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Lactobacillus Casei Thymidylate Synthase Ternary Complex with DUMP and the Phtalimidic Derivative C00
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LCA PDB ENTRY 1LCA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 293 1mM EDTA, 20 mM Tris-HCl, dUMP, 100mM ammonium phopshate, 5% (v/v) PEG 400, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.68 54.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.916 α = 90 b = 77.916 β = 90 c = 224.183 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 EMBL/DESY, HAMBURG BEAMLINE BW7B 1.078 EMBL/DESY, HAMBURG BW7B
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 2.7 33.37 88.6 0.139 0.139 4.3 4 10447 10443 1.7 56.53
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 2.7 2.85 92.3 0.439 0.439 1.7 4.1 1502
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1LCA 2.7 33.37 10443 9511 932 88.6 0.2349 0.22582 0.226 0.32619 0.3224 RANDOM 37.422
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] 0.02 0.01 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.425 r_dihedral_angle_3_deg 24.324 r_dihedral_angle_4_deg 23.758 r_dihedral_angle_1_deg 8.06 r_scangle_it 2.955 r_angle_refined_deg 2.151 r_scbond_it 1.933 r_mcangle_it 1.518 r_mcbond_it 0.86 r_nbtor_refined 0.331
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.425 r_dihedral_angle_3_deg 24.324 r_dihedral_angle_4_deg 23.758 r_dihedral_angle_1_deg 8.06 r_scangle_it 2.955 r_angle_refined_deg 2.151 r_scbond_it 1.933 r_mcangle_it 1.518 r_mcbond_it 0.86 r_nbtor_refined 0.331 r_symmetry_vdw_refined 0.329 r_nbd_refined 0.284 r_symmetry_hbond_refined 0.216 r_xyhbond_nbd_refined 0.166 r_chiral_restr 0.154 r_bond_refined_d 0.019 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2521 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing