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Soluble epoxide hydrolase in complex with RK4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7P4K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 20% PEG6000, 10% ethylene glycol, 0.1M HEPES pH 7.0, 0.1M calcium chloride
Crystal Properties Matthews coefficient Solvent content 2.04 39.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.29 α = 90 b = 90.642 β = 90 c = 188.416 γ = 90
Symmetry Space Group P 21 21 21
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 16M 2023-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 1.47 49.47 99.5 0.062 0.067 0.026 0.999 13.8 6.7 233100
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 1.47 1.49 91.3 1.125 1.218 0.463 0.71 6.9
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 1.47 49.47 221479 11504 99.52 0.18882 0.18752 0.1936 0.21408 0.2188 RANDOM 21.377
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] -1.14 0.69 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.687 r_dihedral_angle_1_deg 6.709 r_dihedral_angle_2_deg 6.632 r_long_range_B_refined 5.938 r_long_range_B_other 5.938 r_scangle_other 4.8 r_scbond_it 3.21 r_scbond_other 3.209 r_mcangle_it 2.874 r_mcangle_other 2.874
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.687 r_dihedral_angle_1_deg 6.709 r_dihedral_angle_2_deg 6.632 r_long_range_B_refined 5.938 r_long_range_B_other 5.938 r_scangle_other 4.8 r_scbond_it 3.21 r_scbond_other 3.209 r_mcangle_it 2.874 r_mcangle_other 2.874 r_mcbond_it 2.044 r_mcbond_other 2.043 r_angle_refined_deg 1.787 r_angle_other_deg 0.63 r_chiral_restr 0.111 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 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 10206 Nucleic Acid Atoms Solvent Atoms 842 Heterogen Atoms 184
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing