☰ Navigation Tabs
Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 1.80 Ang resolution in complex with 5'-deoxy-5'-thioadenosine
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 44.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.304 α = 90 b = 71.426 β = 99.34 c = 81.885 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 2006-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.973 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 99.3 0.062 0.062 17.26 4.9 51346 51004 28
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 1.9 97.4 0.427 0.427 3.3 4.9 8204
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 37.66 48751 48449 2551 99.38 0.16112 0.16112 0.15898 0.1588 0.20176 0.2012 RANDOM 23.657
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 38.207 r_dihedral_angle_4_deg 15.011 r_dihedral_angle_3_deg 12.977 r_dihedral_angle_1_deg 5.54 r_scangle_it 5.391 r_scbond_it 3.5 r_mcangle_it 3.376 r_mcbond_it 2.548 r_angle_refined_deg 1.333 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.207 r_dihedral_angle_4_deg 15.011 r_dihedral_angle_3_deg 12.977 r_dihedral_angle_1_deg 5.54 r_scangle_it 5.391 r_scbond_it 3.5 r_mcangle_it 3.376 r_mcbond_it 2.548 r_angle_refined_deg 1.333 r_nbtor_refined 0.303 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.165 r_xyhbond_nbd_refined 0.153 r_symmetry_hbond_refined 0.141 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 4139 Nucleic Acid Atoms Solvent Atoms 522 Heterogen Atoms 78
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement