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High-resolution structure of bovine (3-367)Arrestin-1 in a pre-activated conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UGU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.1 M imidazole, 0.1 M MES pH 6.5, 10% PEG 4000, 20% glycerol, 20 mM sodium formate; 20 mM ammonium acetate; 20 mM sodium citrate tribasic dihydrate; 20 mM potassium sodium tartrate tetrahydrate; 20 mM sodium oxamate
Crystal Properties Matthews coefficient Solvent content 2.44 49.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.56 α = 90 b = 74.76 β = 90 c = 79.77 γ = 90
Symmetry Space Group P 21 21 21
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 2023-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.979460 SSRL BL12-2
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 1.4 50 99.7 0.096 0.999 13.2 15.8 78726
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 1.4 1.48 2.874 0.398 1.1
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 (All) 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 1.4 42.19 78725 3937 99.707 0.143 0.1406 0.14 0.1798 0.1804 RANDOM 24.644
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] -1.48 1.975 -0.495
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.213 r_dihedral_angle_3_deg 11.987 r_dihedral_angle_1_deg 7.102 r_dihedral_angle_2_deg 6.403 r_lrange_it 4.594 r_lrange_other 4.362 r_rigid_bond_restr 2.649 r_scangle_it 2.107 r_scangle_other 2.107 r_mcangle_it 2.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.213 r_dihedral_angle_3_deg 11.987 r_dihedral_angle_1_deg 7.102 r_dihedral_angle_2_deg 6.403 r_lrange_it 4.594 r_lrange_other 4.362 r_rigid_bond_restr 2.649 r_scangle_it 2.107 r_scangle_other 2.107 r_mcangle_it 2.013 r_mcangle_other 2.013 r_scbond_it 1.503 r_scbond_other 1.503 r_mcbond_it 1.44 r_mcbond_other 1.44 r_angle_refined_deg 1.212 r_angle_other_deg 0.417 r_metal_ion_refined 0.312 r_nbd_refined 0.244 r_symmetry_nbd_other 0.188 r_nbd_other 0.171 r_nbtor_refined 0.167 r_symmetry_xyhbond_nbd_refined 0.159 r_xyhbond_nbd_refined 0.143 r_symmetry_nbd_refined 0.091 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.06 r_gen_planes_refined 0.007 r_bond_refined_d 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2729 Nucleic Acid Atoms Solvent Atoms 543 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing