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Crystal structure of Mycobacterium tuberculosis H37Rv PknF kinase domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5M06
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291.15 PEG 4000, Citrate buffer, Ammonium acetate pH 5.5, 10 mM Ikk16
Crystal Properties Matthews coefficient Solvent content 2.51 51.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.127 α = 90 b = 239.33 β = 90 c = 53.982 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS3 6M 2019-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.979 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.75 39.9 99.41 0.145 0.159 0.065 0.99 11.14 5.8 34601
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.84 98.93 1.57 1.76 0.76 0.6 1.38
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5m06 2.75 39.9 32914 1688 99.53 0.23888 0.2369 0.27887 0.254 RANDOM 64.4
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] 0.87 -2.11 1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.238 r_dihedral_angle_4_deg 16.136 r_dihedral_angle_3_deg 14.057 r_dihedral_angle_1_deg 5.948 r_long_range_B_refined 5.13 r_long_range_B_other 5.111 r_mcangle_other 2.296 r_mcangle_it 2.295 r_scangle_other 2.181 r_angle_refined_deg 1.359
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.238 r_dihedral_angle_4_deg 16.136 r_dihedral_angle_3_deg 14.057 r_dihedral_angle_1_deg 5.948 r_long_range_B_refined 5.13 r_long_range_B_other 5.111 r_mcangle_other 2.296 r_mcangle_it 2.295 r_scangle_other 2.181 r_angle_refined_deg 1.359 r_mcbond_it 1.33 r_mcbond_other 1.33 r_scbond_it 1.265 r_scbond_other 1.265 r_angle_other_deg 1.17 r_chiral_restr 0.054 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 6831 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing