1W0G

Crystal structure of human cytochrome P450 3A4


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1W0EPDB ENTRY 1W0E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.1M HEPES PH 7.5, 0.025M NACL, 7.5% (V/V) ISOPROPANOL, 10
Crystal Properties
Matthews coefficientSolvent content
2.447.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.94α = 90
b = 100.91β = 90
c = 131γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS 42003-11-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU

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
12.744094.70.0410.82.813241
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)
12.742.8997.10.3082.52.7

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 1W0E2.7381.651257768993.90.2380.2340.318RANDOM78.73
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]
-0.360.63-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.691
r_dihedral_angle_3_deg20.273
r_dihedral_angle_4_deg17.719
r_dihedral_angle_1_deg9.32
r_scangle_it4.382
r_mcangle_it4.282
r_mcbond_it3.392
r_scbond_it3.315
r_angle_refined_deg1.753
r_angle_other_deg1.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.691
r_dihedral_angle_3_deg20.273
r_dihedral_angle_4_deg17.719
r_dihedral_angle_1_deg9.32
r_scangle_it4.382
r_mcangle_it4.282
r_mcbond_it3.392
r_scbond_it3.315
r_angle_refined_deg1.753
r_angle_other_deg1.05
r_mcbond_other0.913
r_nbd_refined0.27
r_nbd_other0.205
r_nbtor_refined0.204
r_symmetry_vdw_refined0.181
r_xyhbond_nbd_refined0.178
r_symmetry_vdw_other0.171
r_chiral_restr0.123
r_xyhbond_nbd_other0.123
r_nbtor_other0.092
r_bond_refined_d0.017
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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 Atoms3652
Nucleic Acid Atoms
Solvent Atoms29
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling