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OPR3 Y370F 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 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 2.27 45.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.311 α = 90 b = 92.602 β = 99.235 c = 89.982 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 0.967697 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 1.42 32.6 98.12 0.997 10.4 3.6 287567 17.41
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 1.42 1.475 0.767
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3hgs 1.42 32.6 1.36 146004 7314 98.13 0.1611 0.1598 0.1856 0.2059 23.85
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 21.1234 f_angle_d 0.8294 f_chiral_restr 0.0774 f_bond_d 0.0052 f_plane_restr 0.0052
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5690 Nucleic Acid Atoms Solvent Atoms 613 Heterogen Atoms 93
Software Software Software Name Purpose PHENIX refinement PHASER phasing Aimless data scaling XDS data reduction AutoProcess data processing