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Sterol 14-alpha demethylase (CYP51) from Trypanosoma brucei in complex with the VNI derivative (R)-N-(1-(3,4'-difluorobiphenyl-4-yl)-2-(1H-imidazol-1-yl)ethyl)-4-(5-phenyl-1,3,4-oxadiazol-2-yl)benzamide [VNI/VNF (VFV)]
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 2.49 50.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.947 α = 74.64 b = 79.706 β = 81.2 c = 117.868 γ = 68.96
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) R Sym 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 2.05 29.817 98 0.046 0.046 31 4.6 123297 120831 2.6 2.6 37.85
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 2.05 2.09 97 0.58 2.6 4.5 5970
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 2.05 29.817 117107 114765 6065 98.03 0.16597 0.1627 0.1638 0.22618 0.2271 RANDOM 44.796
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] 0.91 -0.72 0.32 -0.6 0.04 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.073 r_sphericity_free 20.98 r_dihedral_angle_4_deg 20.936 r_sphericity_bonded 16.799 r_dihedral_angle_3_deg 15.321 r_dihedral_angle_1_deg 5.385 r_rigid_bond_restr 2.287 r_angle_refined_deg 1.976 r_chiral_restr 0.076 r_bond_refined_d 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.073 r_sphericity_free 20.98 r_dihedral_angle_4_deg 20.936 r_sphericity_bonded 16.799 r_dihedral_angle_3_deg 15.321 r_dihedral_angle_1_deg 5.385 r_rigid_bond_restr 2.287 r_angle_refined_deg 1.976 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14228 Nucleic Acid Atoms Solvent Atoms 504 Heterogen Atoms 336
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling