4C0C

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-(2,4-difluorophenyl)piperazin-1-yl)-2-fluorobenzamide.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WX2PDB ENTRY 2WX2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
150.4 M AMMONIUM SULFATE, 0.1 M BIS-TRIS PH 5.0, 19% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.5852.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.528α = 90
b = 128.528β = 90
c = 116.721γ = 120
Symmetry
Space GroupP 63 2 2

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
12.04116.7299.90.0914.611366960.542.9
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)
12.042.1599.21.241.57.1

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 2WX22.0480.6834827183399.80.201950.199270.25365RANDOM43.54
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]
-0.13-0.13-0.130.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.618
r_dihedral_angle_4_deg22.358
r_dihedral_angle_3_deg16.757
r_dihedral_angle_1_deg6.456
r_mcangle_it5.149
r_scbond_it4.957
r_mcbond_it3.825
r_mcbond_other3.823
r_angle_refined_deg1.963
r_angle_other_deg0.958
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.618
r_dihedral_angle_4_deg22.358
r_dihedral_angle_3_deg16.757
r_dihedral_angle_1_deg6.456
r_mcangle_it5.149
r_scbond_it4.957
r_mcbond_it3.825
r_mcbond_other3.823
r_angle_refined_deg1.963
r_angle_other_deg0.958
r_chiral_restr0.127
r_bond_refined_d0.018
r_gen_planes_refined0.011
r_gen_planes_other0.005
r_bond_other_d0.001
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 Atoms3529
Nucleic Acid Atoms
Solvent Atoms125
Heterogen Atoms164

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing