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CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01991231
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, 500 mM NaCl, 5% GLYCEROL, 2 mM DTT, PH 7.0,
Crystal Properties Matthews coefficient Solvent content 2.22 44.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.589 α = 90 b = 83.589 β = 90 c = 147.406 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 2019-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.4 147.41 100 0.254 0.272 0.097 0.997 6.5 14.4 21202 57.9
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 2.49 100 5.109 2.014 0.597 0.7 14.1
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 2.4 72.712 21130 1067 99.915 0.237 0.2331 0.2355 0.3081 0.3082 77.859
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] 4.51 4.51 -9.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.381 r_dihedral_angle_6_deg 13.426 r_lrange_other 10.73 r_lrange_it 10.728 r_dihedral_angle_1_deg 8.342 r_mcangle_it 7.894 r_mcangle_other 7.892 r_scangle_it 7.33 r_scangle_other 7.328 r_dihedral_angle_2_deg 6.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.381 r_dihedral_angle_6_deg 13.426 r_lrange_other 10.73 r_lrange_it 10.728 r_dihedral_angle_1_deg 8.342 r_mcangle_it 7.894 r_mcangle_other 7.892 r_scangle_it 7.33 r_scangle_other 7.328 r_dihedral_angle_2_deg 6.02 r_mcbond_it 5.056 r_mcbond_other 5.045 r_scbond_it 4.595 r_scbond_other 4.594 r_angle_refined_deg 1.371 r_angle_other_deg 0.487 r_dihedral_angle_other_2_deg 0.385 r_symmetry_nbd_other 0.212 r_nbd_refined 0.21 r_symmetry_xyhbond_nbd_refined 0.182 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.174 r_nbd_other 0.168 r_symmetry_nbd_refined 0.127 r_symmetry_nbtor_other 0.082 r_symmetry_xyhbond_nbd_other 0.07 r_chiral_restr 0.063 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 3556 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing