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The crystal structure of 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase from Yersinia pestis CO92
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TDT PDB ENTRY 3TDT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 10% PEG3000, 0.1M Cacodinate, 0.2M MgCl2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.28 46.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.792 α = 90 b = 69.695 β = 105.28 c = 106.448 γ = 90
Symmetry Space Group P 1 21 1
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 315r mirrors 2008-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 APS 19-ID
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 1.8 57.64 98.18 0.111 13.57 3.8 71891 70583 2 2
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 1.8 1.847 90.15 0.548 1.14 2.3
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 3TDT 1.8 57.64 71891 70583 3741 98.18 0.22989 0.2271 0.232 0.27198 0.2852 RANDOM 16.957
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] 1.23 1.77 -1.84 1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.684 r_dihedral_angle_4_deg 16.52 r_dihedral_angle_3_deg 16.045 r_dihedral_angle_1_deg 7.397 r_scangle_it 4.243 r_scbond_it 2.881 r_angle_refined_deg 1.83 r_mcangle_it 1.751 r_mcbond_it 1.097 r_angle_other_deg 1.018
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.684 r_dihedral_angle_4_deg 16.52 r_dihedral_angle_3_deg 16.045 r_dihedral_angle_1_deg 7.397 r_scangle_it 4.243 r_scbond_it 2.881 r_angle_refined_deg 1.83 r_mcangle_it 1.751 r_mcbond_it 1.097 r_angle_other_deg 1.018 r_mcbond_other 0.362 r_chiral_restr 0.117 r_bond_refined_d 0.022 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined 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 6288 Nucleic Acid Atoms Solvent Atoms 285 Heterogen Atoms 1
Software Software Software Name Purpose SBC-Collect data collection MERLOT phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling