6CR2

Crystal structure of sterol 14-alpha demethylase (CYP51B) from Aspergillus fumigatus in complex with the VNI derivative N-(1-(2,4-dichlorophenyl)-2-(1H-imidazol-1-yl)ethyl)-4-(5-(2-fluoro-4-(2,2,2-trifluoroethoxy)phenyl)-1,3,4-oxadiazol-2-yl)benzamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4UYMPDB entry 4UYM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.42790.2 M lithium acetate, pH 7.4, 19% w/v PEG3350, 5 mM cyclohexylpentanoyl-N-hydroxyethylglucamide
Crystal Properties
Matthews coefficientSolvent content
2.8156.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.438α = 90
b = 108.438β = 90
c = 90.999γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-300Be lenses2018-02-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

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
12.3893.9196.90.03927.14.94426330.1
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)
12.382.4264.90.6981.74.9

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 REPLACEMENTTHROUGHOUTPDB entry 4UYM2.383044263228296.90.21620.21540.23RANDOM40.37
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]
-0.05-0.02-0.050.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.933
r_dihedral_angle_4_deg21.989
r_dihedral_angle_3_deg17.19
r_long_range_B_refined11.191
r_long_range_B_other11.191
r_dihedral_angle_1_deg7.49
r_scangle_other7.188
r_mcangle_it6.611
r_mcangle_other6.611
r_scbond_it4.804
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.933
r_dihedral_angle_4_deg21.989
r_dihedral_angle_3_deg17.19
r_long_range_B_refined11.191
r_long_range_B_other11.191
r_dihedral_angle_1_deg7.49
r_scangle_other7.188
r_mcangle_it6.611
r_mcangle_other6.611
r_scbond_it4.804
r_scbond_other4.804
r_mcbond_it4.34
r_mcbond_other4.336
r_angle_refined_deg1.118
r_angle_other_deg0.724
r_chiral_restr0.068
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_refined_d0.001
r_bond_other_d
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7486
Nucleic Acid Atoms
Solvent Atoms106
Heterogen Atoms170

Software

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