4G7G

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)]


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3G1QPDB ENTRY 3G1Q

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.3294potassium phosphate, sodium chloride, glycerol, PEG3350, N-tetradecyl-beta-D-maltoside, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.4950.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.947α = 74.64
b = 79.706β = 81.2
c = 117.868γ = 68.96
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDBe Lenses/Diamond Laue Mono2012-04-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.0529.817980.0460.046314.61232971208312.62.637.85
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)
12.052.09970.582.64.55970

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 3G1Q2.0529.817117107114765606598.030.165970.16270.22618RANDOM44.796
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]
0.91-0.720.32-0.60.040.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.073
r_sphericity_free20.98
r_dihedral_angle_4_deg20.936
r_sphericity_bonded16.799
r_dihedral_angle_3_deg15.321
r_dihedral_angle_1_deg5.385
r_rigid_bond_restr2.287
r_angle_refined_deg1.976
r_chiral_restr0.076
r_bond_refined_d0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.073
r_sphericity_free20.98
r_dihedral_angle_4_deg20.936
r_sphericity_bonded16.799
r_dihedral_angle_3_deg15.321
r_dihedral_angle_1_deg5.385
r_rigid_bond_restr2.287
r_angle_refined_deg1.976
r_chiral_restr0.076
r_bond_refined_d0.008
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14228
Nucleic Acid Atoms
Solvent Atoms504
Heterogen Atoms336

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling