6I5E

X-ray structure of apo human soluble Epoxide Hydrolase C-terminal Domain (hsEH CTD)


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
2.3347.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.224α = 90
b = 80.139β = 95.39
c = 104.696γ = 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 I040.97949DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
12.670.5199.90.210.2355.75.07711420222492
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.6001229.60030.7410.831

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 REPLACEMENTTHROUGHOUT3ANS2.670.5121388110199.90.247550.245990.27704RANDOM45.454
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]
-4.081.11-3.26.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.732
r_dihedral_angle_3_deg15.291
r_dihedral_angle_4_deg13.764
r_long_range_B_refined8.989
r_long_range_B_other8.989
r_dihedral_angle_1_deg5.804
r_scangle_other4.708
r_mcangle_it4.618
r_mcangle_other4.618
r_scbond_it2.789
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.732
r_dihedral_angle_3_deg15.291
r_dihedral_angle_4_deg13.764
r_long_range_B_refined8.989
r_long_range_B_other8.989
r_dihedral_angle_1_deg5.804
r_scangle_other4.708
r_mcangle_it4.618
r_mcangle_other4.618
r_scbond_it2.789
r_scbond_other2.785
r_mcbond_it2.784
r_mcbond_other2.778
r_angle_refined_deg1.449
r_angle_other_deg1.001
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.006
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 Atoms5086
Nucleic Acid Atoms
Solvent Atoms13
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
REFMACphasing