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Epoxide hydrolase CorEH without ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QYJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 2 uL reservoir (16% PEG4000, 0.1 M Tris pH 9.5, 0.1 M NaOAc, 0.018 M imidazol pH 7.0) + 2 uL protein solution (10 mg/ml protein, 10 mM Tris pH 7.5, 20 mM NaCl) + 0.66 uL extra (1 M imidazol pH 6.5)
Crystal Properties Matthews coefficient Solvent content 2.31 46.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.016 α = 90 b = 156.57 β = 90 c = 112.581 γ = 90
Symmetry Space Group P 21 21 2
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 2M mirrors 2020-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.918400 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) 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 2.177 50 99.7 0.203 0.22 0.994 9.1 6.7 129462 -3 -3 37.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.177 2.31 98.9 1.41 1.535 0.547 1.3 6.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT FREE R-VALUE 3QYJ 2.177 47.394 129462 6415 99.667 0.176 0.1734 0.1735 0.2262 0.2262 random selection 34.511
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] -0.768 0.19 0.578
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.12 r_dihedral_angle_4_deg 24.222 r_dihedral_angle_3_deg 15.343 r_dihedral_angle_1_deg 7.304 r_lrange_it 4.003 r_lrange_other 3.934 r_scangle_it 1.837 r_scangle_other 1.837 r_angle_refined_deg 1.759 r_mcangle_it 1.583
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.12 r_dihedral_angle_4_deg 24.222 r_dihedral_angle_3_deg 15.343 r_dihedral_angle_1_deg 7.304 r_lrange_it 4.003 r_lrange_other 3.934 r_scangle_it 1.837 r_scangle_other 1.837 r_angle_refined_deg 1.759 r_mcangle_it 1.583 r_mcangle_other 1.583 r_angle_other_deg 1.36 r_scbond_it 1.149 r_scbond_other 1.149 r_mcbond_it 1.022 r_mcbond_other 1.022 r_symmetry_xyhbond_nbd_other 0.255 r_nbd_refined 0.212 r_nbd_other 0.205 r_symmetry_nbd_other 0.177 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.161 r_symmetry_xyhbond_nbd_refined 0.154 r_symmetry_nbd_refined 0.123 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.077 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18055 Nucleic Acid Atoms Solvent Atoms 1112 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing