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Lactobacillus CASEI Thymidylate Synthase Ternary Complex with DUMP and the Phtalimidic Derivative 14C in Multiple Binding Modes-Mode 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LCE PDB ENTRY 1LCE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 293 4mg/mL LcTS, 1mM EDTA, 40mM dUMP, 20mM TRIS HCl,100mM ammonium phosphate, 5% PEG 400 v/v, 10-12% ligand solution in DMSO, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.73 54.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.518 α = 90 b = 78.518 β = 90 c = 224.377 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 MARMOSAIC 225 mm CCD 2005-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.008 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 2.4 50.32 99 0.095 0.095 5.6 10.32 16609 16609 1.4 55.434
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 2.4 2.53 99.1 0.528 0.528 1.4 10.69 2363
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 1LCE 2.4 50.32 1.4 15087 1505 100 0.25541 0.24827 0.2512 0.32615 0.3244 RANDOM 48.242
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] 0.18 0.09 0.18 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.622 r_dihedral_angle_4_deg 23.738 r_dihedral_angle_3_deg 23.055 r_dihedral_angle_1_deg 7.819 r_scangle_it 3.225 r_angle_refined_deg 2.201 r_scbond_it 2.175 r_mcangle_it 1.676 r_mcbond_it 0.959 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.622 r_dihedral_angle_4_deg 23.738 r_dihedral_angle_3_deg 23.055 r_dihedral_angle_1_deg 7.819 r_scangle_it 3.225 r_angle_refined_deg 2.201 r_scbond_it 2.175 r_mcangle_it 1.676 r_mcbond_it 0.959 r_nbtor_refined 0.32 r_nbd_refined 0.253 r_symmetry_vdw_refined 0.241 r_xyhbond_nbd_refined 0.204 r_chiral_restr 0.136 r_symmetry_hbond_refined 0.091 r_bond_refined_d 0.019 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2383 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing