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E.coli thymidylate synthase complexes with 5-NO2dUMP and tetrahydrofolate at 1.4 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2TSC pdb entry 2TSC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 2.5 M ammonium sulfate, 20 mm KH2PO4, 4mm DTT, 4 mM 5-NO2dump, 4MM methylenetetrahydrofolate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.44 49.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.87 α = 90 b = 124.87 β = 90 c = 66.394 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 100 CCD ADSC QUANTUM 4 2002-08-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-D 0.9 APS 14-BM-D
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 1.4 105.41 100 0.076 18.6 6.4 115632 115632
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) 1 1.4 1.45 100 0.45 3.2 6.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 FOURIER SYNTHESIS THROUGHOUT pdb entry 2TSC 1.4 25 109776 5799 99.74 0.17564 0.1742 0.1807 0.20299 0.2074 RANDOM 10.792
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] 0.01 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.845 r_dihedral_angle_4_deg 23.521 r_dihedral_angle_3_deg 13.556 r_dihedral_angle_1_deg 6.453 r_scangle_it 3.394 r_scbond_it 2.271 r_angle_other_deg 1.984 r_angle_refined_deg 1.786 r_mcangle_it 1.511 r_mcbond_it 0.854
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.845 r_dihedral_angle_4_deg 23.521 r_dihedral_angle_3_deg 13.556 r_dihedral_angle_1_deg 6.453 r_scangle_it 3.394 r_scbond_it 2.271 r_angle_other_deg 1.984 r_angle_refined_deg 1.786 r_mcangle_it 1.511 r_mcbond_it 0.854 r_chiral_restr 0.302 r_symmetry_vdw_other 0.302 r_mcbond_other 0.249 r_symmetry_vdw_refined 0.196 r_symmetry_hbond_refined 0.147 r_xyhbond_nbd_refined 0.132 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4306 Nucleic Acid Atoms Solvent Atoms 437 Heterogen Atoms 125
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction CrystalClear data scaling