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Crystal Structure of Glycine--tRNA ligase from Mycobacterium tuberculosis (AMP-Mg bound)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8SLG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 Morpheus A2: 20%(v/v) Ethylene glycol, 10%(w/v) PEG 8000, 100 mM Imidazole/MES, pH 6.5, 30 mM MgCl2 and 30 mM CaCl2. MytuD.19107.a.UW1.PS38711 at 24.9 mg/mL. 10 mM MgCl2, 1 mM ATP added prior to crystallization. ATP hydrolyzed to AMP. plate 13247 well A2 drop 1. Puck: PSL-0301, Cryo: direct
Crystal Properties Matthews coefficient Solvent content 2.73 54.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.355 α = 90 b = 126.355 β = 90 c = 129.027 γ = 120
Symmetry Space Group P 61 2 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 EIGER2 XE 9M 2023-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9795 NSLS-II 19-ID
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 1.65 45.14 100 0.123 0.125 0.021 1 19.4 35.1 73239
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 100 2.489 2.524 0.417 0.886 36.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.65 40.03 1.34 73150 3693 99.97 0.1565 0.1558 0.1653 0.1706 0.1791
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.748 f_angle_d 0.976 f_chiral_restr 0.059 f_plane_restr 0.013 f_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3207 Nucleic Acid Atoms Solvent Atoms 368 Heterogen Atoms 65
Software Software Software Name Purpose PHENIX refinement XDS data reduction PHASER phasing Aimless data scaling