ELECTRON MICROSCOPY

Sample

Quasibacillus thermotolerans T=4 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 44759
Reported Resolution (Å) 2.4
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 79.3
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 four 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
MODEL REFINEMENT Coot 0.9.8.1
MODEL REFINEMENT PHENIX 1.20.1-4487-000
INITIAL EULER ASSIGNMENT cryoSPARC 4.7.1
FINAL EULER ASSIGNMENT cryoSPARC 4.7.1
RECONSTRUCTION cryoSPARC 4.7.1
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?
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