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Crystal structure of the active G-protein-coupled receptor opsin in complex with the finger-loop peptide derived from the full-length arrestin-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DQB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 3.2 M (NH4)2SO4 in 0.1 M 2-(N-morpholino)ethanesulfonic acid (MES), pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 242.622 α = 90 b = 242.622 β = 90 c = 110.216 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 mirrors 2012-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9791 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (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 2.75 40.04 99.6 0.05 0.05 23.1 7.4 32166 32166 70.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.9 99.2 0.944 2 7.3 4645
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3DQB 2.75 40.04 30511 30511 1637 99.66 0.21659 0.21659 0.21476 0.2204 0.25075 0.2579 RANDOM 84.895
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] -1.17 -1.17 -1.17 3.79
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 42.816 r_sphericity_free 40.117 r_dihedral_angle_2_deg 36.438 r_scangle_other 19.421 r_long_range_B_refined 19.062 r_long_range_B_other 19.038 r_scbond_it 16.421 r_scbond_other 16.412 r_mcangle_it 16.286 r_mcangle_other 16.284
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 42.816 r_sphericity_free 40.117 r_dihedral_angle_2_deg 36.438 r_scangle_other 19.421 r_long_range_B_refined 19.062 r_long_range_B_other 19.038 r_scbond_it 16.421 r_scbond_other 16.412 r_mcangle_it 16.286 r_mcangle_other 16.284 r_dihedral_angle_3_deg 15.713 r_mcbond_it 13.846 r_mcbond_other 13.834 r_dihedral_angle_4_deg 12.246 r_rigid_bond_restr 6.208 r_dihedral_angle_1_deg 5.104 r_angle_refined_deg 1.187 r_angle_other_deg 0.798 r_chiral_restr 0.154 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2635 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 159
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling