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Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 2.40 Ang resolution in complex with fragment compound 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 2.22 44.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.632 α = 90 b = 71.338 β = 99.51 c = 82.06 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 MARMOSAIC 225 mm CCD 2007-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 1.117 SRS PX10.1
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 2.39 50 99.7 0.127 0.127 7.5 3.3 21939 21873 35
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 2.39 2.46 99.7 0.458 0.458 3.3 1447
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3COV 2.39 27.86 20910 20730 1120 99.14 0.1612 0.1612 0.15595 0.2614 0.2619 RANDOM 34.708
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 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.04 r_dihedral_angle_3_deg 16.867 r_dihedral_angle_4_deg 14.617 r_dihedral_angle_1_deg 6.879 r_scangle_it 6.794 r_mcangle_it 5.198 r_scbond_it 4.935 r_mcbond_it 3.834 r_angle_refined_deg 1.773 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.04 r_dihedral_angle_3_deg 16.867 r_dihedral_angle_4_deg 14.617 r_dihedral_angle_1_deg 6.879 r_scangle_it 6.794 r_mcangle_it 5.198 r_scbond_it 4.935 r_mcbond_it 3.834 r_angle_refined_deg 1.773 r_nbtor_refined 0.308 r_nbd_refined 0.22 r_symmetry_vdw_refined 0.196 r_xyhbond_nbd_refined 0.175 r_symmetry_hbond_refined 0.174 r_chiral_restr 0.11 r_bond_refined_d 0.018 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4084 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 42
Software Software Software Name Purpose AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling