4C28

Crystal structure of Trypanosoma cruzi CYP51 bound to the inhibitor (R)-N-(3-(1H-indol-3-yl)-1-oxo-1-(pyridin-4-ylamino)propan-2-yl)-4-(4-(4-chlorophenyl)piperazin-1-yl)-2-fluorobenzamide.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4C0CPDB ENTRY 4C0C

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.50.4 M AMMONIUM ACETATE, 0.1 M SODIUM ACETATE PH 4.5, 28% PEG 3350, 5% JEFFAMINE M-600 PH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.3647.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.951α = 90
b = 79.005β = 90
c = 176.839γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARRESERCHMIRRORS2013-07-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.1ALS8.3.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.04176.8486.40.079.93.5568090.528.6
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)
12.042.1547.80.541.62

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 4C0C2.0372.2454178290485.410.188360.185740.23761RANDOM25.021
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]
0.061.31-1.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.689
r_dihedral_angle_4_deg21.349
r_dihedral_angle_3_deg16.471
r_dihedral_angle_1_deg6.371
r_mcangle_it2.809
r_scbond_it2.73
r_angle_refined_deg1.911
r_mcbond_it1.901
r_mcbond_other1.898
r_angle_other_deg0.906
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.689
r_dihedral_angle_4_deg21.349
r_dihedral_angle_3_deg16.471
r_dihedral_angle_1_deg6.371
r_mcangle_it2.809
r_scbond_it2.73
r_angle_refined_deg1.911
r_mcbond_it1.901
r_mcbond_other1.898
r_angle_other_deg0.906
r_chiral_restr0.105
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_gen_planes_other0.004
r_bond_other_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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7033
Nucleic Acid Atoms
Solvent Atoms410
Heterogen Atoms177

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing