ELECTRON MICROSCOPY

Sample

Acidipropionibacterium acidipropionici encapsulin at pH 7.5 in a closed state

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details Additional settings were : Blot force - 20, blot time - 4 seconds, drain time - 0 seconds, wait time - 0 seconds
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 29056
Reported Resolution (Å) 2.9
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 Correlation coefficient
Overall B Value 45.66
Fitting Procedure ?
Details A starting model was created using RosettaFold (Baek, M. 2021). The starting model was placed in the map manually using Chimera. The model was then further refined using Coot and Phenix Real Space Refine.
Data Acquisition
Detector Type GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å2) 41
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TALOS ARCTICA
Minimum Defocus (nm) 800
Maximum Defocus (nm) 1800
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS 2.7
Imaging Mode BRIGHT FIELD
Specimen Holder Model ?
Nominal Magnification 45000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 200
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION cryoSPARC 3.3.1
IMAGE ACQUISITION Leginon ?
CTF CORRECTION cryoSPARC 3.3.1
MODEL FITTING PHENIX 1.19.2-4158
MODEL FITTING UCSF Chimera 1.16
MODEL REFINEMENT Coot 8.9.6
MODEL REFINEMENT PHENIX 1.19.2-4158
INITIAL EULER ASSIGNMENT cryoSPARC 3.3.1
FINAL EULER ASSIGNMENT cryoSPARC 3.3.1
RECONSTRUCTION cryoSPARC 3.3.1
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?