3MCV

Structure of PTR1 from Trypanosoma brucei in ternary complex with 2,4-diamino-5-[2-(2,5-dimethoxyphenyl)ethyl]thieno[2,3-d]-pyrimidine and NADP+


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62912.8 M sodium acetate, 50 mM sodium citrate, 1mM DTT, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.0339.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.502α = 90
b = 89.819β = 115.49
c = 82.26γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97857ESRFID29

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
11.740.76198.50.0610.06119.75.7105672105672
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7997.40.3080.3082.45.515226

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.738.98105645531098.350.1370.1350.167RANDOM13.678
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]
-1.31-0.611.7-0.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.109
r_dihedral_angle_4_deg18.323
r_dihedral_angle_3_deg12.603
r_dihedral_angle_1_deg5.689
r_scangle_it4.728
r_scbond_it3.555
r_mcangle_it2.471
r_mcbond_it2.174
r_angle_refined_deg1.454
r_angle_other_deg0.935
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.109
r_dihedral_angle_4_deg18.323
r_dihedral_angle_3_deg12.603
r_dihedral_angle_1_deg5.689
r_scangle_it4.728
r_scbond_it3.555
r_mcangle_it2.471
r_mcbond_it2.174
r_angle_refined_deg1.454
r_angle_other_deg0.935
r_mcbond_other0.531
r_symmetry_vdw_other0.263
r_nbd_refined0.21
r_nbd_other0.192
r_symmetry_hbond_refined0.18
r_nbtor_refined0.174
r_symmetry_vdw_refined0.172
r_xyhbond_nbd_refined0.148
r_nbtor_other0.086
r_chiral_restr0.075
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7453
Nucleic Acid Atoms
Solvent Atoms793
Heterogen Atoms300

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction