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CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01869767
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 2.24 45.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.983 α = 90 b = 83.983 β = 90 c = 147.324 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 CCD RIGAKU SATURN 944+ 2019-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
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 2.6 46.275 99.7 0.158 0.062 0.988 8.5 13.8 16862 33.02
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 2.6 2.72 97.5 0.522 0.222 0.972 2.3 11.5
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 2.601 46.275 16807 841 99.638 0.235 0.2318 0.2344 0.2921 0.2916 55.198
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] 2.976 2.976 -5.952
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.54 r_dihedral_angle_6_deg 12.665 r_dihedral_angle_1_deg 7.293 r_lrange_it 7.016 r_lrange_other 7.011 r_dihedral_angle_2_deg 5.181 r_mcangle_it 4.656 r_mcangle_other 4.656 r_scangle_it 4.387 r_scangle_other 4.386
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.54 r_dihedral_angle_6_deg 12.665 r_dihedral_angle_1_deg 7.293 r_lrange_it 7.016 r_lrange_other 7.011 r_dihedral_angle_2_deg 5.181 r_mcangle_it 4.656 r_mcangle_other 4.656 r_scangle_it 4.387 r_scangle_other 4.386 r_mcbond_it 2.882 r_mcbond_other 2.87 r_scbond_it 2.611 r_scbond_other 2.611 r_angle_refined_deg 1.102 r_dihedral_angle_other_2_deg 0.506 r_angle_other_deg 0.413 r_symmetry_nbd_other 0.2 r_nbd_refined 0.191 r_symmetry_xyhbond_nbd_refined 0.174 r_nbtor_refined 0.172 r_nbd_other 0.163 r_xyhbond_nbd_refined 0.151 r_symmetry_nbtor_other 0.079 r_symmetry_nbd_refined 0.061 r_chiral_restr 0.051 r_chiral_restr_other 0.027 r_bond_other_d 0.007 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3551 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building