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Crystal structure of bovine rod opsin in complex with a nanobody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.16 277.15 25% PEG 600
0.1 M Tricine pH 8.16
5 mM EDTA
5 mM beta mercaptoethanol
10 mM hydroxylamine
50 mM CYGLU-4
* reservoir solution contained 30% PEG 600
Crystal Properties Matthews coefficient Solvent content 4.54 72.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.065 α = 90 b = 120.065 β = 90 c = 230.943 γ = 120
Symmetry Space Group P 31 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 EIGER X 16M 2022-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.71 50 99.9 0.055 0.999 15.83 10 20961
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.71 3.94 3.659 0.221 0.65
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FOURIER SYNTHESIS THROUGHOUT 3.71 47.41 19956 1033 99.68 0.2921 0.2919 0.2938 0.2953 0.3053 RANDOM 230.952
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] 0.44 0.22 0.44 -1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.946 r_dihedral_angle_2_deg 7.797 r_dihedral_angle_1_deg 5.488 r_angle_refined_deg 0.67 r_angle_other_deg 0.246 r_chiral_restr 0.037 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6629 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 203
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling REFMAC phasing