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Design and structural analysis of aromatic inhibitors of type II dehydroquinate dehydratase from Mycobacterium tuberculosis - compound 49e [5-[(3-nitrobenzyl)amino]benzene-1,3-dicarboxylic acid]
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.8 298 0.15M KBr, 30% PEG 5000, pH 7.8, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.34 47.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.71 α = 90 b = 135.22 β = 97.18 c = 143.91 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 MAR CCD 165 mm 2009-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97160 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.57 142.781 85.7 0.139 7.3 4.1 99630 99630 2 2
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 2.57 2.71 85.3 0.747 0.747 1 4.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.57 67.61 99630 94578 4996 85.21 0.20195 0.19716 0.29379 0.285 RANDOM 37.068
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] 0.06 0.01 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.192 r_dihedral_angle_3_deg 19.537 r_dihedral_angle_4_deg 17.982 r_dihedral_angle_1_deg 6.402 r_mcangle_it 3.105 r_scbond_it 2.083 r_mcbond_it 1.905 r_angle_refined_deg 1.471 r_chiral_restr 0.097 r_bond_refined_d 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.192 r_dihedral_angle_3_deg 19.537 r_dihedral_angle_4_deg 17.982 r_dihedral_angle_1_deg 6.402 r_mcangle_it 3.105 r_scbond_it 2.083 r_mcbond_it 1.905 r_angle_refined_deg 1.471 r_chiral_restr 0.097 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25342 Nucleic Acid Atoms Solvent Atoms 1101 Heterogen Atoms 506
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction DNA data collection MOSFLM data reduction MOLREP phasing