ELECTRON MICROSCOPY

Sample

Cargo-loaded Myxococcus xanthus EncA encapsulin engineered pore mutant with T=4 icosahedral symmetry

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details Blot force: 20 Blot time: 4 seconds Wait time: 0 seconds
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 4386
Reported Resolution (Å) 3.46
Resolution Method FSC 0.143 CUT-OFF
Other Details Homogeneous refinement was performed against the intial ab-initio map using I symmetry, per-particle defocus optimization, per-group CTF parameterization, and Ewald sphere correction.
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol FLEXIBLE FIT
Refinement Target cross-correlation coefficient
Overall B Value 60.6
Fitting Procedure ?
Details ChimeraX v1.2.5 was first used to place the starting model (PDB: 7S4Q) in the cryo-EM map by using the fit in map command. The model was then manually refined using Coot v 0.9.8.1, followed by iterative real-space refinements in Phenix v1.20.1-4487-000. BioMT operators were identified from the cryo-EM map using map_symmetry command in Phenix then applied to the model using the apply_ncs command to assemble the complete shell. Real-space refinement was repeated in Phenix with NCS constraints applied. The BioMT operators were then identified using find_ncs command in Phenix and applied to the header of a protomer of the NCS-refined model.
Data Acquisition
Detector Type GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å2) 39.56
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TECNAI ARCTICA
Minimum Defocus (nm) 1000
Maximum Defocus (nm) 1800
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS ?
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 4.10.0
IMAGE ACQUISITION Leginon ?
CTF CORRECTION cryoSPARC 4.10.0
MODEL FITTING UCSF ChimeraX 1.2.5
MODEL REFINEMENT Coot 0.9.8.1
MODEL REFINEMENT PHENIX 1.20.1-4487-000
INITIAL EULER ASSIGNMENT cryoSPARC 4.10.0
FINAL EULER ASSIGNMENT cryoSPARC 4.10.0
RECONSTRUCTION cryoSPARC 4.10.0
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?