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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
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4UYM PDB entry 4UYM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 279 0.2 M lithium acetate, pH 7.4, 19% w/v PEG3350, 5 mM cyclohexylpentanoyl-N-hydroxyethylglucamide
Crystal Properties Matthews coefficient Solvent content 2.81 56.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.438 α = 90 b = 108.438 β = 90 c = 90.999 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-300 Be lenses 2018-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.38 93.91 96.9 0.039 27.1 4.9 44263 30.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.38 2.42 64.9 0.698 1.7 4.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 4UYM 2.38 30 44263 2282 96.9 0.2162 0.2154 0.2209 0.23 0.2286 RANDOM 40.37
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 -0.05 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.933 r_dihedral_angle_4_deg 21.989 r_dihedral_angle_3_deg 17.19 r_long_range_B_refined 11.191 r_long_range_B_other 11.191 r_dihedral_angle_1_deg 7.49 r_scangle_other 7.188 r_mcangle_it 6.611 r_mcangle_other 6.611 r_scbond_it 4.804
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.933 r_dihedral_angle_4_deg 21.989 r_dihedral_angle_3_deg 17.19 r_long_range_B_refined 11.191 r_long_range_B_other 11.191 r_dihedral_angle_1_deg 7.49 r_scangle_other 7.188 r_mcangle_it 6.611 r_mcangle_other 6.611 r_scbond_it 4.804 r_scbond_other 4.804 r_mcbond_it 4.34 r_mcbond_other 4.336 r_angle_refined_deg 1.118 r_angle_other_deg 0.724 r_chiral_restr 0.068 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_refined_d 0.001 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 Atoms Number Protein Atoms 7486 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 170
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing