6I5G

X-ray structure of human soluble Epoxide Hydrolase C-terminal Domain (hsEH CTD)in complex with 15d-PGJ2


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.4277.1522.5% PEG 3350, 0.2 M malic acid
Crystal Properties
Matthews coefficientSolvent content
2.3547.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.49α = 90
b = 79.992β = 96.78
c = 104.544γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97949DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
1271.8399.20.0960.1210.05310.24.9948933
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.050.7020.790.354

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 REPLACEMENTTHROUGHOUT3ANS271.8346528240399.160.17430.172030.21699RANDOM33.996
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]
0.471.33-2.171.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.197
r_dihedral_angle_3_deg15.958
r_dihedral_angle_4_deg15.581
r_long_range_B_refined7.349
r_long_range_B_other7.349
r_dihedral_angle_1_deg7.24
r_scangle_other5.546
r_mcangle_it3.91
r_mcangle_other3.909
r_scbond_it3.679
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.197
r_dihedral_angle_3_deg15.958
r_dihedral_angle_4_deg15.581
r_long_range_B_refined7.349
r_long_range_B_other7.349
r_dihedral_angle_1_deg7.24
r_scangle_other5.546
r_mcangle_it3.91
r_mcangle_other3.909
r_scbond_it3.679
r_scbond_other3.678
r_mcbond_it2.769
r_mcbond_other2.768
r_angle_refined_deg2.062
r_angle_other_deg1.212
r_chiral_restr0.147
r_bond_refined_d0.017
r_gen_planes_refined0.01
r_bond_other_d0.003
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 Atoms5088
Nucleic Acid Atoms
Solvent Atoms226
Heterogen Atoms94

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
REFMACphasing