EMD-5584 Experiments and Validation

Life in the extremes: atomic structure of Sulfolobus Turreted Icosahedral Virus

Single particle reconstruction
Overview of EMD-5584
Sample name: Mature Sulfolobus Turreted Icosahedral Virus
Organism: Sulfolobus turreted icosahedral virus
Fitted atomic model: 3j31

Map parameters

Minimum density: -0.191
Maximum density: 0.333
Average density: -0.001
Standard deviation: 0.014
Recommended contour level: 0.05 (author)

Sample information

Sample name: Mature Sulfolobus Turreted Icosahedral Virus
Virus: Sulfolobus turreted icosahedral virus

Validation information

Experimental information

 

Image processing

Applied symmetry: I
Software: Frealign
Number of particles: 8903
Reconstruction protocol: Projection matching
CTF correction: Each particle
Details: The final reconstruction was sharpened with a negative temperature factor of 400A2.

Fitting

Fitting 1
Initial atomic model: 2BBD
Fitting software: CNS
Refinement space: RECIPROCAL
Details: Positional (xyz) minimization and isotropic B factor refinement. Real space refinement was also carried out using Coot.
Fitting 2
Initial atomic model: 4IL7
Fitting software: CNS
Refinement space: RECIPROCAL
Details: Positional (xyz) minimization and isotropic B factor refinement. Real space refinement was also carried out using Coot. Only the N-terminal domain was refined using CNS (residues 3-134). The C-terminal domain (residues 135-222) was only rigid-body fit using Coot and an arbitrary B-factor value of 150 A2 was assigned to it.

Imaging

Session
Microscope model: FEI TITAN KRIOS
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 18.0
Nominal CS (mm): 2.70
Defocus max (nm): 2,500.00
Defocus min (nm): 800.00
Tilt max (degrees): 0.00
Tilt min (degrees): 0.00
Holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Details: Nanoprobe mode was used
Acquisition
Number of images: 878

Specimen

Preparation
Specimen state: particle
Buffer: 23 mM KH2PO4, 19 mM (NH4)2SO4, 1 mM MgSO4, 2 mM CaCl2
Specimen support: glow-discharged C-flat holey carbon grids (CF-2/2-4C, Protochips)
Vitrification
Apparatus: HOMEMADE PLUNGER
Cryogen: ETHANE
Details: Vitrification carried out at room temperature