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CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01993593
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 2.22 44.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.669 α = 90 b = 83.669 β = 90 c = 147.261 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 2019-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91188 Diamond I04-1
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 2.28 147.26 100 0.142 0.043 0.991 11.1 12.7 24663
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 2.28 2.32 100 1.702 0.495 0.894 0.9 12.8
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 2.28 72.853 24587 1232 99.951 0.217 0.214 0.2168 0.2769 0.2765 66.897
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] 2.656 2.656 -5.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.473 r_dihedral_angle_6_deg 14.122 r_lrange_it 10.224 r_lrange_other 10.223 r_dihedral_angle_1_deg 7.746 r_scangle_it 7.692 r_scangle_other 7.69 r_mcangle_it 7.447 r_mcangle_other 7.445 r_dihedral_angle_2_deg 5.244
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.473 r_dihedral_angle_6_deg 14.122 r_lrange_it 10.224 r_lrange_other 10.223 r_dihedral_angle_1_deg 7.746 r_scangle_it 7.692 r_scangle_other 7.69 r_mcangle_it 7.447 r_mcangle_other 7.445 r_dihedral_angle_2_deg 5.244 r_mcbond_it 4.975 r_mcbond_other 4.974 r_scbond_other 4.97 r_scbond_it 4.968 r_angle_refined_deg 1.379 r_dihedral_angle_other_2_deg 0.854 r_angle_other_deg 0.501 r_symmetry_xyhbond_nbd_refined 0.299 r_symmetry_nbd_other 0.209 r_nbd_refined 0.204 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.163 r_nbd_other 0.16 r_symmetry_nbd_refined 0.112 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.066 r_symmetry_xyhbond_nbd_other 0.036 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3591 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing Coot model building