1JUT

E. coli Thymidylate Synthase Bound to dUMP and LY338529, A Pyrrolo(2,3-d)pyrimidine-based Antifolate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2KCEPDB entry 2KCE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8296KPO4, MgCl2, DTT, EDTA, ammonium sulphate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
2.5150.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.8α = 90
b = 125.8β = 90
c = 67.063γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray296IMAGE PLATERIGAKU RAXIS IV1998-04-28MSINGLE 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
12.7301000.16385.81686616866-344.9
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)
12.72.8990.61.9

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 2KCE2.729.591671916719115599.50.220.2180.25RANDOM30.8
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]
-0.67-1.4-0.671.34
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d25.2
c_angle_deg1.8
c_improper_angle_d1.17
c_bond_d0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4306
Nucleic Acid Atoms
Solvent Atoms82
Heterogen Atoms98

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing