6TUP

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	351381

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.