X-ray Diffraction Analysis of Protein Crystals

X-ray diffraction data sets for the native and mercury-derivatized protein crystals were collected on beamline X06SA at SLS and beamline BL32XU at SPring-8, using a 1-μm-wide, 15-μm-high microbeam³⁸ . Data were indexed and scaled with the programs XDS^{39 (link)} and SCALA^{40 (link)}, or with DENZO and SCALEPACK from the HKL2000 program suite (HKL Research). Experimental phases were determined by the MAD method, using the four Hg sites identified with the program SHELX^{41 (link)}. Subsequent refinements of the heavy atom parameters and phase calculations were performed with the program SHARP⁴² . The data collection and phasing statistics are shown in Supplementary Table 1. The initial model structure of C1C2 was built with the program Phyre⁴³ , using the Anabaena sensory rhodopsin structure (PDB accession 1XIO) as the template. The resultant structure was manually modified to fit into the experimental electron density maps, using the program Coot^{44 (link)}. The structure was then refined with the program Phenix^{45 (link)}. Figures were prepared with Cuemol (http://www.cuemol.org).