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Pantothenate kinase from Mycobacterium tuberculosis (MtPanK) in complex with GDP and Phosphopantothenate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GEV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 1.4-1.8M tri sodium citrate, 0.05-0.1M sodium acetate, 10% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.93 68.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.64 α = 90 b = 103.64 β = 90 c = 90.41 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 100 IMAGE PLATE MAR scanner 345 mm plate Mirrors 2009-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54
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 2.2 40 99.9 0.064 13.9 4.5 28891 51.1
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 2.2 2.32 99.9 0.522 2.3 3.5 4159
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 2GEV 2.2 34.06 27379 1408 100 0.20511 0.20318 0.1975 0.24252 0.2335 RANDOM 41.597
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] 1.21 0.61 1.21 -1.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.793 r_dihedral_angle_4_deg 20.877 r_dihedral_angle_3_deg 17.079 r_scangle_it 8.373 r_dihedral_angle_1_deg 7.666 r_scbond_it 5.57 r_mcangle_it 3.505 r_mcbond_it 1.992 r_angle_refined_deg 1.497 r_chiral_restr 0.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.793 r_dihedral_angle_4_deg 20.877 r_dihedral_angle_3_deg 17.079 r_scangle_it 8.373 r_dihedral_angle_1_deg 7.666 r_scbond_it 5.57 r_mcangle_it 3.505 r_mcbond_it 1.992 r_angle_refined_deg 1.497 r_chiral_restr 0.113 r_gen_planes_refined 0.017 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2480 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 126
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling