ELECTRON MICROSCOPY

Sample

Klebsiella pneumoniae family 1 encapsulin-associated DyP peroxidase

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details Blot force: 5 Blot time: 2 seconds
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 431317
Reported Resolution (Å) 2.39
Resolution Method FSC 0.143 CUT-OFF
Other Details Unmasked local refinement was performed with D3 symmetry imposed.
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 107.7
Fitting Procedure ?
Details Initial fitting was performed using ChimeraX v1.2.5. The model was then manually refined and mutated using Coot v9.8.1 followed by real-space refinement using Phenix v1.20.1-4487-000.
Data Acquisition
Detector Type GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å2) 50.02
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
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 105000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION cryoSPARC 4.4.0+231114
IMAGE ACQUISITION SerialEM ?
CTF CORRECTION cryoSPARC 4.4.0+231114
MODEL FITTING UCSF ChimeraX 1.2.5
MODEL FITTING Coot 0.9.8
MODEL REFINEMENT PHENIX 1.20.1-4487-000
INITIAL EULER ASSIGNMENT cryoSPARC 4.4.0+231114
FINAL EULER ASSIGNMENT cryoSPARC 4.4.0+231114
RECONSTRUCTION cryoSPARC 4.4.0+231114
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?