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Crystal structure of tetrahydrodipicolinate N-succinyltransferase from E. coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TDT PDB entry 1tdt
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 0.9M tri-sodium citrate, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.4 63.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.924 α = 90 b = 102.924 β = 90 c = 69.229 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 210 mirrors 2007-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.9772 CHESS A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 50 99.9 0.114 14.5 9.8 26875 26848 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 100 0.375 6 9.1 1934
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 (All) 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 1tdt 2 44.59 26848 1434 99.65 0.176 0.176 0.17499 0.184 0.20547 0.2151 RANDOM 21.878
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] 0.06 0.03 0.06 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.829 r_dihedral_angle_3_deg 14.705 r_dihedral_angle_4_deg 12.689 r_dihedral_angle_1_deg 6.366 r_scangle_it 3.21 r_scbond_it 2.057 r_angle_refined_deg 1.359 r_mcangle_it 1.272 r_mcbond_it 0.769 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.829 r_dihedral_angle_3_deg 14.705 r_dihedral_angle_4_deg 12.689 r_dihedral_angle_1_deg 6.366 r_scangle_it 3.21 r_scbond_it 2.057 r_angle_refined_deg 1.359 r_mcangle_it 1.272 r_mcbond_it 0.769 r_nbtor_refined 0.303 r_nbd_refined 0.196 r_symmetry_vdw_refined 0.159 r_xyhbond_nbd_refined 0.158 r_symmetry_hbond_refined 0.155 r_chiral_restr 0.104 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2114 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing