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Crystal structure of bovine opsin with citronellol bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CAP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 3.1-3.3M ammonium sulfate, 0.1M sodium acetate buffer, pH 5.5
Crystal Properties Matthews coefficient Solvent content 7.75 84.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 243.412 α = 90 b = 243.412 β = 90 c = 108.44 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 173 PIXEL DECTRIS EIGER R 4M 2016-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033 APS 23-ID-B
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 3.186 39.756 99.9 0.081 0.09 0.037 0.998 12.5 5.7 20603
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 3.186 3.197 99 0.549 0.596 0.229 0.927 6.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3CAP 3.186 39.756 1.38 20585 1047 99.84 0.2139 0.2121 0.2193 0.2477 0.2529
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.358 f_angle_d 0.834 f_chiral_restr 0.045 f_plane_restr 0.006 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2673 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 98
Software Software Software Name Purpose PHENIX refinement XDS data reduction autoPROC data scaling PHASER phasing