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Crystal structure of sterol 14-alpha demethylase (CYP51) from Candida albicans in complex with the tetrazole-based antifungal drug candidate VT1161 (VT1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FSA PDB entry 5FSA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 291 0.1 M HEPES, pH 7.4, 0.2 M sodium chloride, 10% PEG6000, 0.03 mM n-Tridecyl-b-D-maltoside
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.64 α = 90 b = 71.44 β = 96.63 c = 79.19 γ = 90
Symmetry Space Group C 1 2 1
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 MARMOSAIC 225 mm CCD 2016-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97849 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 49.61 98.8 0.075 0.943 12.8 5 65813
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 2.05 96.4 0.691 2 4.6
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 5FSA 2 49.61 62497 3313 98.61 0.218 0.21766 0.2309 0.22442 0.2526 RANDOM 41.745
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] 3.92 0.99 -2.67 -1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.08 r_dihedral_angle_4_deg 16.402 r_dihedral_angle_3_deg 15.996 r_long_range_B_refined 13.676 r_long_range_B_other 13.639 r_scangle_other 7.017 r_mcangle_it 6.872 r_mcangle_other 6.872 r_dihedral_angle_1_deg 5.286 r_scbond_it 4.809
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.08 r_dihedral_angle_4_deg 16.402 r_dihedral_angle_3_deg 15.996 r_long_range_B_refined 13.676 r_long_range_B_other 13.639 r_scangle_other 7.017 r_mcangle_it 6.872 r_mcangle_other 6.872 r_dihedral_angle_1_deg 5.286 r_scbond_it 4.809 r_scbond_other 4.808 r_mcbond_it 4.677 r_mcbond_other 4.672 r_angle_refined_deg 0.985 r_angle_other_deg 0.759 r_chiral_restr 0.05 r_gen_planes_refined 0.013 r_bond_other_d 0.006 r_gen_planes_other 0.006 r_bond_refined_d 0.002 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 7857 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms 160
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data scaling xia2 data scaling xia2 data reduction PHASER phasing