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Crystal structure of dimeric biodegradative threonine deaminase (TdcB) from Salmonella typhimurium at 2.2A resolution (Triclinic form with one dimer of TdcB in the asymmetric unit)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GN0 BIODEGRADATIVE THREONINE DEAMINASE FROM SALMONELLA TYPHIMURIUM (PDB CODE 1GN0)
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 10% 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.06 40.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.317 α = 103.09 b = 55.3 β = 94.7 c = 67.235 γ = 112.94
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 2005-12-24 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 2.2 30 94.7 0.053 22.18 12.19 29556 31.42
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 2.2 2.28 84.5 0.222 4.98 2494
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT BIODEGRADATIVE THREONINE DEAMINASE FROM SALMONELLA TYPHIMURIUM (PDB
CODE 1GN0) 2.2 25 26557 26557 1405 94.32 0.21183 0.20964 0.25291 0.2551 RANDOM 32.816
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] 1.76 2.34 0.94 2.5 0.92 -1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.666 r_dihedral_angle_3_deg 12.703 r_dihedral_angle_4_deg 12.482 r_dihedral_angle_1_deg 5.47 r_scangle_it 1.538 r_angle_refined_deg 1.025 r_scbond_it 0.885 r_angle_other_deg 0.741 r_mcangle_it 0.563 r_mcbond_it 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.666 r_dihedral_angle_3_deg 12.703 r_dihedral_angle_4_deg 12.482 r_dihedral_angle_1_deg 5.47 r_scangle_it 1.538 r_angle_refined_deg 1.025 r_scbond_it 0.885 r_angle_other_deg 0.741 r_mcangle_it 0.563 r_mcbond_it 0.312 r_nbd_refined 0.18 r_symmetry_vdw_refined 0.175 r_symmetry_vdw_other 0.168 r_nbtor_refined 0.163 r_nbd_other 0.157 r_xyhbond_nbd_refined 0.145 r_symmetry_metal_ion_refined 0.104 r_symmetry_hbond_refined 0.088 r_nbtor_other 0.079 r_mcbond_other 0.057 r_chiral_restr 0.056 r_metal_ion_refined 0.043 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4789 Nucleic Acid Atoms Solvent Atoms 274 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing