Computational protocol: Crystal Structure of Cruxrhodopsin-3 from Haloarcula vallismortis

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Protocol publication

[…] X-ray diffraction data were collected on beamline BL38B1 at SPring-8, where a crystal kept at 100 K was exposed to a monochromatic X-ray beam at a wavelength of 1.0 Å with an X-ray flux rate of ∼2×1012 photons/mm2/sec. Diffraction data were collected with an oscillation range of 1° and an X-ray flux of ∼1×1013 photons/mm2 per image. Indexing and integration of diffraction spots were carried out using MOSFILM 6.1 . The scaling of data was accomplished using SCALA in the CCP4 program suite . Structural analysis was performed with CNS and XtalView . Firstly the structure of bR (pdb entry: 1IW6) was modified using Swiss-Model , by which non-conserved residues between bR and cR3 were automatically replaced, and the whole part of the modified polypeptide was used as an input model of the molecular replacement. (The root mean square deviation between the input model and the final model of cR3 is 0.64 Å for 193 Cα atoms). After a rotational and translational searching with MOLREP , retinal, water and lipid molecules were added and the protein conformation was modified manually on the ground of the 2Fo-Fc map. Subsequent refinements including simulated annealing and individual B-factor refinement resulted in an R cryst of 23.1% and an R free of 25.4% (). […]

Pipeline specifications

Software tools SWISS-MODEL, Molrep
Applications Small-angle scattering, Protein structure analysis
Chemicals Retinaldehyde