3IBD

Crystal structure of a cytochrome P450 2B6 genetic variant in complex with the inhibitor 4-(4-chlorophenyl)imidazole


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Q6NENSEMBLE OF PDB ID 2Q6N (A CHAIN), 1SUO, 2BDM, 3G5N (A CHAIN) EACH WITH RESIDUES 101-120, 205-232 OMITTED
experimental modelPDB 1SUOENSEMBLE OF PDB ID 2Q6N (A CHAIN), 1SUO, 2BDM, 3G5N (A CHAIN) EACH WITH RESIDUES 101-120, 205-232 OMITTED
experimental modelPDB 2BDMENSEMBLE OF PDB ID 2Q6N (A CHAIN), 1SUO, 2BDM, 3G5N (A CHAIN) EACH WITH RESIDUES 101-120, 205-232 OMITTED
experimental modelPDB 3G5NENSEMBLE OF PDB ID 2Q6N (A CHAIN), 1SUO, 2BDM, 3G5N (A CHAIN) EACH WITH RESIDUES 101-120, 205-232 OMITTED

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.52910.1 M sodium acetate (pH 5.5), 0.2 M potassium thiocyanate, 10% (w/v) PEG 1000, 10% (w/v) PEG 8000, vapor diffusion, sitting drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.2545.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.573α = 90
b = 55.74β = 96.51
c = 99.09γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2009-06-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-1SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.99898.45198.30.1310.13111.86.932536
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.1188.10.4870.4871.44.1

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTENSEMBLE OF PDB ID 2Q6N (A CHAIN), 1SUO, 2BDM, 3G5N (A CHAIN) EACH WITH RESIDUES 101-120, 205-232 OMITTED298.453254532494164098.10.1810.1780.228RANDOM21.92
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]
0.88-0.26-0.69-0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.825
r_dihedral_angle_4_deg19.742
r_dihedral_angle_3_deg17.358
r_dihedral_angle_1_deg6.384
r_scangle_it4.813
r_scbond_it3.03
r_mcangle_it1.925
r_angle_refined_deg1.767
r_mcbond_it1.061
r_symmetry_vdw_refined0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.825
r_dihedral_angle_4_deg19.742
r_dihedral_angle_3_deg17.358
r_dihedral_angle_1_deg6.384
r_scangle_it4.813
r_scbond_it3.03
r_mcangle_it1.925
r_angle_refined_deg1.767
r_mcbond_it1.061
r_symmetry_vdw_refined0.32
r_nbtor_refined0.316
r_nbd_refined0.232
r_symmetry_hbond_refined0.198
r_xyhbond_nbd_refined0.173
r_chiral_restr0.122
r_metal_ion_refined0.035
r_bond_refined_d0.018
r_gen_planes_refined0.007
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_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 Atoms3699
Nucleic Acid Atoms
Solvent Atoms176
Heterogen Atoms89

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction