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Human Thymidylate Synthase Bound to dUMP and LY231514, a Pyrrolo(2,3-d)pyrimidine-based Antifolate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other thymidylate synthase from Leishmania major
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 296 PEG-monomethyl ether 5000, sodium cacodylate, ammonium sulfate, KCL, TRIS, EDTA, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.48 50.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.14 α = 90 b = 98.14 β = 110.7 c = 111.97 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 296 IMAGE PLATE RIGAKU RAXIS II 1997-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3 40 84 0.145 5.8 2.1 23396 23396 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3 3.09 78 0.43 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MIR THROUGHOUT thymidylate synthase from Leishmania major 3 37.96 22378 22378 2221 79.5 0.273 0.268 0.2676 0.311 0.3076 RANDOM 25.2
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] -2.77 0.36 -1.1 3.87
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.6 c_angle_deg 1.5 c_improper_angle_d 0.86 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9208 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 204
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement CNS phasing