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Sterol 14-alpha demethylase (CYP51) from Trypanosoma brucei in complex with the VNI derivative (R)-N-(1-(2,4-dichlorophenyl)-2-(1H-1,2,4-triazol-1-yl)ethyl)-4-(5-phenyl-1,3,4-oxadiazol-2-yl)benzamide [R-VNI-triazole (VNT)]
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3G1Q PDB ENTRY 3G1Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 294 potassium phosphate, sodium chloride, glycerol, PEG3350, N-tetradecyl-beta-D-maltoside, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.44 49.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.013 α = 74.59 b = 79.48 β = 79.28 c = 116.353 γ = 68.48
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 Be Lenses/Diamond Laue Mono 2012-04-03 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 1.82 29.926 98 0.048 28.3 4.6 162337 159091 2.4 2.4
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 1.82 1.85 96 0.621 2.4 4.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3G1Q 1.83 29.926 162098 157414 8328 97.11 0.17158 0.16898 0.1689 0.22019 0.2198 RANDOM 36.427
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] -0.01 -0.19 0.31 -0.74 0.06 0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.004 r_sphericity_free 21.377 r_dihedral_angle_4_deg 19.555 r_dihedral_angle_3_deg 16.169 r_sphericity_bonded 13.635 r_rigid_bond_restr 7.61 r_dihedral_angle_1_deg 6.848 r_scbond_it 4.888 r_mcangle_it 3.988 r_mcbond_it 3.552
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.004 r_sphericity_free 21.377 r_dihedral_angle_4_deg 19.555 r_dihedral_angle_3_deg 16.169 r_sphericity_bonded 13.635 r_rigid_bond_restr 7.61 r_dihedral_angle_1_deg 6.848 r_scbond_it 4.888 r_mcangle_it 3.988 r_mcbond_it 3.552 r_angle_refined_deg 0.919 r_chiral_restr 0.056 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_mcangle_other 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 Atoms Number Protein Atoms 14228 Nucleic Acid Atoms Solvent Atoms 703 Heterogen Atoms 312
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling