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Sak Single Strand Annealing Protein from Staphylococcal Bacteriophage 80a - dCTD
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
in silico model
AlphaFold
Sample
18-mer ring cryoEM structure of the 80a-Sak NTD in apo state
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
75703
Reported Resolution (Å)
3.21
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Symmetry expanded to C18, multiplying the stack by 18, from 75703 to 1365300 particles.
Refinement Type
Symmetry Type
POINT
Point Symmetry
C18
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Fitting of the truncated AlphaFold prediction was done with ChimeraX and then subjected to real space refinement in PHENIX. The output was then repeat ...
Fitting of the truncated AlphaFold prediction was done with ChimeraX and then subjected to real space refinement in PHENIX. The output was then repeatedly adjusted with Coot and verified in PHENIX.
Data Acquisition
Detector Type
TFS FALCON 4i (4k x 4k)
Electron Dose (electrons/Å**2)
50
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
TFS GLACIOS
Minimum Defocus (nm)
1600
Maximum Defocus (nm)
2900
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
2.7
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
190000
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
200
Imaging Details
EM Software
Task
Software Package
Version
PARTICLE SELECTION
cryoSPARC
4.2.1
IMAGE ACQUISITION
EPU
2.13.0
CTF CORRECTION
cryoSPARC
4.2.1
MODEL FITTING
UCSF ChimeraX
1.4
MODEL REFINEMENT
PHENIX
1.20.1
MODEL REFINEMENT
Coot
0.9.8.4 EL
INITIAL EULER ASSIGNMENT
cryoSPARC
4.2.1
FINAL EULER ASSIGNMENT
cryoSPARC
4.2.1
RECONSTRUCTION
cryoSPARC
4.2.1
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
CTF correction was applied on-the-fly during data collection with CryoSPARC Live.