshots, leading to a final MD-revised structure Rf (bottom left; 2FoFc density in blue at 1σ with traces of positive 3σ FoFc density visible in green).

Journal logoSTRUCTURAL
ISSN: 2059-7983
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