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Crystal structure of the microbial rhodopsin from Sphingomonas paucimobilis (SpaR)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C3W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 293 1.6M Ammonium Phosphate pH 5.2
Crystal Properties Matthews coefficient Solvent content 2.96 58.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 233.339 α = 90 b = 65.027 β = 90 c = 124.689 γ = 90
Symmetry Space Group C 1 2 1
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 2017-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.975997 ESRF ID29
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 2.8 46.32 96.4 0.171 0.218 0.133 0.995 4.6 2.3 44606
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 2.8 2.91 97.3 1.245 1.592 0.98 0.396 2.3
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 1c3w 2.8 19.91 42268 2215 95.44 0.2761 0.2746 0.2804 0.3033 0.3078 RANDOM 52.68
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] -0.48 0.36 4.93 -4.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.064 r_dihedral_angle_4_deg 28.901 r_dihedral_angle_3_deg 23.943 r_dihedral_angle_1_deg 4.168 r_angle_refined_deg 1.082 r_angle_other_deg 1.037 r_chiral_restr 0.029 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.064 r_dihedral_angle_4_deg 28.901 r_dihedral_angle_3_deg 23.943 r_dihedral_angle_1_deg 4.168 r_angle_refined_deg 1.082 r_angle_other_deg 1.037 r_chiral_restr 0.029 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10354 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 162
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing