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Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 1.95 Ang resolution in complex with 5'-deoxy-5'-((R)-3,4-dihydroxybutylthio)-adenosine
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 Li2SO4, 100 mM imidazole, pH 8.0,
2-4% v/v ethanol, 10% v/v glycerol and 20 mM MgCl2., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.21 44.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.382 α = 90 b = 71.259 β = 99.35 c = 81.871 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 4 2006-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.1 1.488 SRS PX14.1
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 1.95 50 92.5 0.065 0.065 10.84 2.38 40275 37247 29
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 1.95 2.07 94.5 0.388 0.388 2.5 2.24 6463
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 1.95 33.84 38172 35374 1862 92.67 0.16754 0.16754 0.16428 0.1652 0.22974 0.2311 RANDOM 25.947
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.657 r_dihedral_angle_4_deg 14.067 r_dihedral_angle_3_deg 13.987 r_dihedral_angle_1_deg 6.044 r_scangle_it 5.726 r_mcangle_it 4.041 r_scbond_it 4.022 r_mcbond_it 3.171 r_angle_refined_deg 1.539 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.657 r_dihedral_angle_4_deg 14.067 r_dihedral_angle_3_deg 13.987 r_dihedral_angle_1_deg 6.044 r_scangle_it 5.726 r_mcangle_it 4.041 r_scbond_it 4.022 r_mcbond_it 3.171 r_angle_refined_deg 1.539 r_nbtor_refined 0.305 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.194 r_symmetry_hbond_refined 0.189 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.104 r_bond_refined_d 0.016 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4177 Nucleic Acid Atoms Solvent Atoms 443 Heterogen Atoms 78
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement