EMD-20437 Experiments and Validation

Kaposi's sarcoma-associated herpesvirus (KSHV), C12 portal dodecamer structure

Single particle reconstruction
Overview of EMD-20437
Sample name: Human gammaherpesvirus 8
Organisms: Human gammaherpesvirus 8, HHV-8
Fitted atomic model: 6ppi
Related EM entries by publication: EMD-20430, EMD-20431, EMD-20432, EMD-20433, EMD-20436

Map parameters

Recommended contour level: 0.015 (author)
Number of grid points: 192 × 192 × 192
Voxel size: 1.03 × 1.03 × 1.03 Å
Minimum density: -0.022
Maximum density: 0.038
Average density: 0.003
Standard deviation: 0.004

Sample information

Sample name: Human gammaherpesvirus 8
Protein: Portal protein
Virus: Human gammaherpesvirus 8

Validation information

Experimental information

 

Image processing

Applied symmetry: C12
Software: RELION
Number of particles: 39073
Reconstruction protocol: FOURIER SPACE

Fitting

Target criteria: Correlation coefficient
Overall B value: 200.0
Refinement space: REAL

Imaging

Session
Microscope model: FEI TITAN KRIOS
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 25.0
Nominal CS (mm): 2.70
Nominal magnification: 14000.0
Holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Acquisition
Number of images: 8007
Sampling interval (μm): 2.5

Specimen

Preparation
Specimen state: particle
Vitrification
Apparatus: HOMEMADE PLUNGER
Cryogen: ETHANE
Details: The sample was manually blotted and frozen with a homemade plunger..