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Hybrid model of a dimer of BrxC-BrxB fusion complexed with PglZ from the Acinetobacter BREX system
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
in silico model
AlphaFold
Sample
Dimer of BrxC-BrxB fusion complexed with PglZ
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
195504
Reported Resolution (Å)
6.94
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
Initial model consisted of a fusion of N-terminal BrxC and BrxB complexed with PglZ. The entire model was initially placed into the volume using the C ...
Initial model consisted of a fusion of N-terminal BrxC and BrxB complexed with PglZ. The entire model was initially placed into the volume using the ChimeraX Fit in Map tool. Individual domains were then manually rotated/translated into the volume and adjusted with Fit in Map. The interface between BrxB and PglZ was preserved by treating the N-terminal domain of PglZ as part of the fusion. The model was then minimally refined with ISOLDE to resolve bond distortions from rigid domain fitting.
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
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
200
Imaging Details
EM Software
Task
Software Package
Version
PARTICLE SELECTION
cryoSPARC
4.5.3
PARTICLE SELECTION
cryoSPARC
4.5.3
CTF CORRECTION
cryoSPARC
4.5.3
MODEL FITTING
ISOLDE
MODEL FITTING
UCSF ChimeraX
1.1
INITIAL EULER ASSIGNMENT
cryoSPARC
4.5.3
INITIAL EULER ASSIGNMENT
cryoSPARC
4.5.3
FINAL EULER ASSIGNMENT
cryoSPARC
4.5.3
RECONSTRUCTION
cryoSPARC
4.5.3
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
343194
Blob picking on a 500 denoised micrograph resulted in 343,194 particles, which were rigorously sorted/classified and used to generate templates for template picking on the full dataset which resulted in 2,679,070 particles.