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Pantothenate kinase from Mycobacterium tuberculosis (MtPanK) in complex with a coenzyme A derivative, Form-I (RT)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ESM PDB ENTRY 1ESM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 10-15%(w/v) PEG8000, 0.05M NaCl, 0.05-0.1M NaOAc in 0.1M Na-Cacodylate buffer of pH 6.5, 0.001M Beta-mercaptoethanol was present in the protein buffer, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.8 55.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.304 α = 90 b = 78.304 β = 90 c = 115.449 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 IMAGE PLATE MAR scanner 345 mm plate 2004-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU ULTRAX 18 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.4 19.5 99.2 0.083 13.5 5.8 16374 -3 39.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 97.1 0.526 2.5 3 1562
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1ESM 2.4 19.49 16374 822 98.9 0.188 0.188 0.1879 0.232 0.2316 RANDOM 50.3
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] 0.61 2.87 2.48 -3.08
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.6 c_scangle_it 3.48 c_mcangle_it 2.66 c_scbond_it 2.29 c_mcbond_it 1.54 c_angle_deg 1.4 c_improper_angle_d 0.95 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2477 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 52
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement MAR345 data collection CCP4 data scaling AMoRE phasing