ELECTRON MICROSCOPY

Sample

Complex of BREX proteins BrxB / PglZ from Salmonella Typhimurium str. D23580

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 123964
Reported Resolution (Å) 4.45
Resolution Method FSC 0.143 CUT-OFF
Other Details ?
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol RIGID BODY FIT
Refinement Target ?
Overall B Value ?
Fitting Procedure ?
Details AlphaFold model, split into domains at "hinge" points, was rigid fit into the cryo-EM map. The following domains were used: (1) BrxB + 1-96 PglZ, (2) 97-292 PglZ, (3) 293-748 PglZ, and (4) 749-867 PglZ. The model was then simulated in the ISOLDE plug-in for ChimeraX to resolve distortions from rigid domain fitiing.
Data Acquisition
Detector Type GATAN K3 (6k x 4k)
Electron Dose (electrons/Å2) 50
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model TFS GLACIOS
Minimum Defocus (nm) 800
Maximum Defocus (nm) 2000
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS 2.7
Imaging Mode BRIGHT FIELD
Specimen Holder Model ?
Nominal Magnification 36000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 200
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION cryoSPARC 4.2.1
PARTICLE SELECTION cryoSPARC 4.2.1
IMAGE ACQUISITION SerialEM ?
CTF CORRECTION cryoSPARC 4.2.1
MODEL FITTING UCSF ChimeraX 1.9
MODEL FITTING ISOLDE 1.6
INITIAL EULER ASSIGNMENT cryoSPARC 4.2.1
FINAL EULER ASSIGNMENT cryoSPARC 4.2.1
CLASSIFICATION cryoSPARC 4.2.1
RECONSTRUCTION cryoSPARC 4.2.1
MODEL REFINEMENT PHENIX ?
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?