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OPR3 Y190F variant in complex with ethyl (Z)-2-(hydroxyimino)-3-oxobutanoate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HGS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293.15 100 mM (Tris (base); BICINE) pH 8.5; 20 mM Sodium formate; 20 mM Ammonium acetate; 20 mM Sodium citrate tribasic dihydrate; 20 mM Potassium sodium tartrate tetrahydrate; 20 mM Sodium oxamate; 20% v/v Ethylene glycol; 10 % w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.35 47.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.456 α = 90 b = 92.724 β = 99.314 c = 90.343 γ = 90
Symmetry Space Group P 1 21 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 4M 2021-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.967700 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.57 40.17 94.97 0.998 12.31 1.8 210187 17.43
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.57 1.626 0.862
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3hgs 1.57 40.17 1.06 109997 1155 97.25 0.1547 0.1546 0.1548 0.1634 0.1612 21.95
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.4963 f_angle_d 0.7814 f_chiral_restr 0.0541 f_plane_restr 0.0086 f_bond_d 0.0054
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5728 Nucleic Acid Atoms Solvent Atoms 587 Heterogen Atoms 92
Software Software Software Name Purpose PHENIX refinement PHASER phasing Aimless data scaling XDS data reduction AutoProcess data processing