4BMM

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)-2',3, 5'-trifluoro-(1,1'-biphenyl)-4-carboxamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YMCPDB ENTRY 2YMC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.50.1 M AMMONIUM ACETATE, 0.1 M BIS-TRIS PH 5.5, 17% PEG 10K
Crystal Properties
Matthews coefficientSolvent content
2.448.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 272.469α = 90
b = 66.452β = 110.65
c = 122.219γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARRESEARCHMIRRORS2012-09-29MSINGLE 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
12.84127.4899.90.0973.8487411.583.9
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)
12.842.9999.90.721.53.8

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 2YMC2.84114.6346238246999.720.194270.189080.29005RANDOM78.461
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]
-2.95-0.176.66-2.84
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free81.608
r_dihedral_angle_2_deg40.054
r_sphericity_bonded24.66
r_dihedral_angle_3_deg21.775
r_dihedral_angle_4_deg18.963
r_mcangle_it7.159
r_dihedral_angle_1_deg6.845
r_mcbond_it5.316
r_mcbond_other5.316
r_scbond_it5.028
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free81.608
r_dihedral_angle_2_deg40.054
r_sphericity_bonded24.66
r_dihedral_angle_3_deg21.775
r_dihedral_angle_4_deg18.963
r_mcangle_it7.159
r_dihedral_angle_1_deg6.845
r_mcbond_it5.316
r_mcbond_other5.316
r_scbond_it5.028
r_rigid_bond_restr2.861
r_angle_refined_deg1.57
r_angle_other_deg0.85
r_chiral_restr0.08
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_gen_planes_other0.003
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13726
Nucleic Acid Atoms
Solvent Atoms38
Heterogen Atoms324

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing