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Hybrid model of a complex of BREX proteins BrxB and PglZ from Salmonella typhimurium
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
in silico model
AlphaFold
Sample
Complex of BREX proteins BrxB / PglZ from Salmonella Typhimurium str. D23580
Specimen Preparation
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) ...
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/Å**2)
50
Imaging Experiment
1
Date of Experiment
Temperature (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
EM Software
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
15593169
10,876,932 from blob picking on dataset 1
4,716,237 from template picking on dataset 2