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CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01866774
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 2.23 44.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.929 α = 90 b = 83.929 β = 90 c = 147.289 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 2018-07-08 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 2.4 147.29 96.4 0.113 0.056 0.999 8.5 7.6 20488 63.98
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 2.4 2.49 99 2.311 1.17 0.508 0.6 7.7
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.4 55.417 20418 970 95.81 0.253 0.25 0.32 0.2854 89.058
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] 5.248 5.248 -10.497
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.961 r_dihedral_angle_6_deg 14.463 r_lrange_it 11.968 r_lrange_other 11.967 r_dihedral_angle_2_deg 10.135 r_mcangle_it 8.502 r_mcangle_other 8.5 r_dihedral_angle_1_deg 8.354 r_scangle_it 7.849 r_scangle_other 7.847
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.961 r_dihedral_angle_6_deg 14.463 r_lrange_it 11.968 r_lrange_other 11.967 r_dihedral_angle_2_deg 10.135 r_mcangle_it 8.502 r_mcangle_other 8.5 r_dihedral_angle_1_deg 8.354 r_scangle_it 7.849 r_scangle_other 7.847 r_mcbond_it 5.358 r_mcbond_other 5.355 r_scbond_it 4.685 r_scbond_other 4.683 r_angle_refined_deg 1.361 r_dihedral_angle_other_2_deg 0.813 r_angle_other_deg 0.485 r_nbd_refined 0.232 r_symmetry_nbd_other 0.221 r_symmetry_xyhbond_nbd_refined 0.201 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.172 r_nbd_other 0.161 r_symmetry_xyhbond_nbd_other 0.132 r_symmetry_nbd_refined 0.128 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.062 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_chiral_restr_other 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3572 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building