9ZN5 | pdb_00009zn5

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)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 
Sample
Dimer of BrxC-BrxB fusion complexed with PglZ
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles195504
Reported Resolution (Å)6.94
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
DetailsInitial 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 TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)50
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS GLACIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC4.5.3
PARTICLE SELECTIONcryoSPARC4.5.3
CTF CORRECTIONcryoSPARC4.5.3
MODEL FITTINGISOLDE
MODEL FITTINGUCSF ChimeraX1.1
INITIAL EULER ASSIGNMENTcryoSPARC4.5.3
INITIAL EULER ASSIGNMENTcryoSPARC4.5.3
FINAL EULER ASSIGNMENTcryoSPARC4.5.3
RECONSTRUCTIONcryoSPARC4.5.3
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION343194Blob 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.