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Crystal structure of human soluble epoxide hydrolase C-terminal domain in complex with an N-benzylpiperidine-based inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6I5E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 277.15 20% PEG 3350, 0.2 M malic acid, 0.05 M HEPES, 10% Ethylene Glycol
Crystal Properties Matthews coefficient Solvent content 2.38 48.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.027 α = 90 b = 80.092 β = 91.45 c = 104.278 γ = 90
Symmetry Space Group I 1 2 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 PILATUS 6M 2024-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.6199 Diamond I24
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 1.9 68.99 100 0.998 12.9 2 58440 21.62
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 1.9 1.968 0.921
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.9 68.99 1.41 58422 2959 99.97 0.1714 0.1694 0.1692 0.211 0.2106 26.81
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 8.7391 f_angle_d 0.9818 f_chiral_restr 0.0565 f_plane_restr 0.0088 f_bond_d 0.0083
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5092 Nucleic Acid Atoms Solvent Atoms 503 Heterogen Atoms 68
Software Software Software Name Purpose PHENIX refinement xia2 data reduction Aimless data scaling PHASER phasing