3ANS

Human soluble epoxide hydrolase in complex with a synthetic inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VJ5PDB ENTRY 1VJ5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.327720%(w/v) PEG 8000, 200mM sodium iodide, pH 7.3, vapor diffusion, sitting drop, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4148.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.63α = 90
b = 80.35β = 126.2
c = 88.69γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDRAYONIX MX225HE2008-07-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.00SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.9840.1898.70.04516.83.7750573
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.982.0598.80.1475.83.765037

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1VJ51.9831.2150570256698.740.22060.21860.2596RANDOM34.0078
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.829
r_dihedral_angle_4_deg15.456
r_dihedral_angle_3_deg14.587
r_dihedral_angle_1_deg5.892
r_scangle_it2.715
r_scbond_it1.651
r_mcangle_it1.278
r_angle_refined_deg1.242
r_mcbond_it0.683
r_chiral_restr0.088
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.829
r_dihedral_angle_4_deg15.456
r_dihedral_angle_3_deg14.587
r_dihedral_angle_1_deg5.892
r_scangle_it2.715
r_scbond_it1.651
r_mcangle_it1.278
r_angle_refined_deg1.242
r_mcbond_it0.683
r_chiral_restr0.088
r_bond_refined_d0.01
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5066
Nucleic Acid Atoms
Solvent Atoms242
Heterogen Atoms40

Software

Software
Software NamePurpose
d*TREKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing