3E4E

Human cytochrome P450 2E1 in complex with the inhibitor 4-methylpyrazole


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3E6ICYP2E1 IN COMPLEX WITH INDAZOLE (PDB ENTRY 3E6I)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.529312% iso-propanol, 14% PEG 2000 MME, 0.1 M NaHEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6152.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.193α = 90
b = 71.193β = 90
c = 225.888γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRRORS2008-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-1SSRLBL9-1

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
12.6113.21000.06116.33.832629
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)
2.62.671000.3733.13.8

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 REPLACEMENTTHROUGHOUTCYP2E1 IN COMPLEX WITH INDAZOLE (PDB ENTRY 3E6I)2.638.153262917671000.2010.1970.277RANDOM50.82
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]
-0.01-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.878
r_dihedral_angle_4_deg23.696
r_dihedral_angle_3_deg21.916
r_dihedral_angle_1_deg9.719
r_scangle_it3.822
r_scbond_it2.392
r_angle_refined_deg2.021
r_mcangle_it1.485
r_mcbond_it0.843
r_symmetry_hbond_refined0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.878
r_dihedral_angle_4_deg23.696
r_dihedral_angle_3_deg21.916
r_dihedral_angle_1_deg9.719
r_scangle_it3.822
r_scbond_it2.392
r_angle_refined_deg2.021
r_mcangle_it1.485
r_mcbond_it0.843
r_symmetry_hbond_refined0.45
r_nbtor_refined0.324
r_nbd_refined0.255
r_symmetry_vdw_refined0.226
r_xyhbond_nbd_refined0.185
r_chiral_restr0.128
r_bond_refined_d0.019
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7543
Nucleic Acid Atoms
Solvent Atoms66
Heterogen Atoms98

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing