Fig. 4: Time-dependence of difference electron density features in NpSRII.

a Difference electron density (blue positive density, mustard negative density, arbitrary units) is represented as a function of sequence according to the procedure described by Wickstrand et al.³⁸ Similar difference electron density features are observed for bR and NpSRII during continuous illumination, and within the time-resolved data following a 5 ms laser-flash. Transmembrane helices of bR are indicated in transparent purple and those of SRII in transparent pink. Helix boundaries for bR are helix A, residues 6 –32; B, 37 –58; C, 80 –100; D, 105 –127; E, 131 –160; F, 165 –191; G, 201 –224. Helix boundaries for SRII are helix A, residues 3 –26; B, 33 –56; C, 70 –92; D, 94 –118; E, 122 –150; F, 153 –181; G, 189 –219. b Root mean square deviations (rmsd) of Cα atomic displacements after partial occupancy refinement are shown averaged over the time-delays Δt = 0 ms to 90 ms (blue line) and for the photostationary state (red line). Coordinate error bars are estimated from procedures developed in reference 64: 100 sets of refined coordinates are generated from 100 sets of bootstrap resampled data, and the standard-deviations (error bar estimates) of the mean separations between coordinates from light and dark data are calculated. c Quantification of difference electron density features averaged over the time-delays Δt = 0 ms to 90 ms (blue line) and for the photostationary state (red line). Error bars associated with difference electron density observations are estimated from procedures developed in references 64 and 38: difference electron density maps are calculated from 100 sets of bootstrap resampled light and dark data, and the standard deviations (error bar estimates) of difference electron density features are quantify. d Time-dependence of the mean amplitude of difference electron density changes associated with the extracellular portions of helix C (Pro71 to Pro81, blue data), the extracellular portions of helices D and E (Val118 to Tyr124, red data), the cytoplasmic portions of helix F and the F/G loop (Gly143 to Pro171, mustard data), and the mid-portions of helix G (Ile197 to Leu213, purple data). Error bars associated with difference electron density observations are estimated using the same procedures as in panel c. Source data are provided as a Source Data file.