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Crystal structure of S/T protein kinase PknG from Mycobacterium tuberculosis in complex with inhibitor L2W
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Y12
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 292 Mother Liquor: 0.2M CaCl2, 0.2 M TRIS, pH 8.5 and 20 % (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.03 39.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.327 α = 90 b = 37.016 β = 105.5 c = 106.781 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 196 PIXEL DECTRIS EIGER2 X 16M 2021-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9763 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.35 51.5 98.4 0.999 1.67 6.8 12303 62.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.43 98.1 0.699 6.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4Y12 2.35 51.502 12246 627 98.377 0.218 0.215 0.2135 0.2676 0.2661 74.413
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] 3.035 1.561 1.17 -4.395
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.721 r_dihedral_angle_3_deg 15.893 r_lrange_it 12.976 r_dihedral_angle_4_deg 10.975 r_scangle_it 8.401 r_mcangle_it 7.626 r_dihedral_angle_1_deg 7.1 r_scbond_it 5.827 r_mcbond_it 5.161 r_angle_refined_deg 1.246
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.721 r_dihedral_angle_3_deg 15.893 r_lrange_it 12.976 r_dihedral_angle_4_deg 10.975 r_scangle_it 8.401 r_mcangle_it 7.626 r_dihedral_angle_1_deg 7.1 r_scbond_it 5.827 r_mcbond_it 5.161 r_angle_refined_deg 1.246 r_nbtor_refined 0.312 r_symmetry_xyhbond_nbd_refined 0.311 r_symmetry_nbd_refined 0.28 r_nbd_refined 0.227 r_metal_ion_refined 0.162 r_xyhbond_nbd_refined 0.141 r_chiral_restr 0.092 r_gen_planes_refined 0.005 r_bond_refined_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2401 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing