Extended Data Fig. 1: Rhodopsin molecules crystal packing and lattice translation correction.
From: Ultrafast structural changes direct the first molecular events of vision
a-c.) Rhodopsin molecules packing in the crystal lattice of space group P 2 21 21. Bovine rhodopsin crystals obtained with the lipidic cubic phase method reveal a typical molecule packing of type I, consisting of a well-ordered stacking of 2D-crystals (a.) The 2D-crystals contact each other through the glycosyl groups of Asn2 and Asn15 of the rhodopsin N-termini, generating head-to-head crystal contacts in the c-dimension. (b.) View of the potential physiological dimer35 contacting the transmembrane domains 1 (in blue) of each of the two rhodopsin molecules. (c.) top view of the molecules arrangement. The “Spectrum” rainbow colour transforms gradually from the TM1 in blue to the TM7 and the amphipathic helix 8 in red. d-i) Lattice translation correction. Despite a straightforward molecular replacement (Phaser MR, Phenix75, see Methods) and a solution harbouring a P 2 21 21 space group, the dark rhodopsin data analysis indicated the presence of more than one off-origin peaks in the Patterson function36. In particular, the Patterson peak at td = (0,0.245,0)(SwissFEL) and (0,0.243,0)(SACLA) were attributed to the presence of two translation-related domains within the crystals. Accordingly, a ghost density was identified (d) in the Fo-Fc map (in green and red, contoured at 3.83 rmsd) partially overlapping with the 2Fo-Fc map (blue, 2.7 rmsd) from which the rhodopsin model was built in. e) After correction of the single ___domain X-ray intensities36 according to Wang et al.72 (see Methods), the overall rhodopsin electron density map 2Fo-Fc displays less ghost electron density (green and red). More locally at a few affected amino acid residues locations, e.g. compare the electron density of P34(1.29)/A in the lower panel (g) (corrected) to upper (f) (original). h-i) Importantly, the retinal binding pocket of rhodopsin was not affected by the density overlapping and correction, and the density after correction (i) shows only minor changes in the difference map compared to the original data (h).
