Extended Data Fig. 4: Comparison of observed and calculated difference electron density maps at the three time-delays 1, 10 and 100 ps of rhodopsin photoactivation, showing that the refined models (right panels) are in good agreement with raw difference electron density data (left panels).

Difference Fourier electron density maps were created directly from the starting experimental electron density maps (Fobs(light)-Fobs(dark)) (left panels) or from the calculated atomic structure model factors (Fcalc(light)-Fcalc(dark)) (right panels) and compared for the 1 ps dataset (a versus b; g versus h), 10 ps (c versus d), 100 ps datasets (e versus f). The panels show the retinal binding pocket of rhodopsin in the dark state (all panels) (or superimposed with the 1 ps photoactivated structure (g-f)) with retinal in red (or in yellow for the 1 ps structure (g-f)) and contoured with the 2Fobs-Fcalc electron density map (grey mesh) (a—f). Highlighted in colour, the difference Fourier electron density signals between photoactivated and dark rhodopsin are displaying features appearing with time, in blue (positive density) that are correlated with disappearing features in gold (negative density). The mesh contouring at various rmsd values was adjusted for easier side to side comparison of the different types of maps and clarity of the figure (see the values in the panels a—h).