Figure 3.

Comparison of experimental and simulation-derived SAXS profiles of DNA-free form of EcoO109I in solution. The SAXS profiles from the experiments (pink dots) and the 150-ns MD simulation (blue curves) are shown in logarithmic plot (A) and Guinier plot (range of R_gQ, <1.3) (B). (C) Time evolution of protein-water R_g estimated from Guinier plot for time-window of 500 ps shifting through 150-ns MD trajectory (cyan curve) and 20-ns restraint-MD trajectory (yellow-green curve). Average R_g is also shown for 150-ns trajectory (blue horizontal line) and 20-ns trajectory (green horizontal line). Pink horizontal line with error bar shows protein-water Rg estimated from Guinier plot of experimental SAXS profile. Protein R_g was calculated from protein structures without water molecules in 150-ns trajectory (black).