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Structure of Human Aspartate--tRNA ligase 3-154 with linker and FC : ATYR0101
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
in silico model
AlphaFold
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
6.578
f_angle_d
0.669
f_chiral_restr
0.049
f_plane_restr
0.007
f_bond_d
0.005
Sample
Human Aspartate--tRNA ligase 3-154: -Linker-Fcv14
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
To prepare cryo-grids, 3 ul samples were applied to glow discharged Quantifoil Cu grids (R1.2/1.3), which were subsequently blotted with filter paper ...
To prepare cryo-grids, 3 ul samples were applied to glow discharged Quantifoil Cu grids (R1.2/1.3), which were subsequently blotted with filter paper (Ted Pella) for 3 seconds at 18oC and 100% humidity. The grids were immediately plunge frozen in liquid ethane using a FEI Vitrobot IV (ThermoFisher)
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
142250
Reported Resolution (Å)
4.96
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
AB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
Details
Initial local fitting was done using Chimera X, followed by manual fitting using Coot. Finally it was refined using Phenix real space refinement
Data Acquisition
Detector Type
FEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)
50
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
TFS KRIOS
Minimum Defocus (nm)
1200
Maximum Defocus (nm)
2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode
OTHER
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source
OTHER
Acceleration Voltage (kV)
300
Imaging Details
EM Software
Task
Software Package
Version
PARTICLE SELECTION
cryoSPARC
4.7.0
MODEL REFINEMENT
PHENIX
"2.0_5885"
RECONSTRUCTION
cryoSPARC
4.7.0
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
After Inspect Particle Picks (NCC score > 0.670, 10 < local power score < 59) and Extract From Micrographs (Extraction box size 200 pix), a total of 2,771,298 particles were extracted