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Lactobacillus casei Thymidylate Synthase in Ternary Complex with dUMP and the Phtalimidic Derivative 7C1
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 298K
Crystal Properties Matthews coefficient Solvent content 2.73 54.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.197 α = 90 b = 78.197 β = 90 c = 226.663 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 2.1 75.59 99.9 0.106 0.106 27.7 17.2 24969 1 2 30.599
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 2.1 2.21 100 0.384 0.384 6.2 18.8 3531
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 2.1 67.72 2 24900 23614 1265 99.92 0.2086 0.20597 0.2043 0.25817 0.2571 RANDOM 36.607
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 36.049 r_dihedral_angle_4_deg 24.079 r_dihedral_angle_3_deg 18.903 r_dihedral_angle_1_deg 6.62 r_scangle_it 3.5 r_scbond_it 2.344 r_angle_refined_deg 1.843 r_mcangle_it 1.708 r_mcbond_it 0.933 r_chiral_restr 0.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.049 r_dihedral_angle_4_deg 24.079 r_dihedral_angle_3_deg 18.903 r_dihedral_angle_1_deg 6.62 r_scangle_it 3.5 r_scbond_it 2.344 r_angle_refined_deg 1.843 r_mcangle_it 1.708 r_mcbond_it 0.933 r_chiral_restr 0.125 r_bond_refined_d 0.016 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2566 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 41
Software Software Software Name Purpose MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling