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Crystal Structure of Glycine tRNA ligase from Mycobacterium thermoresistibile (AMP bound)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold G7CIG9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 JCSG+ H8: 25% (w/v) PEG 3350, 0.2M NaCl, 0.1M Bis-Tris pH 5.5, MythA.19107.a.A1.PW39162 at 17 mg/mL. Plate:Clover 1/12/2023 AMP, A4. Puck: PSL-1512, Cryo: 25% PEG200 + 85% crystallant. 2mM AMP added prior to crystallization
Crystal Properties Matthews coefficient Solvent content 3.27 62.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173.757 α = 90 b = 86.297 β = 104.2 c = 98.986 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 2022-02-14 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 2.9 47.98 99.6 0.063 0.075 0.04 0.998 9 3.5 31541
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 2.9 3.06 99.8 0.502 0.589 0.305 0.912 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 2.9 42.6 1.22 31468 1562 99.36 0.1854 0.1834 0.1854 0.2239 0.2215
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 13.057 f_angle_d 0.744 f_chiral_restr 0.045 f_plane_restr 0.008 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6662 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 49
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing