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Crystal structure of dimeric biodegradative threonine deaminase (TdcB) from Salmonella typhimurium at 1.7 A resolution (Triclinic form with one complete subunit built in alternate conformation)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TDJ Biosynthetic threonine deaminase (1TDJ)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 0.1 M citrate buffer pH 6.0, 20% PEG 3350 and 15% t-butanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.06 40.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.675 α = 66.12 b = 76.827 β = 89.16 c = 78.501 γ = 77.08
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate Osmic mirror 2005-08-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.542
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.7 30 93.1 0.041 26.58 15.64 128680 128680 26
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 86.9 0.426 2.76 11167
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 (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 Biosynthetic threonine deaminase (1TDJ) 1.7 20 113742 5998 92.92 0.1901 0.18842 0.2251 0.22154 0.2532 RANDOM 22.819
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] 0.8 0.33 0.31 -0.64 0.01 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.148 r_dihedral_angle_4_deg 11.526 r_dihedral_angle_3_deg 11.49 r_dihedral_angle_1_deg 5.106 r_scangle_it 1.979 r_scbond_it 1.187 r_angle_refined_deg 1.031 r_angle_other_deg 0.712 r_mcangle_it 0.666 r_mcbond_it 0.367
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.148 r_dihedral_angle_4_deg 11.526 r_dihedral_angle_3_deg 11.49 r_dihedral_angle_1_deg 5.106 r_scangle_it 1.979 r_scbond_it 1.187 r_angle_refined_deg 1.031 r_angle_other_deg 0.712 r_mcangle_it 0.666 r_mcbond_it 0.367 r_nbd_refined 0.195 r_symmetry_vdw_other 0.19 r_symmetry_vdw_refined 0.181 r_nbtor_refined 0.166 r_nbd_other 0.16 r_symmetry_hbond_refined 0.14 r_xyhbond_nbd_refined 0.117 r_symmetry_metal_ion_refined 0.103 r_mcbond_other 0.092 r_nbtor_other 0.079 r_metal_ion_refined 0.078 r_chiral_restr 0.057 r_symmetry_hbond_other 0.034 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9636 Nucleic Acid Atoms Solvent Atoms 780 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing