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CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01839469
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7QI8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 reservoir: 0.25 M NaOAc, 14% W/V PEG 3350
Protein buffer: 25 mM HEPES, 0.5 M NaCl, 5% glycerol, 2 mM DTT, pH 7
Crystal Properties Matthews coefficient Solvent content 2.3 46.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.999 α = 90 b = 84.999 β = 90 c = 148.045 γ = 90
Symmetry Space Group P 41 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 100 PIXEL DECTRIS PILATUS 6M 2018-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97625 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.3 85 92.1 0.117 0.056 0.999 10.7 10 22947 42.38
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 99.9 1.218 0.546 0.96 2 11.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.3 60.176 22880 1144 92.124 0.258 0.2548 0.2588 0.3106 0.3136 72.847
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] 4.03 4.03 -8.059
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.129 r_dihedral_angle_6_deg 13.713 r_lrange_it 13.53 r_lrange_other 13.529 r_mcangle_it 10.014 r_mcangle_other 10.012 r_scangle_it 9.652 r_scangle_other 9.65 r_dihedral_angle_1_deg 9.136 r_dihedral_angle_2_deg 7.547
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.129 r_dihedral_angle_6_deg 13.713 r_lrange_it 13.53 r_lrange_other 13.529 r_mcangle_it 10.014 r_mcangle_other 10.012 r_scangle_it 9.652 r_scangle_other 9.65 r_dihedral_angle_1_deg 9.136 r_dihedral_angle_2_deg 7.547 r_mcbond_it 6.694 r_mcbond_other 6.687 r_scbond_it 6.272 r_scbond_other 6.271 r_angle_refined_deg 1.653 r_dihedral_angle_other_2_deg 1.48 r_angle_other_deg 0.562 r_symmetry_xyhbond_nbd_refined 0.38 r_nbd_refined 0.236 r_symmetry_nbd_other 0.21 r_xyhbond_nbd_refined 0.204 r_nbtor_refined 0.185 r_symmetry_nbd_refined 0.169 r_nbd_other 0.152 r_symmetry_xyhbond_nbd_other 0.114 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.074 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3627 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building