4ZV8

Structure of CYP2B6 (Y226H/K262R) with additional mutation Y244W in complex with alpha-Pinene


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4I91PDB entry 4I91

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52910.1 M HEPES sodium, pH 7.5, 20% w/v Polyethylene glycol 10,000
Crystal Properties
Matthews coefficientSolvent content
3.2262

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.24α = 90
b = 77.24β = 90
c = 204.25γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2015-04-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.98SSRLBL12-2

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
12.2468.08970.1137.94.833577
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.242.3788.43.14.6

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 REPLACEMENTTHROUGHOUTPDB entry 4I912.2468.0831737169996.340.172150.169040.23218RANDOM38.051
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]
1.670.841.67-2.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.784
r_dihedral_angle_4_deg21.655
r_dihedral_angle_3_deg14.611
r_dihedral_angle_1_deg6.349
r_scangle_it5.717
r_scbond_it3.534
r_mcangle_it2.113
r_angle_refined_deg1.992
r_mcbond_it1.131
r_chiral_restr0.124
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.784
r_dihedral_angle_4_deg21.655
r_dihedral_angle_3_deg14.611
r_dihedral_angle_1_deg6.349
r_scangle_it5.717
r_scbond_it3.534
r_mcangle_it2.113
r_angle_refined_deg1.992
r_mcbond_it1.131
r_chiral_restr0.124
r_bond_refined_d0.023
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_other
r_mcangle_other
r_scbond_other
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 Atoms3736
Nucleic Acid Atoms
Solvent Atoms267
Heterogen Atoms98

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
Cootmodel building