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CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR DDD018870911
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 44.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.701 α = 90 b = 83.701 β = 90 c = 147.691 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+ 2018-10-03 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 2.59 46.225 99.7 0.36 0.161 0.988 4.8 11.2 16852 51.64
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 2.71 98.1 2.404 0.808 0.589 0.8 9.6
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 2.597 46.225 16796 843 99.555 0.263 0.2601 0.2617 0.3181 0.3162 64.121
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] 2.824 2.824 -5.648
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.966 r_dihedral_angle_6_deg 14.125 r_lrange_it 9.884 r_lrange_other 9.884 r_dihedral_angle_1_deg 8.254 r_mcangle_it 6.697 r_mcangle_other 6.696 r_scangle_it 6.492 r_scangle_other 6.491 r_dihedral_angle_2_deg 5.653
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.966 r_dihedral_angle_6_deg 14.125 r_lrange_it 9.884 r_lrange_other 9.884 r_dihedral_angle_1_deg 8.254 r_mcangle_it 6.697 r_mcangle_other 6.696 r_scangle_it 6.492 r_scangle_other 6.491 r_dihedral_angle_2_deg 5.653 r_mcbond_it 4.189 r_mcbond_other 4.18 r_scbond_it 4.042 r_scbond_other 4.041 r_angle_refined_deg 1.212 r_angle_other_deg 0.46 r_nbd_refined 0.218 r_symmetry_nbd_other 0.213 r_symmetry_xyhbond_nbd_refined 0.18 r_nbtor_refined 0.176 r_nbd_other 0.166 r_xyhbond_nbd_refined 0.157 r_symmetry_nbtor_other 0.079 r_symmetry_nbd_refined 0.066 r_chiral_restr 0.06 r_dihedral_angle_other_2_deg 0.043 r_chiral_restr_other 0.017 r_bond_refined_d 0.004 r_gen_planes_refined 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 3627 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing