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OPR3 Y190F variant in complex with ethyl (Z)-2-(hydroxyimino)-3-oxopentanoate
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 7.5 293.15 100 mM (Sodium HEPES; MOPS (acid)) pH 7.5; 30 mM Sodium nitrate; 30 mM Sodium phosphate dibasic; 30 mM Ammonium sulphate; 20% v/v Glycerol; 10% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.26 45.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.38 α = 90 b = 92.1 β = 99.11 c = 89.96 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 EIGER2 X 16M 2021-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033190 PETRA III, DESY P11
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 1.35 45.92 95.14 0.999 16.19 1.8 317534 14.42
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 1.35 1.398 0.967
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 1.35 45.92 1.36 165582 2099 95 0.1647 0.1645 0.1644 0.1836 0.1826 20.38
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 13.8613 f_angle_d 0.8276 f_chiral_restr 0.0796 f_plane_restr 0.0086 f_bond_d 0.0052
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5718 Nucleic Acid Atoms Solvent Atoms 645 Heterogen Atoms 126
Software Software Software Name Purpose PHENIX refinement PHASER phasing Aimless data scaling XDS data reduction AutoProcess data processing