EMD-5742 Experiments and Validation

Zernike Phase Contrast electron cryo-tomography of cyanophage Syn5 assembly intermediates

Subtomogram averaging
Overview of EMD-5742
Sample name: Cyanophage Syn5 assembly intermediate inside cyanobacteria Synechococcus WH8109 cells
Organism: Synechococcus phage Syn5
Related EM entries by publication: EMD-5743, EMD-5744, EMD-5745, EMD-5746

Map parameters

Minimum density: -50.291
Maximum density: 55.094
Average density: 0.51
Standard deviation: 4.559
Recommended contour level: 4.00 (author)

Sample information

Sample name: Cyanophage Syn5 assembly intermediate inside cyanobacteria Synechococcus WH8109 cells
Virus: Synechococcus phage Syn5

Validation information

Experimental information

 

Image processing

Applied symmetry: C1
Software: IMOD
Number of subtomograms averaged: 78
Number of class averages: 1
Reconstruction protocol: back projection

Imaging

Session
Microscope model: JEOL 2200FS
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 1.0
Energy filter: in-column GIF energy filter
Energy window (eV): 15.00
Nominal CS (mm): 4.10
Nominal magnification: 25000.0
Defocus max (nm): 1,000.00
Defocus min (nm): 0.00
Tilt max (degrees): 60.00
Tilt min (degrees): -60.00
Holder model: GATAN LIQUID NITROGEN
Acquisition
Number of images: 42

Specimen

Preparation
Specimen state: particle
Buffer: artificial sea water
Specimen support: 200 mesh Quantifoil holey grids, glow discharged
Vitrification
Apparatus: FEI VITROBOT MARK III
Cryogen: ETHANE
Humidity: 95
Protocol: Blot for 3 seconds before plunging