4OD0 | pdb_00004od0

Crystal structure of human soluble epoxide hydrolase complexed with 1-(1-propanoylpiperidin-4-yl)-3-[4-(trifluoromethoxy)phenyl]urea


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1S8OPDB ENTRY 1S8O

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.527730% PEG3350, 0-10% sucrose, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3848.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.136α = 90
b = 92.136β = 90
c = 243.354γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMIRRORS2011-11-21MSINGLE 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
12.92401000.11115.65.61409614096-382.1
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)
12.923.021000.7451.85.81360

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1S8O2.9240133341333469799.820.196170.196170.193210.190.252020.24RANDOM51.396
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]
3.021.513.02-4.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.298
r_dihedral_angle_4_deg20.118
r_dihedral_angle_3_deg18.592
r_dihedral_angle_1_deg6.581
r_angle_refined_deg1.522
r_angle_other_deg0.91
r_chiral_restr0.074
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_gen_planes_other0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.298
r_dihedral_angle_4_deg20.118
r_dihedral_angle_3_deg18.592
r_dihedral_angle_1_deg6.581
r_angle_refined_deg1.522
r_angle_other_deg0.91
r_chiral_restr0.074
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_gen_planes_other0.003
r_bond_other_d0.001
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4328
Nucleic Acid Atoms
Solvent Atoms16
Heterogen Atoms31

Software

Software
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling