1JU6

Human Thymidylate Synthase Complex with dUMP and LY231514, A Pyrrolo(2,3-d)pyrimidine-based Antifolate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherthymidylate synthase portion of the Leishmania major DHFR-TS bifunctional enzyme

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5296PEG-monomethyl ether 5000, sodium cacodylate, ammonium sulfate, KCL, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
2.2545.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.138α = 71.67
b = 69.633β = 85.72
c = 73.958γ = 75.11
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray103.2IMAGE PLATERIGAKU RAXIS IV1997-09-01MSINGLE WAVELENGTH
21x-ray103.2IMAGE PLATERIGAKU RAXIS IV1997-09-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54178

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
1,22.823880.1387.41.92465924659-341.9
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)
2.82.88740.3332

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTthymidylate synthase portion of the Leishmania major DHFR-TS bifunctional enzyme2.8922.952337623376231583.80.2390.2360.264RANDOM23.8
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]
1.65-1.996.33-4.36-1.092.71
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.3
c_angle_deg1.5
c_improper_angle_d0.83
c_bond_d0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9236
Nucleic Acid Atoms
Solvent Atoms48
Heterogen Atoms209

Software

Software
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing