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Human soluble epoxide hydrolase in complex with a synthetic inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VJ5 PDB ENTRY 1VJ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.3 277 20%(w/v) PEG 8000, 200mM sodium iodide, pH 7.3, vapor diffusion, sitting drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.41 48.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.63 α = 90 b = 80.35 β = 126.2 c = 88.69 γ = 90
Symmetry Space Group C 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 CCD RAYONIX MX225HE 2008-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.00 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.98 40.18 98.7 0.045 16.8 3.77 50573
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.05 98.8 0.147 5.8 3.76 5037
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 PDB ENTRY 1VJ5 1.98 31.21 50570 2566 98.74 0.2206 0.2186 0.2147 0.2596 0.2536 RANDOM 34.0078
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 r_dihedral_angle_2_deg 34.829 r_dihedral_angle_4_deg 15.456 r_dihedral_angle_3_deg 14.587 r_dihedral_angle_1_deg 5.892 r_scangle_it 2.715 r_scbond_it 1.651 r_mcangle_it 1.278 r_angle_refined_deg 1.242 r_mcbond_it 0.683 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.829 r_dihedral_angle_4_deg 15.456 r_dihedral_angle_3_deg 14.587 r_dihedral_angle_1_deg 5.892 r_scangle_it 2.715 r_scbond_it 1.651 r_mcangle_it 1.278 r_angle_refined_deg 1.242 r_mcbond_it 0.683 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5066 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 40
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection CrystalClear data reduction CrystalClear data scaling MOLREP phasing