3HBB

Structures of dihydrofolate reductase-thymidylate synthase of Trypanosoma cruzi in the folate-free state and in complex with two antifolate drugs, trimetrexate and methotrexate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2H2Q2H2Q, chain A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52951.5-1.7 M ammonium sulfate, 0.01 M magnesium chloride, 5% ethylene glycol and 0.05 M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
4.1770.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 176.571α = 90
b = 176.571β = 90
c = 251.848γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2006-08-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.0APS17-ID

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
1324.9797.20.1520.1527.96.777643776431154
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)
133.1198.30.4720.47236.87755

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2H2Q, chain A319.947356873568389897.140.2030.2030.201120.23885RANDOM38.7
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]
0.370.37-0.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.956
r_dihedral_angle_4_deg17.837
r_dihedral_angle_3_deg17.785
r_dihedral_angle_1_deg5.578
r_scangle_it1.336
r_angle_refined_deg1.137
r_scbond_it0.752
r_mcangle_it0.645
r_mcbond_it0.336
r_chiral_restr0.074
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.956
r_dihedral_angle_4_deg17.837
r_dihedral_angle_3_deg17.785
r_dihedral_angle_1_deg5.578
r_scangle_it1.336
r_angle_refined_deg1.137
r_scbond_it0.752
r_mcangle_it0.645
r_mcbond_it0.336
r_chiral_restr0.074
r_bond_refined_d0.007
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16134
Nucleic Acid Atoms
Solvent Atoms190
Heterogen Atoms488

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling