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Crystal structure of Bos taurus opsin at 2.7 Angstrom
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4J4Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 contained 2.8-3.4 M ammonium sulfate in 0.05-0.1 M NaAcO buffer, pH 5.2-5.6
Crystal Properties Matthews coefficient Solvent content 84.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 242.66 α = 90 b = 242.66 β = 90 c = 111.77 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 100 PIXEL DECTRIS PILATUS 6M-F 2014-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97890 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.7 50 100 20.9 22.8 34545
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 FOURIER SYNTHESIS THROUGHOUT 4J4Q 2.7 49.34 32815 1725 99.95 0.24541 0.24496 0.2518 0.25378 0.2555 RANDOM 94.944
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] -3.82 -1.91 -3.82 12.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.25 r_dihedral_angle_3_deg 12.665 r_dihedral_angle_4_deg 11.276 r_long_range_B_refined 7.181 r_long_range_B_other 7.18 r_dihedral_angle_1_deg 4.492 r_scangle_other 3.976 r_mcangle_it 3.692 r_mcangle_other 3.691 r_scbond_it 2.342
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.25 r_dihedral_angle_3_deg 12.665 r_dihedral_angle_4_deg 11.276 r_long_range_B_refined 7.181 r_long_range_B_other 7.18 r_dihedral_angle_1_deg 4.492 r_scangle_other 3.976 r_mcangle_it 3.692 r_mcangle_other 3.691 r_scbond_it 2.342 r_scbond_other 2.342 r_mcbond_it 2.194 r_mcbond_other 2.19 r_angle_refined_deg 0.866 r_angle_other_deg 0.697 r_chiral_restr 0.047 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2592 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 154
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing