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Pantothenate kinase from Mycobacterium tuberculosis (MtPanK) in complex with GDP and Pantothenate
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 trisodium citrate, 0.05-0.1M sodium acetate, 10% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.01 69.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.73 α = 90 b = 104.73 β = 90 c = 90.4 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 2009-05-19 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 2.5 40 99.9 0.063 13 3.9 20208 65.7
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 2.5 2.64 99.8 0.548 2 3.6 2893
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 2.5 34.28 19194 981 100 0.2088 0.20651 0.2017 0.2539 0.2509 RANDOM 49.796
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] 1.3 0.65 1.3 -1.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.224 r_dihedral_angle_4_deg 21.405 r_dihedral_angle_3_deg 18.314 r_dihedral_angle_1_deg 7.659 r_scangle_it 6.868 r_scbond_it 4.314 r_mcangle_it 2.868 r_mcbond_it 1.538 r_angle_refined_deg 1.271 r_chiral_restr 0.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.224 r_dihedral_angle_4_deg 21.405 r_dihedral_angle_3_deg 18.314 r_dihedral_angle_1_deg 7.659 r_scangle_it 6.868 r_scbond_it 4.314 r_mcangle_it 2.868 r_mcbond_it 1.538 r_angle_refined_deg 1.271 r_chiral_restr 0.099 r_gen_planes_refined 0.014 r_bond_refined_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2474 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 98
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling