Figure 4.

Structure refinement aided by Monte Carlo simulations. The case of the wild-type I₃ intermediate is shown as an example. Starting from 360 random initial structures generated from Monte Carlo simulations, we minimized the χ² value (i.e., the degree of discrepancy between the experimental curve and the theoretical curve calculated from one of the starting structures) by exploring the structural space via Monte Carlo simulations guided by MD force fields and simulated annealing. (a) The χ² values between the experimental curve and the theoretical curve for the initial structure (black circles) and the refined structures (red and blue circles) are plotted as functions of the rmsd vs an arbitrary reference structure (4sdh). Those corresponding to the best structures are circled in blue. (b, c) Displacement plots for (b) 50 arbitrary structures chosen from among the 360 initial structures and (c) the 76 best refined structures. The displacement was calculated with respect to the 3sdh structure of HbI(CO)₂. Helices are labeled at the top of the plots. (d, e) Comparison of the experimental species-associated scattering curve with the theoretical scattering curves of (d) the 50 arbitrary structures and (e) the 76 best refined structures.