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Crystal structure of the viral rhodopsin OLPVR1 in P21212 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 6000, 100mM Tris (pH 8.2), monopalmitolein
Crystal Properties Matthews coefficient Solvent content 2.64 53.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.525 α = 90 b = 115.796 β = 90 c = 53.529 γ = 90
Symmetry Space Group P 21 21 2
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 1.4 48.59 100 0.072 0.078 0.031 0.998 12.3 6.3 57845
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 1.4 1.42 99.9 1.81 1.972 0.775 0.453 6.3
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 1.4 20 54864 2896 99.87 0.1451 0.1427 0.1434 0.1879 0.1855 RANDOM 24.189
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] -0.39 0.89 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.743 r_dihedral_angle_4_deg 23.378 r_dihedral_angle_3_deg 16.011 r_rigid_bond_restr 10.934 r_dihedral_angle_1_deg 6.665 r_angle_other_deg 1.388 r_angle_refined_deg 1.048 r_chiral_restr 0.065 r_gen_planes_refined 0.01 r_bond_refined_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.743 r_dihedral_angle_4_deg 23.378 r_dihedral_angle_3_deg 16.011 r_rigid_bond_restr 10.934 r_dihedral_angle_1_deg 6.665 r_angle_other_deg 1.388 r_angle_refined_deg 1.048 r_chiral_restr 0.065 r_gen_planes_refined 0.01 r_bond_refined_d 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1920 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 219
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing