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Crystal structure of the light-driven proton pump Coccomyxa subellipsoidea Rhodopsin CsR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AM6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 1-(9Z-octadecenoyl)-rac-glycerol, 10 % cholesterol, 42 % v/v polyethylene glycol 400; 100 mM MES; pH 6.5, 150 mM sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.62 53.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.078 α = 90 b = 78.078 β = 90 c = 143.951 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 2M 2016-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8729 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2 32.91 100 0.066 0.997 6.8 4.4 22100
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 100 0.901 0.357 0.8 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3AM6 2 32.91 20932 1155 99.98 0.19398 0.19231 0.2022 0.22493 0.2295 RANDOM 43.432
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.59 0.29 0.59 -1.9
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 42.288 r_dihedral_angle_2_deg 37.1 r_dihedral_angle_4_deg 13.223 r_dihedral_angle_3_deg 11.955 r_sphericity_bonded 6.341 r_dihedral_angle_1_deg 5.159 r_long_range_B_refined 2.983 r_long_range_B_other 2.969 r_mcangle_it 2.764 r_mcangle_other 2.764
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 42.288 r_dihedral_angle_2_deg 37.1 r_dihedral_angle_4_deg 13.223 r_dihedral_angle_3_deg 11.955 r_sphericity_bonded 6.341 r_dihedral_angle_1_deg 5.159 r_long_range_B_refined 2.983 r_long_range_B_other 2.969 r_mcangle_it 2.764 r_mcangle_other 2.764 r_angle_other_deg 2.297 r_scangle_other 2.284 r_mcbond_it 2.21 r_mcbond_other 2.181 r_scbond_it 2.011 r_scbond_other 1.982 r_angle_refined_deg 1.973 r_rigid_bond_restr 1.291 r_chiral_restr 0.193 r_bond_refined_d 0.013 r_bond_other_d 0.009 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1706 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing