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Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 2.50 Ang resolution in complex with 5'-deoxy-5'-(benzyldisulfanyl)-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 2.22 44.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.591 α = 90 b = 71.485 β = 100.03 c = 82.044 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 2007-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9763 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 2.5 50 99.3 0.094 0.094 13.54 3.67 19422 19277
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 2.5 2.65 97.9 0.457 0.457 3.1 3.7
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 (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 2.5 39.78 18433 18332 941 99.45 0.1664 0.16163 0.1618 0.26106 0.2589 RANDOM 38.004
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] -0.04 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.379 r_dihedral_angle_3_deg 18.897 r_dihedral_angle_4_deg 16.615 r_dihedral_angle_1_deg 7.276 r_scangle_it 7.273 r_mcangle_it 5.636 r_scbond_it 5.274 r_mcbond_it 4.209 r_angle_refined_deg 2.088 r_nbtor_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.379 r_dihedral_angle_3_deg 18.897 r_dihedral_angle_4_deg 16.615 r_dihedral_angle_1_deg 7.276 r_scangle_it 7.273 r_mcangle_it 5.636 r_scbond_it 5.274 r_mcbond_it 4.209 r_angle_refined_deg 2.088 r_nbtor_refined 0.323 r_symmetry_vdw_refined 0.244 r_nbd_refined 0.24 r_symmetry_hbond_refined 0.205 r_xyhbond_nbd_refined 0.179 r_chiral_restr 0.124 r_bond_refined_d 0.021 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 3996 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 66
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement