EMD-2437 Experiments and Validation

Mechanism of Membranous Tunnelling Nanotube Formation in Viral Genome Delivery

Subtomogram averaging
Overview of EMD-2437
Sample name: Lipid-containing bacteriophage PRD1
Organism: Enterobacteria phage PRD1
Related EM entries by publication: EMD-2438, EMD-2439, EMD-2440

Map parameters

Recommended contour level: 1.10 (author)
Number of grid points: 48 × 48 × 48
Voxel size: 8.80 × 8.80 × 8.80 Å
Minimum density: -2.417
Maximum density: 3.308
Average density: -0.006
Standard deviation: 0.705

Sample information

Sample name: Lipid-containing bacteriophage PRD1
Virus: Enterobacteria phage PRD1

Validation information

Experimental information

 

Image processing

Applied symmetry: C1
Software: IMOD, Dynamo
Number of subtomograms averaged: 138
Number of class averages: 1
Reconstruction protocol: Weighted Back projection

Fitting

Initial atomic model: 1W8X
Fitting software: Chimera
Fitting protocol: rigid body
Refinement space: REAL
Details: For the docking, please, see the protocol described in the primary reference

Imaging

Session
Microscope model: JEOL 2200FS
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 100.0
Energy filter: In-column Omega filter
Energy window (eV): 10.00
Nominal CS (mm): 2.00
Nominal magnification: 25000.0
Defocus max (nm): 8,000.00
Defocus min (nm): 5,000.00
Tilt max (degrees): 64.00
Tilt min (degrees): -64.00
Holder model: GATAN LIQUID NITROGEN
Acquisition

Specimen

Preparation
Specimen state: particle
Specimen concentration (mg/mL): 0.60
Buffer: 20 mM Phosphate Buffer 1 mM MgCl2
Specimen support: 200 mesh QUANTIFOIL R 2/1 (or R 3.5/1) copper grid, glow discharged in air atmosphere
Vitrification
Apparatus: FEI VITROBOT MARK III
Cryogen: ETHANE
Humidity: 95
Protocol: Blot for 4 seconds before plunging