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Complex of translation initiation factors eIF2 and eIF2B
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK III
Cryogen Name
ETHANE
Sample Vitrification Details
Blot for 2 seconds before plunging
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
64541
Reported Resolution (Å)
3.93
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
C2
Map-Model Fitting and Refinement
Id
1 (5B04, 3JAP)
2 (3JAP, 3JAP, 3JAP)
Refinement Space
REAL
REAL
Refinement Protocol
FLEXIBLE FIT
RIGID BODY FIT
Refinement Target
correlation coeficient
Cross-correlation coefficient
Overall B Value
Fitting Procedure
Details
Modeller was used to build homology model of S. cerevisiae eIF2B structure based on S. pombe crystal structure. Subunits of the homology model, along ...
Modeller was used to build homology model of S. cerevisiae eIF2B structure based on S. pombe crystal structure. Subunits of the homology model, along with eIF2 alpha domains 1 and 2, were then rigid body fitted into our map using UCSF Chimera. The model then was refined using phenix and manually adjusted in Coot.
eIF2 alpha domain 3, eIF2 gamma, and eIF2 beta (3JAP) were rigid body fitted into our map using Chimera.
Data Acquisition
Detector Type
GATAN K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å**2)
40
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI TITAN KRIOS
Minimum Defocus (nm)
1500
Maximum Defocus (nm)
4000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
2.7
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification
37313
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
Tilt at zero and 35 degrees.
EM Software
Task
Software Package
Version
PARTICLE SELECTION
RELION
2.01
IMAGE ACQUISITION
EPU
CTF CORRECTION
Gctf
MODEL FITTING
MODELLER
MODEL FITTING
UCSF Chimera
MODEL FITTING
Coot
INITIAL EULER ASSIGNMENT
RELION
2.1
FINAL EULER ASSIGNMENT
RELION
2.1
CLASSIFICATION
RELION
2.1
RECONSTRUCTION
RELION
2.1
MODEL REFINEMENT
PHENIX
MODEL FITTING
UCSF Chimera
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
CTF determination was performed per micrograph initially.
After particle picking and initial reconstruction, per particle CTF determination was performed.
655000
Initially, approximately 3000 particles were picked manually and used for 2D classification. Then 4 best looking 2D class average images were used as references for automated particle picking in RELION.
For the zero tilt data collection, 406000 particles were picked.
For the 35 degree tilt data collection, 249000 particles were picked