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Crystal structure of the viral rhodopsin OLPVR1 in P1 space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SQG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 8.2 293 10 mM CaCl2, 10 mM MgCl2, 24% PEG 550, 100mM Tris (pH 8.2), monoolein
Crystal Properties Matthews coefficient Solvent content 2.39 48.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.177 α = 113.9 b = 56.968 β = 90.01 c = 62.34 γ = 91.49
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 PILATUS 6M-F 2018-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.97625 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.6 40.16 95.2 0.058 0.069 0.036 0.998 6.1 3.5 63486
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 94.5 1.161 1.366 0.714 0.533 3.6
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 6sqg 1.6 20 60315 3142 95.18 0.1896 0.1884 0.2007 0.2132 0.2225 RANDOM 29.79
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] 1.72 -0.36 -0.22 -0.18 0.13 -1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.938 r_dihedral_angle_4_deg 21.953 r_dihedral_angle_3_deg 16.234 r_dihedral_angle_1_deg 6.397 r_angle_other_deg 1.167 r_angle_refined_deg 1.066 r_chiral_restr 0.059 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_gen_planes_other 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.938 r_dihedral_angle_4_deg 21.953 r_dihedral_angle_3_deg 16.234 r_dihedral_angle_1_deg 6.397 r_angle_other_deg 1.167 r_angle_refined_deg 1.066 r_chiral_restr 0.059 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_gen_planes_other 0.001 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3842 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 288
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing