ELECTRON MICROSCOPY

Sample

Nuclear Pore Complex

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK III
Cryogen Name ETHANE
Sample Vitrification Details ?
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 29655
Reported Resolution (Å) 8.1
Resolution Method FSC 0.143 CUT-OFF
Other Details multibody in RELION followed by refinements in cryosparc
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 Molecular dynamics flexible fitting after docking Alphafold2 CSMs for Nups into the 3D map of double Y complex ring with Chimera
Data Acquisition
Detector Type GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å2) 40
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) 1500
Maximum Defocus (nm) 3500
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 37651
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details Preliminary grid screening done manually with individual images of low magnification montages of candidate meshes.
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION Gautomatch Gautomatch_v0.56_sm61_cu7.5
IMAGE ACQUISITION SerialEM ?
CTF CORRECTION Gctf Gctf-v0.1.06_sm_20_cu7.5_x86_64
CTF CORRECTION RELION 3.0.7
MODEL FITTING UCSF Chimera 1.14
MODEL REFINEMENT MDFF ?
MODEL REFINEMENT Coot 0.8.9.2
INITIAL EULER ASSIGNMENT RELION 3.0.7
FINAL EULER ASSIGNMENT cryoSPARC 3.3.2
CLASSIFICATION RELION 3.0.7
RECONSTRUCTION cryoSPARC 3.3.2
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION CTF correction applied in RELION during the alignment and reconstruction