8T5N

Crystal Structure of Glycine--tRNA ligase from Mycobacterium tuberculosis (AMP-Mg bound)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8SLG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5291Morpheus 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 coefficientSolvent content
2.7354.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.355α = 90
b = 126.355β = 90
c = 129.027γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 9M2023-05-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 19-ID0.9795NSLS-II19-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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.6545.141000.1230.1250.021119.435.173239
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)RedundancyNumber Unique Reflections (All)
11.651.681002.4892.5240.4170.88636.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.6540.031.3473150369399.970.15650.15580.1706
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.748
f_angle_d0.976
f_chiral_restr0.059
f_plane_restr0.013
f_bond_d0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3207
Nucleic Acid Atoms
Solvent Atoms368
Heterogen Atoms65

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
Aimlessdata scaling