6BM7

Crystal structure of Trypanosoma brucei AdoMetDC/prozyme heterodimer in complex with pyrimidineamine inhibitor UTSAM568


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5TVMPDB entry 5TVM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72931 uL 4 mg/mL protein in crystallization buffer (50 mM Bis-Tris propane, pH 7.2, 50 mM sodium chloride, 4 mM TCEP, 2 mM putrescine, 0.5 mM N4-(3,5-dibromophenyl)-6-methylpyrimidine-2,4-diamine [UTSAM568], 1% DMSO) + 1 uL reservoir solution (17% PEG6000, 100 mM Bis-Tris propane, pH 7.0) + 0.5 uL unliganded protein microseeds obtained using Seed-Bead method in stabilization solution (100 mM Bis-Tris propane, pH 8.9, 50 mM HEPES, pH 7.2, 19% PEG6000, 50 mM sodium chloride, 4 mM TCEP, 2 mM putrescine)
Crystal Properties
Matthews coefficientSolvent content
2.652.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.09α = 90
b = 96.25β = 102.426
c = 98.84γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.91905APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)Rpim I (All)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
12.985099.80.1940.074106.83029449.2238648407
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
133.0599.10.7121.876.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEPDB entry 5TVM2.9848.26232335321.3378980514750644252084.60266283560.2023353565150.1995896236240.25485727003758.4151476361
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.4170911814
f_angle_d0.558602768216
f_chiral_restr0.0446252615216
f_plane_restr0.00364942909324
f_bond_d0.00314584829052
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10193
Nucleic Acid Atoms
Solvent Atoms7
Heterogen Atoms117

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing