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Crystal structure of 2,3,4,5-Tetrahydropyridine-2-carboxylate N-Succinyltransferase from Brucella melitensis biovar abortus 2308
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BXY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 HAMPTON INDEX B11: 2.1M DL MALIC ACID, PH 7.0, VAPOR DIFFUSION, TEMPERATURE 298K, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.07 40.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.808 α = 90 b = 67.808 β = 90 c = 154.83 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 2008-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9774 ALS 5.0.1
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 1.87 25.8 98.6 0.097 0.097 12.2 3.3 21653 21653 14.7
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) 1.87 1.97 91.3 0.442 0.442 2 2.2 2915
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MR, MR THROUGHOUT 3BXY 1.87 25.8 21642 21642 1113 98.6 0.132 0.132 0.13 0.166 RANDOM 14.32
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] 0.83 0.83 -1.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.168 r_dihedral_angle_3_deg 14.841 r_dihedral_angle_4_deg 10.226 r_dihedral_angle_1_deg 7.096 r_scangle_it 4.191 r_scbond_it 2.735 r_angle_refined_deg 1.683 r_mcangle_it 1.573 r_angle_other_deg 1.015 r_mcbond_it 0.954
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.168 r_dihedral_angle_3_deg 14.841 r_dihedral_angle_4_deg 10.226 r_dihedral_angle_1_deg 7.096 r_scangle_it 4.191 r_scbond_it 2.735 r_angle_refined_deg 1.683 r_mcangle_it 1.573 r_angle_other_deg 1.015 r_mcbond_it 0.954 r_mcbond_other 0.29 r_chiral_restr 0.105 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 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 2114 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms
Software Software Software Name Purpose BOS data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling