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E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH CB3717 AND 2',5'-DIDEOXYURIDINE (DDURD)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TDU PDB ENTRY 1TDU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 CRYSTALLIZATION WAS CONDUCTED IN HANGING DROPS CONTAINING 4.2 MG/ML E. COLI TS, 0.38 MM DURD, 3.8 MM DTT, 1.0 MM CB3717 AND 1.2 M (NH4)2SO4, PH 7.8 (20 MM KPO4) OVER A WELL SOLUTION CONTAINING 2.4 M (NH4)2SO4 AND 1.0 MM DTT., vapor diffusion - hanging drop
Crystal Properties Matthews coefficient Solvent content 2.56 52.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.405 α = 90 b = 127.405 β = 90 c = 68.203 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 IMAGE PLATE RIGAKU 1996-11-02 M
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH2R
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.1 50 70.1 0.068 0.068 5.1 2.6 37027 14.1
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) Redundancy Number Unique Reflections (All) 2.1 2.16 49.8 0.252 0.252 1.6 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION DIFFERENCE FOURIER THROUGHOUT PDB ENTRY 1TDU 2.1 8 2 15938 1688 78.4 0.188 0.188 0.272 SHELLS 24.3
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]
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 26 x_scangle_it 3.27 x_angle_deg 3.1 x_mcangle_it 2.24 x_scbond_it 2.12 x_mcbond_it 1.35 x_improper_angle_d 1.15 x_bond_d 0.013 x_bond_d_na x_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 26 x_scangle_it 3.27 x_angle_deg 3.1 x_mcangle_it 2.24 x_scbond_it 2.12 x_mcbond_it 1.35 x_improper_angle_d 1.15 x_bond_d 0.013 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot x_dihedral_angle_d_na x_dihedral_angle_d_prot x_improper_angle_d_na x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4298 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 120
Software Software Software Name Purpose X-PLOR model building X-PLOR refinement DENZO data reduction SCALEPACK data scaling X-PLOR phasing