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Crystal structure of Bos taurus opsin regenerated with 6-carbon ring retinal chromophore
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G87
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 2.8-3.4 M ammonium sulfate in 0.05-0.1 M MES, pH 6.1-6.6, or 0.05-0.1 M NaAcO buffer, pH 5.2-5.6
Crystal Properties Matthews coefficient Solvent content 4.94 75.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.725 α = 90 b = 81.725 β = 90 c = 200.012 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 PILATUS 6M-F 2016-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97920 APS 24-ID-C
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 4.01 50 99.8 0.243 0.999 6.33 10.6 6944
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 2G87 4.01 48.53 6594 348 99.77 0.31633 0.31419 0.3225 0.35719 0.3683 RANDOM 310.92
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] 5.03 2.51 5.03 -16.3
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 62.711 r_long_range_B_other 62.708 r_mcangle_it 46.387 r_mcangle_other 46.373 r_scangle_other 41.486 r_dihedral_angle_2_deg 30.726 r_mcbond_it 30.023 r_mcbond_other 30.008 r_scbond_it 25.681 r_scbond_other 25.673
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 62.711 r_long_range_B_other 62.708 r_mcangle_it 46.387 r_mcangle_other 46.373 r_scangle_other 41.486 r_dihedral_angle_2_deg 30.726 r_mcbond_it 30.023 r_mcbond_other 30.008 r_scbond_it 25.681 r_scbond_other 25.673 r_dihedral_angle_3_deg 14.712 r_dihedral_angle_4_deg 12.463 r_dihedral_angle_1_deg 5.642 r_angle_refined_deg 1.229 r_angle_other_deg 0.952 r_chiral_restr 0.065 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2749 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing