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Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 1.8 Ang resolution in a ternary complex with fragment compounds 5-methoxyindole and 1-benzofuran-2-carboxylic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3COV PDB entry 3COV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 11-14% w/v PEG3000, 100-150 mM lithium sulfate, 100 mM imidazole, pH 8.0,
2-4% v/v ethanol, 10% v/v glycerol and 20 mM magnesium chloride., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.21 44.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.48 α = 90 b = 71.22 β = 99.4 c = 81.8 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 2008-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9788 ESRF ID29
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 1.8 50 99.7 0.061 0.061 16.6 4.1 50986 50816 29.5
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 1.8 1.91 99.4 0.529 0.529 2.76 4.1 8124
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3COV 1.8 38.49 48410 48270 2543 99.71 0.16978 0.16978 0.16773 0.1678 0.20909 0.209 RANDOM 27.439
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 37.147 r_dihedral_angle_4_deg 15.113 r_dihedral_angle_3_deg 13.223 r_dihedral_angle_1_deg 5.67 r_scangle_it 5.406 r_mcangle_it 3.728 r_scbond_it 3.55 r_mcbond_it 2.815 r_angle_refined_deg 1.401 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.147 r_dihedral_angle_4_deg 15.113 r_dihedral_angle_3_deg 13.223 r_dihedral_angle_1_deg 5.67 r_scangle_it 5.406 r_mcangle_it 3.728 r_scbond_it 3.55 r_mcbond_it 2.815 r_angle_refined_deg 1.401 r_nbtor_refined 0.307 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.169 r_xyhbond_nbd_refined 0.15 r_symmetry_hbond_refined 0.096 r_chiral_restr 0.094 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4126 Nucleic Acid Atoms Solvent Atoms 382 Heterogen Atoms 73
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement