ELECTRON MICROSCOPY

Sample

Pseudomonas virus Pf1

Specimen Preperation
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 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
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 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/Å2) 43
Imaging Experiment
Date of Experiment ?
Temprature (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 ?
Imaging Experiment
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