5TZ1

Crystal structure of sterol 14-alpha demethylase (CYP51) from Candida albicans in complex with the tetrazole-based antifungal drug candidate VT1161 (VT1)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5FSAPDB entry 5FSA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.42910.1 M HEPES, pH 7.4, 0.2 M sodium chloride, 10% PEG6000, 0.03 mM n-Tridecyl-b-D-maltoside
Crystal Properties
Matthews coefficientSolvent content
2.3247

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 177.64α = 90
b = 71.44β = 96.63
c = 79.19γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2016-06-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97849APS21-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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1249.6198.80.0750.94312.8565813
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)
122.0596.40.69124.6

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 5FSA249.6162497331398.610.2180.217660.22442RANDOM41.745
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]
3.920.99-2.67-1.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.08
r_dihedral_angle_4_deg16.402
r_dihedral_angle_3_deg15.996
r_long_range_B_refined13.676
r_long_range_B_other13.639
r_scangle_other7.017
r_mcangle_it6.872
r_mcangle_other6.872
r_dihedral_angle_1_deg5.286
r_scbond_it4.809
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.08
r_dihedral_angle_4_deg16.402
r_dihedral_angle_3_deg15.996
r_long_range_B_refined13.676
r_long_range_B_other13.639
r_scangle_other7.017
r_mcangle_it6.872
r_mcangle_other6.872
r_dihedral_angle_1_deg5.286
r_scbond_it4.809
r_scbond_other4.808
r_mcbond_it4.677
r_mcbond_other4.672
r_angle_refined_deg0.985
r_angle_other_deg0.759
r_chiral_restr0.05
r_gen_planes_refined0.013
r_bond_other_d0.006
r_gen_planes_other0.006
r_bond_refined_d0.002
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 AtomsNumber
Protein Atoms7857
Nucleic Acid Atoms
Solvent Atoms320
Heterogen Atoms160

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data scaling
xia2data scaling
xia2data reduction
PHASERphasing