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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 3ANS PDB ENTRY 3ANS
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 2.42 49.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.384 α = 90 b = 80.296 β = 125.88 c = 88.867 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 2009-03-04 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 2.4 50 99.2 0.059 16.4 3.7 28466
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 2.4 2.44 94.9 0.179 3.4 1372
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 3ANS 2.4 35.07 28433 1439 98.7 0.2014 0.1994 0.195 0.2375 0.2283 RANDOM 36.4799
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] -0.01 -0.04 -0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.819 r_dihedral_angle_3_deg 15.335 r_dihedral_angle_4_deg 12.905 r_dihedral_angle_1_deg 5.603 r_scangle_it 2.594 r_scbond_it 1.522 r_angle_refined_deg 1.204 r_mcangle_it 1.164 r_mcbond_it 0.604 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.819 r_dihedral_angle_3_deg 15.335 r_dihedral_angle_4_deg 12.905 r_dihedral_angle_1_deg 5.603 r_scangle_it 2.594 r_scbond_it 1.522 r_angle_refined_deg 1.204 r_mcangle_it 1.164 r_mcbond_it 0.604 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5066 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 52
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing