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Crystal Structure of Glycine--tRNA ligase active site chimera from Mycobacterium thermoresistibile/tuberculosis (G5A bound)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8SBO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 Index F12: 25% (w/v) Polyethylene glycol 3,350, 0.1 M HEPES pH 7.5, 0.2 M Sodium chloride. MythA.19107.a.UX11.PW39208 at 20.4 mg/mL. 2mM G5A added prior to crystallization. Plate 13386 F12 drop 3. Puck: PSL-1203, Cryo: 20% Glycerol + 80% Crystallant.
Crystal Properties Matthews coefficient Solvent content 3.29 62.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 171.286 α = 90 b = 87.388 β = 104.12 c = 99.152 γ = 90
Symmetry Space Group C 1 2 1
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 2023-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9785 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 2.45 48.08 99.6 0.086 0.101 0.053 0.997 9.8 3.5 52055
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 2.45 2.53 99.8 0.887 1.037 0.533 0.756 3.7
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 2.45 41.53 1.34 51956 2606 99.34 0.1864 0.1852 0.1876 0.2092 0.2115
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 14.126 f_angle_d 0.572 f_chiral_restr 0.043 f_plane_restr 0.006 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6659 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 63
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing