Figure 4. Difference Fourier electron density map and structural changes around TM7 and TM3.

Views of the |F_obs|^light− |F_obs|^dark difference Fourier electron density maps and the structural changes around TM7 (a–e) and TM3 (f–j) for 1 μs (a and f), 50 μs (b and g), 250 μs (c and h), 1 ms (d and i), and 4 ms (e and j). Green and purple meshes indicate positive and negative difference electron densities, respectively (contoured at ±3.1 to 3.3σ, see also Figure 4—figure supplement 1). The difference Fourier maps were calculated by using the phases from the coordinates of the dark-adapted C1C2 structure (gray). Paired negative and positive difference electron densities indicate the downward shift of TM7 and the outward shift of TM3. The structural model (blue) was refined against the extrapolated data of each time point and the model was superimposed upon the initial-state C1C2 model (gray). Movements of the residues and the TM helices are indicated by arrows. Probably due to the variations in the crystal quality (Table 1), the difference density in the 250 μs time-delay seems rather weak.

Figure 4—figure supplement 1. Overview of the |F_obs|^light− |F_obs|^dark difference Fourier electron density maps for five time points.

Green represents positive difference electron density (contoured at +3.1 to 3.3σ, where sigma represents the root mean square electron density of the unit cell) and purple represents negative difference electron density (contoured at −3.1 to −3.3σ). The initial-state C1C2 structure was used for the phases in calculating these difference Fourier maps and is shown in blue. Significant density changes were only observed in the protein regions.

Figure 4—figure supplement 2. Stereo views of the difference Fourier electron density maps and structural changes.

Stereo views of the |F_obs|^light− |F_obs|^dark difference Fourier electron density maps and the structural changes of C1C2. Each time point is indicated in the respective maps. The structural model (blue) was refined against the extrapolated data of each time point and the model was superimposed upon the initial-state C1C2 model (gray).

Figure 4—figure supplement 3. Electron density of extrapolated map.

A stereo view of the extrapolated electron density map for the retinal binding pocket, shown as a mesh representation contoured at 1.2σ. The 13-cis retinal and the surrounding residues are indicated by sticks. The red spheres indicate water molecules.

Figure 4—figure supplement 4. Calculated difference |F_calc|^light− |F_calc|^dark map and structural changes around TM7 and TM3.

Views of the structural changes around TM7 (a–e) and TM3 (f–j) for 1 μs (a and f), 50 μs (b and g), 250 μs (c and h), 1 ms (d and i), and 4 ms (e and j). Light green and orange mesh indicate positive and negative difference electron densities, respectively (contoured at ±3.9 to 4.2 σ, see also Figure 4—figure supplement 1). The structural model (blue) was refined against the extrapolated data of each time point and the model was superimposed upon the initial-state C1C2 model (gray). Movements of the residues and the TM helices are indicated by arrows.

Figure 4—figure supplement 5. Difference Fourier maps along the putative ion pore.

Difference maps of different time delays are shown for the inner-gate (left), central-gate (middle), and extracellular water access channel (right). Each time point and contour level is indicated in the respective maps.