9NNA | pdb_00009nna

Crystal structure of CYP46A1 with [(1R,5S)-3-oxa-8-azabicyclo[3.2.1]octan-8-yl][(4R,8M)-8-(1,3-oxazol-5-yl)-6-(trifluoromethyl)imidazo[1,2-a]pyridin-3-yl]methanone (compound 3k)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7LRL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.1518.5% PEG3350, 0.4 M calcium chloride
Crystal Properties
Matthews coefficientSolvent content
2.1342.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.478α = 90
b = 63.633β = 90
c = 124.615γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2012-06-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.30.976ALS5.0.3

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
11.675099.60.1029.56.854937
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)
11.671.794.60.7514.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.673052157270899.380.172140.170270.2090.207390.2343RANDOM9.055
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]
0.83-0.870.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.906
r_sphericity_free16.713
r_dihedral_angle_4_deg16.632
r_dihedral_angle_3_deg12.534
r_dihedral_angle_1_deg5
r_sphericity_bonded4.31
r_rigid_bond_restr3.81
r_angle_refined_deg2.061
r_angle_other_deg0.946
r_chiral_restr0.082
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.906
r_sphericity_free16.713
r_dihedral_angle_4_deg16.632
r_dihedral_angle_3_deg12.534
r_dihedral_angle_1_deg5
r_sphericity_bonded4.31
r_rigid_bond_restr3.81
r_angle_refined_deg2.061
r_angle_other_deg0.946
r_chiral_restr0.082
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_gen_planes_other0.005
r_bond_other_d0.001
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3499
Nucleic Acid Atoms
Solvent Atoms284
Heterogen Atoms71

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing