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Soluble epoxide hydrolase in complex with AK191
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8QMZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 25% w/v PEG 3350, 0.1M Bis-Tris, pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.14 42.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.296 α = 90 b = 79.85 β = 94.99 c = 102.429 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 EIGER2 XE 16M 2025-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.1 69.69 100 0.121 0.131 0.049 0.998 8.7 7.1 41484
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 100 1.026 1.105 0.409 0.888 7.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.1 64.01 39452 2024 99.98 0.18448 0.18201 0.1912 0.23095 0.2324 RANDOM 45.483
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] -2.45 -0.21 -5.96 8.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.315 r_dihedral_angle_2_deg 13.95 r_long_range_B_refined 8.831 r_long_range_B_other 8.83 r_dihedral_angle_1_deg 6.845 r_scangle_other 6.727 r_mcangle_it 5.511 r_mcangle_other 5.511 r_scbond_it 4.496 r_scbond_other 4.495
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.315 r_dihedral_angle_2_deg 13.95 r_long_range_B_refined 8.831 r_long_range_B_other 8.83 r_dihedral_angle_1_deg 6.845 r_scangle_other 6.727 r_mcangle_it 5.511 r_mcangle_other 5.511 r_scbond_it 4.496 r_scbond_other 4.495 r_mcbond_it 3.859 r_mcbond_other 3.858 r_angle_refined_deg 1.56 r_angle_other_deg 0.538 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5121 Nucleic Acid Atoms Solvent Atoms 268 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing PDB_EXTRACT data extraction