ELECTRON MICROSCOPY

Sample

Myxococcus xanthus EncA encapsulin engineered pore mutant with T=1 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 61808
Reported Resolution (Å) 2.86
Resolution Method FSC 0.143 CUT-OFF
Other Details CryoSPARC homogeneous refinement was performed with I symmetry, per-particle defocus optimization, per-group CTF-parameterization, and Ewald sphere correction enabled.
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 126.4
Fitting Procedure ?
Details ChimeraX v1.2.5 was first used to place the starting model (PDB: 7S21) 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) 39.18
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 3.10.0
IMAGE ACQUISITION Leginon ?
CTF CORRECTION cryoSPARC 3.10.0
MODEL FITTING UCSF ChimeraX 1.2.5
INITIAL EULER ASSIGNMENT cryoSPARC 3.10.0
FINAL EULER ASSIGNMENT cryoSPARC 3.10.0
RECONSTRUCTION cryoSPARC 3.10.0
MODEL REFINEMENT PHENIX v1.20.1-4487-000
MODEL REFINEMENT Coot v0.9.8.1
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?