6TUP | pdb_00006tup

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 StateFILAMENT
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsSamples 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 MethodHELICAL
Number of Particles185002
Reported Resolution (Å)3.2
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypeHELICAL
Axial SymmetryC1
Axial Rise3.14
Angular Rotation65.9
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolBACKBONE TRACE
Refinement TargetCorrelation coefficient
Overall B Value93.74
Fitting Procedure
DetailsThe 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 TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)43
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)-1000
Maximum Defocus (nm)-3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification105000
Calibrated Magnification105000
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION2.0
IMAGE ACQUISITIONEPU
CTF CORRECTIONRELION2.0
MODEL FITTINGCoot
MODEL REFINEMENTPHENIX
INITIAL EULER ASSIGNMENTRELION2.0
FINAL EULER ASSIGNMENTRELION2.0
CLASSIFICATIONRELION3.0
RECONSTRUCTIONRELION3.0
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTIONWiener filter implemented in the RELION refinement algorithm351381