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Lactobacillus casei Thymidylate Synthase in Ternary Complex with dUMP and the Phtalimidic Derivative 20C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2TDM PDB ENTRY 2TDM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 298 10% saturated Ammonium sulfate, 1mM DTT, 20mM Potassium phosphate
, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.69 54.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.985 α = 90 b = 77.985 β = 90 c = 224.718 γ = 120
Symmetry Space Group P 61 2 2
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 315r 2008-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.983 ESRF ID23-1
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 2.25 74.95 99.9 0.079 0.079 37.7 19.9 20159 1 2 33.669
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) 1 2.25 2.37 100 0.286 0.286 10.8 20.9 2868
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2TDM 2.25 67.54 2 20103 19048 1024 99.85 0.21457 0.21164 0.2049 0.27083 0.2636 RANDOM 37.159
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] 0.03 0.01 0.03 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.501 r_dihedral_angle_4_deg 22.565 r_dihedral_angle_3_deg 18.809 r_dihedral_angle_1_deg 6.677 r_scangle_it 4.36 r_scbond_it 2.858 r_mcangle_it 2.076 r_angle_refined_deg 2.027 r_mcbond_it 1.123 r_chiral_restr 0.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.501 r_dihedral_angle_4_deg 22.565 r_dihedral_angle_3_deg 18.809 r_dihedral_angle_1_deg 6.677 r_scangle_it 4.36 r_scbond_it 2.858 r_mcangle_it 2.076 r_angle_refined_deg 2.027 r_mcbond_it 1.123 r_chiral_restr 0.136 r_bond_refined_d 0.019 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2561 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 42
Software Software Software Name Purpose MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling