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Structure of tetrahydrodipicolinate N-succinyltransferase (Rv1201c; DapD) from Mycobacterium tuberculosis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 190 mM magnesium acetate tetrahydrate, 100 mM sodium cacodylate pH 6.5, 10 %(w/v) PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.48 50.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 216.99 α = 90 b = 216.99 β = 90 c = 216.99 γ = 90
Symmetry Space Group I 21 3
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 MARMOSAIC 225 mm CCD 2008-06-13 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1.0000 MAX II I911-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.15 37.21 100 10.4 91741 91416 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.19 99.7 8.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.15 30 90536 90238 1126 99.67 0.16856 0.16793 0.172 0.21945 0.2182 RANDOM 30.215
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.299 r_dihedral_angle_4_deg 19.042 r_dihedral_angle_3_deg 14.173 r_scangle_it 6.976 r_dihedral_angle_1_deg 6.417 r_scbond_it 4.645 r_mcangle_it 1.966 r_angle_refined_deg 1.724 r_mcbond_it 1.075 r_chiral_restr 0.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.299 r_dihedral_angle_4_deg 19.042 r_dihedral_angle_3_deg 14.173 r_scangle_it 6.976 r_dihedral_angle_1_deg 6.417 r_scbond_it 4.645 r_mcangle_it 1.966 r_angle_refined_deg 1.724 r_mcbond_it 1.075 r_chiral_restr 0.119 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10866 Nucleic Acid Atoms Solvent Atoms 570 Heterogen Atoms 53
Software Software Software Name Purpose MxCuBE data collection Auto-Rickshaw phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling