4ENH

Crystal Structure of Human Cytochrome P450 CYP46A1 with Fluvoxamine Bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Q9FPDB ENTRY 2Q9F

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.8290Crystals were grown after mixing 1 ul of an ~40 mg/ml P450 solution with 1 ul of precipitant solution (15% PEG 8000, 50 M FLX, 50 mM potassium phosphate, 20% glycerol), pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.550.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.13α = 90
b = 121.13β = 90
c = 141.9γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152011-04-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-11.09717SSRLBL7-1

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
12.592.1291000.1016.2718625
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)
12.52.641000.61.3

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 2Q9F2.560.571858095099.660.21330.21040.2721RANDOM44.5623
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]
0.60.6-1.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.34
r_dihedral_angle_3_deg18.541
r_dihedral_angle_4_deg15.368
r_dihedral_angle_1_deg5.245
r_scangle_it2.823
r_scbond_it1.699
r_mcangle_it1.228
r_angle_refined_deg1.185
r_mcbond_it0.654
r_chiral_restr0.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.34
r_dihedral_angle_3_deg18.541
r_dihedral_angle_4_deg15.368
r_dihedral_angle_1_deg5.245
r_scangle_it2.823
r_scbond_it1.699
r_mcangle_it1.228
r_angle_refined_deg1.185
r_mcbond_it0.654
r_chiral_restr0.095
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3430
Nucleic Acid Atoms
Solvent Atoms132
Heterogen Atoms65

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
XDSdata reduction
PHASERphasing