ELECTRON MICROSCOPY

Sample

yeast NPC

Specimen Preperation
Sample Aggregation State CELL
Vitrification Instrument ?
Cryogen Name ETHANE-PROPANE
Sample Vitrification Details A custom-built vitrification device (Max Planck Institute for Biochemistry, Munich)
3D Reconstruction
Reconstruction Method SUBTOMOGRAM AVERAGING
Number of Particles 518
Reported Resolution (Å) 37.0
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 FLEXIBLE FIT
Refinement Target cross-correlation
Overall B Value ?
Fitting Procedure ?
Details Manual docking and limited molecular dynamics flexible fitting
Data Acquisition
Detector Type GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å2) 4.5
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) 2500
Maximum Defocus (nm) 6000
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS ?
Imaging Mode BRIGHT FIELD
Specimen Holder Model ?
Nominal Magnification 42000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details Tilt series collection: dose-symmetric & bi-directional
Imaging Experiment
Task Software Package Version
IMAGE ACQUISITION SerialEM ?
CTF CORRECTION EMAN2 2.9
MODEL FITTING UCSF Chimera 1.14
MODEL REFINEMENT VMD 1.9.3
RECONSTRUCTION EMAN2 2.9
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING ONLY e2spt_ctf.py was used to identify the precise z height of the particle in the tomogram. This precise height was then used for computing the CTF and performing the CTF correction.