3ANT

Human soluble epoxide hydrolase in complex with a synthetic inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ANSPDB ENTRY 3ANS

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
2.4249.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.384α = 90
b = 80.296β = 125.88
c = 88.867γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDRAYONIX MX225HE2009-03-04MSINGLE 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
12.45099.20.05916.43.728466
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)
12.42.4494.90.1793.41372

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 3ANS2.435.0728433143998.70.20140.19940.2375RANDOM36.4799
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.819
r_dihedral_angle_3_deg15.335
r_dihedral_angle_4_deg12.905
r_dihedral_angle_1_deg5.603
r_scangle_it2.594
r_scbond_it1.522
r_angle_refined_deg1.204
r_mcangle_it1.164
r_mcbond_it0.604
r_chiral_restr0.083
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.819
r_dihedral_angle_3_deg15.335
r_dihedral_angle_4_deg12.905
r_dihedral_angle_1_deg5.603
r_scangle_it2.594
r_scbond_it1.522
r_angle_refined_deg1.204
r_mcangle_it1.164
r_mcbond_it0.604
r_chiral_restr0.083
r_bond_refined_d0.009
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5066
Nucleic Acid Atoms
Solvent Atoms121
Heterogen Atoms52

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing