Extended Data Fig. 9: Examples of the FAD geometry correlation analysis.
(a) Superposition of all three steady-state real space correlation analysis (Eox/ss, Str1, in shades of grey, Esemi/ss, Str12, in shades of green, and Ered/ss, Str23, in shades of blue). The overall restraint space derived from our computational analysis is shown as a dotted square surrounding the data extracted from Phenix refinement. Individual data points represent the actual ρC and ρN values obtained from the refined structures. Values corresponding to good fits (top 95 to 100% CC values) are highlighted by a darker shade. (b) Real space correlation analysis examples of the first time-resolved series. The dark control structure (Eox/dark, Str2) results are shown in black, while the ones for the 10 µs time-point (Eox/10µs, Str7) in shades of orange, with good fits in a dark shade, while bad fits in a light one. As the conformational space for FAD•- was unknown, the restraint space for Eox/10µs varied from -90 to 90 degrees. (c) Real space correlation analysis results for the control dark structure (Esemi/dark, Str13) of the second time-resolved series. For real space correlation analysis, the FADH− restraint space was used, and accordingly, data is shown in shades of blue (dark blue for good fits, light blue for bad fits). (d) Real space correlation analysis results for the 300 ns time-point (Esemi/300ns, Str17) of the second time-resolved series. For real space correlation analysis, the FADH− restraint space was used, and accordingly, data is shown in shades of blue (dark blue for good fits, light blue for bad fits). (e - g) 2D ρC and ρN heat maps for the initial computational analysis. Occupancy of each bin is shown in a blue (low occupancy) to red (high occupancy) scale. (e) Oxidized state computational analysis. (f) Semiquinone state computational analysis. (g) Reduced state computational analysis assuming a neutral Arg378-Asp409 pair.
