ELECTRON MICROSCOPY

Sample

Quasibacillus thermotolerans T=3 encapsulin pore mutant variant Letter11

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details ?
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 18327
Reported Resolution (Å) 2.42
Resolution Method FSC 0.143 CUT-OFF
Other Details The final map was generated using homogeneous refinement against the ab-initio map with I symmetry imposed, per-particle defocus optimization, per-group CTF parameterization, spherical aberration fitting enabled, tetrafoil fitting enabled, anisotropic magnification fitting enabled, and Ewald sphere correcting enabled with a negative curvature sign.
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 71.2
Fitting Procedure ?
Details A starting model of a single protomer was generated using AlphaFold 3, and individual protomers were fit into the volume of an asymmetric unit using UCSF ChimeraX v 1.8. The model containing a single asymmetric unit consisting of three protomers was then manually refined using Coot v 0.9.8.1, followed by real-space refinement in PHENIX v 1.20.1-4487-000. Non-crystallographic symmetry (NCS) operators were then applied to generate a complete NCS-expanded shell, which was refined against the map using PHENIX real-space refinement.
Data Acquisition
Detector Type GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å2) 51.5
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model TFS KRIOS
Minimum Defocus (nm) 800
Maximum Defocus (nm) 1200
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS ?
Imaging Mode BRIGHT FIELD
Specimen Holder Model ?
Nominal Magnification ?
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION cryoSPARC 4.7.1
IMAGE ACQUISITION SerialEM ?
CTF CORRECTION cryoSPARC 4.7.1
MODEL FITTING UCSF ChimeraX 1.8
INITIAL EULER ASSIGNMENT cryoSPARC 4.7.1
FINAL EULER ASSIGNMENT cryoSPARC 4.7.1
RECONSTRUCTION cryoSPARC 4.7.1
MODEL REFINEMENT Coot 0.9.8.1
MODEL REFINEMENT PHENIX 1.20.1-4487-000
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?
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