Figure 2: Comparison of bR dark-state structures. Overall structures determined by SFX (purple), SMX (blue) and conventional cryo-crystallography (green).

(a) Overall structures are highly similar with only minor deviations in loop regions and the termini. (b–d) Comparison of electron density maps in the retinal-binding pocket (SFX (b), SMX (c) and Cryo (d)). The electron density maps (blue, 2Fo−Fc, 1 σ) are well defined in all three cases and strong positive density is observed when retinal (yellow sticks; left panel) is omitted during refinement (green, Fo−Fc, 2.5 σ). Flexible regions of the retinal β-ionone ring (insets), which are not part of the retinal conjugated double bond system, can be clearly identified in the two room temperature structures.