Effects of crystallization parameters on active site geometry. (A) Whole-molecule view of our crystal structure model, with length of long-range restraints and participating residues indicated. (Top inset) Short-range restraints and participating residues in our Xtal simulations. (Bottom inset) A 100-psec-averaged snapshot from a Xtal_U-1+ simulation (gold) is overlaid with a 100-psec-averaged snapshot from a U-1+ simulation (navy). The adjacent P4 loop interacts with U23 and C22 resulting in increased distances of these residues from U-1. As a result, interactions important for stabilizing favorable fitness cannot easily form. (B) Comparison of in-line fitness values in Xtal_dU-1+ and dU-1+ simulations. (C) Comparison of in-line fitness “equivalent” values (see the Results section for definition) in dUGG+, Xtal_dUGG+, and dUGG simulations. (D) Comparison of C75(N3)…G1(O5′) heavy atom distances in dUGG+ and dUGG simulations.
