Figure 1.

Simulations of distance distributions between nitroxide probes using RosettaDEER. (A) An example of an experimentally observed distance distribution in apo Mhp1 51/278, shown in black. Distance distributions were simulated using RosettaDEER, MMM, and MDDS from the occluded Mhp1 structure (PDB: 2JLN). The average distance between C_β atoms and the average distance calculated using the CONE model shown in light gray and dark gray, respectively. (B) The estimated average time required to simulate distance distributions (^∗the lower limit of quantitation exceeded the C_β-C_β distance compute time). (C) Coarse-grained rotameric ensemble representation of the methanethiosulfonate spin label. Centers of mass, shown in purple, are used for clash evaluation, whereas electron coordinates, shown in gray, serve as measurement coordinates. (D) Distance distributions between residues are simulated by superimposing coordinates, evaluating clashes and measuring all resulting pairwise distances.