EMD-2133 Experiments and Validation

The Structure of Lactococcal Phage TP901-1 by electron microscopy: the capsid

Single particle reconstruction
Overview of EMD-2133
Sample name: Icosahedral capsid of the lactococcal phage TP901-1
Organism: Lactococcus phage TP901-1
Related EM entry by publication: EMD-2227, EMD-2228

Map parameters

Minimum density: -2.32
Maximum density: 8.48
Average density: 0.1
Standard deviation: 0.67
Recommended contour level: 0.1 (author)

Sample information

Sample name: Icosahedral capsid of the lactococcal phage TP901-1
Virus: Lactococcus phage TP901-1

Validation information

Experimental information

 

Image processing

Applied symmetry: I
Software: IMAGIC
Number of particles: 1500
Reconstruction protocol: Icosahedral
CTF correction: Images

Fitting

Initial atomic model: 1OHG
Fitting software: Chimera
Fitting protocol: rigid body
Overall B value: 10.0
Refinement space: REAL
Details: Protocol: Rigid body. Manually fitted 60 copies of the hexamer of HK97. Every hexamer was refined using Chimera.

Imaging

Session
Microscope model: FEI/PHILIPS CM200FEG
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 10.0
Energy filter: FEI
Nominal CS (mm): 2.2
Nominal magnification: 50000.0
Defocus max (nm): 3,000
Defocus min (nm): 1,500
Holder model: GATAN LIQUID NITROGEN
Acquisition
Number of images: 200

Specimen

Preparation
Specimen state: particle
Buffer: SM buffer (100 mM sodium chloride, 10 mM magnesium sulfate, 50 mM Tris [pH 7.5], and 0.01% [wt/vol] gelatin)
Specimen support: Quantifoil grids were glow discharged for 20 seconds
Vitrification
Apparatus: FEI VITROBOT MARK I
Cryogen: ETHANE
Humidity: 100
Protocol: Blot for 2 seconds before plunging