5TE8

Crystal structure of the midazolam-bound human CYP3A4


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TQN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29312% polyethilene glycol 3350, 0.1M sodium malonate pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.3347.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.289α = 90
b = 117.98β = 90
c = 205.649γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray103CCDOXFORD TITAN CCD2015-01-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.21.0ALS8.2.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
12.7102.3499.40.1650.9765.85.6435492
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.899.30.8220.7171.55.9

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 REPLACEMENTTHROUGHOUT1TQN2.7102.3441161217898.770.227480.224060.2918RANDOM75.677
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]
-1.380.730.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.007
r_dihedral_angle_3_deg18.164
r_dihedral_angle_4_deg16.976
r_long_range_B_refined6.712
r_dihedral_angle_1_deg6.293
r_mcangle_it2.897
r_scbond_it1.768
r_mcbond_it1.675
r_angle_refined_deg1.334
r_chiral_restr0.091
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.007
r_dihedral_angle_3_deg18.164
r_dihedral_angle_4_deg16.976
r_long_range_B_refined6.712
r_dihedral_angle_1_deg6.293
r_mcangle_it2.897
r_scbond_it1.768
r_mcbond_it1.675
r_angle_refined_deg1.334
r_chiral_restr0.091
r_bond_refined_d0.007
r_gen_planes_refined0.006
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_it
r_scangle_other
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 Atoms11364
Nucleic Acid Atoms
Solvent Atoms111
Heterogen Atoms198

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing