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Crystal structure of the intracellular domain of the M. tuberculosis Ser/Thr kinase PknA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O6Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 4.3 M NaCl, 0.1 M Hepes-Na pH 8.0
Crystal Properties Matthews coefficient Solvent content 3.43 63.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.31 α = 90 b = 150.18 β = 96.98 c = 96.54 γ = 90
Symmetry Space Group C 1 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 CCD ADSC QUANTUM 210 2008-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
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 2.9 43.6 99.6 0.107 8.3 3.6 31961
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 2.9 3.06 99.1 1.197 1.1 3.5
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 1o6y 2.9 43.56 30353 1606 99.57 0.22033 0.21912 0.2186 0.24302 0.2423 RANDOM 91.212
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] -3.57 1.5 -0.5 3.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.047 r_dihedral_angle_3_deg 16.555 r_dihedral_angle_4_deg 12.339 r_long_range_B_refined 7.878 r_long_range_B_other 7.878 r_scangle_other 6.291 r_mcangle_it 5.214 r_mcangle_other 5.214 r_scbond_it 4.077 r_scbond_other 4.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.047 r_dihedral_angle_3_deg 16.555 r_dihedral_angle_4_deg 12.339 r_long_range_B_refined 7.878 r_long_range_B_other 7.878 r_scangle_other 6.291 r_mcangle_it 5.214 r_mcangle_other 5.214 r_scbond_it 4.077 r_scbond_other 4.076 r_mcbond_it 3.377 r_mcbond_other 3.369 r_dihedral_angle_1_deg 3.188 r_angle_refined_deg 1.289 r_angle_other_deg 1.144 r_chiral_restr 0.063 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.004 r_gen_planes_other 0.004 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6017 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing