4I3Q

Crystal structure of human CYP3A4 coordinated to a water molecule


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WOEPDB ENTRY 1WOE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1microbatch under oil6298PEG 3350, sodium malonate, pH 6.0, microbatch under oil, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3547.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.11α = 90
b = 101.47β = 90
c = 130.54γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDADSC QUANTUM 315mirrors2012-02-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-11.127SSRLBL7-1

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
12.665.398.40.08210.37.116524162602
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)
12.62.6797.50.5162.34.5

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONPHASERTHROUGHOUTPDB ENTRY 1WOE2.60265.271543281998.390.223550.219990.220.298140.29RANDOM93.672
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]
0.09-0.05-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.998
r_dihedral_angle_3_deg19.75
r_dihedral_angle_4_deg18.884
r_dihedral_angle_1_deg6.541
r_angle_refined_deg1.998
r_chiral_restr0.101
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3749
Nucleic Acid Atoms
Solvent Atoms6
Heterogen Atoms43

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling