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Crystal structure of human soluble epoxide hydrolase complexed with trans-4-[4-(3-trifluoromethoxyphenyl-l-ureido)-cyclohexyloxy]-benzoic acid.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S8O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 277 30% PEG 3350, 0-10% sucrose
Crystal Properties Matthews coefficient Solvent content 2.41 49.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.713 α = 90 b = 92.713 β = 90 c = 243.736 γ = 120
Symmetry Space Group P 65 2 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 CCD MAR CCD 165 mm MIRRORS 2011-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CAMD BEAMLINE GCPCC 1.38079 CAMD GCPCC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.95 40 98.7 0.11 9.8 2.8 13636 78.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.95 3.06 97.7 0.66 1.6 2.9
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 (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 1S8O 2.95 36.89 12929 674 98.87 0.19616 0.19307 0.1985 0.2546 0.2519 RANDOM 51.387
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] -0.45 -0.23 -0.45 1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.069 r_dihedral_angle_4_deg 18.097 r_dihedral_angle_3_deg 16.698 r_dihedral_angle_1_deg 6.52 r_long_range_B_refined 2.132 r_long_range_B_other 2.132 r_angle_refined_deg 1.407 r_angle_other_deg 0.945 r_mcangle_it 0.925 r_mcangle_other 0.925
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.069 r_dihedral_angle_4_deg 18.097 r_dihedral_angle_3_deg 16.698 r_dihedral_angle_1_deg 6.52 r_long_range_B_refined 2.132 r_long_range_B_other 2.132 r_angle_refined_deg 1.407 r_angle_other_deg 0.945 r_mcangle_it 0.925 r_mcangle_other 0.925 r_scangle_other 0.866 r_scbond_it 0.585 r_scbond_other 0.585 r_mcbond_it 0.525 r_mcbond_other 0.525 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 4331 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing