2J0D

Crystal structure of human P450 3A4 in complex with erythromycin


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5HANGING DROP CRYSTALLISATION USING 1:1 RATIO OF PROTEIN AT 20-27 MG/ML AGAINST 0.1 M HEPES PH 7-7.5, 0.2 M LITHIUM SULFATE,0.8-1.0 M LITHIUM CHLORIDE AND 30% PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.753

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.254α = 90
b = 210.706β = 90
c = 161.246γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2005-07-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
12.7529.899.90.116.47.2302912
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)
12.752.821000.563.97.4

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 1W0E2.753027971148397.30.2420.2380.315RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.899
r_dihedral_angle_3_deg21.009
r_dihedral_angle_4_deg15.935
r_dihedral_angle_1_deg5.835
r_scangle_it1.839
r_angle_refined_deg1.332
r_scbond_it1.141
r_mcangle_it0.965
r_mcbond_it0.533
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.899
r_dihedral_angle_3_deg21.009
r_dihedral_angle_4_deg15.935
r_dihedral_angle_1_deg5.835
r_scangle_it1.839
r_angle_refined_deg1.332
r_scbond_it1.141
r_mcangle_it0.965
r_mcbond_it0.533
r_nbtor_refined0.313
r_symmetry_hbond_refined0.285
r_xyhbond_nbd_refined0.225
r_nbd_refined0.219
r_symmetry_vdw_refined0.217
r_chiral_restr0.089
r_bond_refined_d0.011
r_gen_planes_refined0.004
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_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 Atoms7140
Nucleic Acid Atoms
Solvent Atoms49
Heterogen Atoms137

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing