6AUM

Crystal structure of human soluble epoxide hydrolase complexed with trans-4-[4-(3-trifluoromethoxyphenyl-l-ureido)-cyclohexyloxy]-benzoic acid.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1S8O 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.527730% PEG 3350, 0-10% sucrose
Crystal Properties
Matthews coefficientSolvent content
2.4149.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.713α = 90
b = 92.713β = 90
c = 243.736γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMIRRORS2011-11-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCAMD BEAMLINE GCPCC1.38079CAMDGCPCC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.954098.70.119.82.81363678.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.953.0697.70.661.62.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1S8O2.9536.891292967498.870.196160.193070.2546RANDOM51.387
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]
-0.45-0.23-0.451.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.069
r_dihedral_angle_4_deg18.097
r_dihedral_angle_3_deg16.698
r_dihedral_angle_1_deg6.52
r_long_range_B_refined2.132
r_long_range_B_other2.132
r_angle_refined_deg1.407
r_angle_other_deg0.945
r_mcangle_it0.925
r_mcangle_other0.925
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.069
r_dihedral_angle_4_deg18.097
r_dihedral_angle_3_deg16.698
r_dihedral_angle_1_deg6.52
r_long_range_B_refined2.132
r_long_range_B_other2.132
r_angle_refined_deg1.407
r_angle_other_deg0.945
r_mcangle_it0.925
r_mcangle_other0.925
r_scangle_other0.866
r_scbond_it0.585
r_scbond_other0.585
r_mcbond_it0.525
r_mcbond_other0.525
r_chiral_restr0.071
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
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 AtomsNumber
Protein Atoms4331
Nucleic Acid Atoms
Solvent Atoms25
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing