2FTO

Y94F mutant of thymidylate synthase bound to thymidine-5'-phosphate and 10-propargyl-5,8-dideazafolid acid


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52982.5 M ammonium sulfate, 20 mM KH2PO4, 4 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.8356.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.08α = 90
b = 72.08β = 90
c = 115.21γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293DIFFRACTOMETERENRAF-NONIUS FASTgraphite monochromator1996-06-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR5711.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
1250890.0692443124431

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (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 DIFFRACTIONStarted with coordinates from isomorphous structure 1TSN28.4193841840597980.730.159190.158070.17917RANDOM24.703
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]
1.080.541.08-1.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.969
r_dihedral_angle_4_deg17.738
r_dihedral_angle_3_deg14.871
r_dihedral_angle_1_deg6.505
r_scangle_it4.103
r_scbond_it2.628
r_mcangle_it1.63
r_angle_refined_deg1.507
r_mcbond_it0.98
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.969
r_dihedral_angle_4_deg17.738
r_dihedral_angle_3_deg14.871
r_dihedral_angle_1_deg6.505
r_scangle_it4.103
r_scbond_it2.628
r_mcangle_it1.63
r_angle_refined_deg1.507
r_mcbond_it0.98
r_nbtor_refined0.311
r_symmetry_hbond_refined0.222
r_nbd_refined0.214
r_symmetry_vdw_refined0.173
r_xyhbond_nbd_refined0.131
r_chiral_restr0.101
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2152
Nucleic Acid Atoms
Solvent Atoms98
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
MADNESSdata reduction
PROCORdata scaling