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Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 2.05 Ang resolution- in complex with sulphonamide inhibitor 3
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 final soak solution: 12% PEG3000, 0.1 M imidazole, 4% ethanol, 10% glycerol, 6 mM of inhibitor 3, 3% v/v DMSO, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.21 44.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.49 α = 90 b = 71.2 β = 99.8 c = 81.85 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 315 2007-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.979 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 2.05 50.5 98.3 0.07 0.07 9.3 4.6 35124 34527 2.5 31.1
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 2.05 2.1 97.1 0.466 0.466 4.3 2307
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 FOURIER SYNTHESIS THROUGHOUT PDB entry 3COV 2.03 44.59 33640 32796 1730 97.49 0.16904 0.16904 0.16625 0.1655 0.22106 0.2168 RANDOM 38.096
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] 0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.599 r_dihedral_angle_4_deg 19.348 r_dihedral_angle_3_deg 16.026 r_dihedral_angle_1_deg 5.664 r_scangle_it 4.91 r_mcangle_it 3.807 r_scbond_it 3.508 r_mcbond_it 2.911 r_angle_refined_deg 1.394 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.599 r_dihedral_angle_4_deg 19.348 r_dihedral_angle_3_deg 16.026 r_dihedral_angle_1_deg 5.664 r_scangle_it 4.91 r_mcangle_it 3.807 r_scbond_it 3.508 r_mcbond_it 2.911 r_angle_refined_deg 1.394 r_nbtor_refined 0.305 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.18 r_xyhbond_nbd_refined 0.14 r_symmetry_hbond_refined 0.126 r_chiral_restr 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4133 Nucleic Acid Atoms Solvent Atoms 369 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling CCP4 phasing