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Cryo-EM structure of Pf4 bacteriophage coat protein with single-stranded DNA
ELECTRON MICROSCOPY
Sample
Pseudomonas virus Pf1
Sample Components
Pseudomonas virus Pf1
DNA
Specimen Preparation
Sample Aggregation State
FILAMENT
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
Samples for cryo-EM were prepared by pipetting 2.5 ul of the sample onto freshly glow-discharged Quantifoil grids (Cu/Rh R2/2, 200 mesh). Grids were b ...
Samples for cryo-EM were prepared by pipetting 2.5 ul of the sample onto freshly glow-discharged Quantifoil grids (Cu/Rh R2/2, 200 mesh). Grids were blotted for 2.5 seconds with a blot force of -15, 0.5 second drain and 0 second wait times.
3D Reconstruction
Reconstruction Method
HELICAL
Number of Particles
185002
Reported Resolution (Å)
3.2
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
HELICAL
Axial Symmetry
C1
Axial Rise
3.14
Angular Rotation
65.9
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
BACKBONE TRACE
Refinement Target
Correlation coefficient
Overall B Value
93.74
Fitting Procedure
Details
The helical filament symmetry is only applied to the Pf4 coat protein and not the DNA. The reason for this is that the DNA bases are not resolved clea ...
The helical filament symmetry is only applied to the Pf4 coat protein and not the DNA. The reason for this is that the DNA bases are not resolved clearly due to averaging along the ssDNA genome of the phage, meaning that refinement of the protein into the map is of a higher quality than the ssDNA, where a poly-adenine model has been built.
Data Acquisition
Detector Type
GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)
43
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI TITAN KRIOS
Minimum Defocus (nm)
-1000
Maximum Defocus (nm)
-3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
2.7
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
105000
Calibrated Magnification
105000
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
EM Software
Task
Software Package
Version
PARTICLE SELECTION
RELION
2.0
IMAGE ACQUISITION
EPU
CTF CORRECTION
RELION
2.0
MODEL FITTING
Coot
MODEL REFINEMENT
PHENIX
INITIAL EULER ASSIGNMENT
RELION
2.0
FINAL EULER ASSIGNMENT
RELION
2.0
CLASSIFICATION
RELION
3.0
RECONSTRUCTION
RELION
3.0
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
Wiener filter implemented in the RELION refinement algorithm