EMD-5588 Experiments and Validation

Electron cryo-microscopy of the yeast Mediator Cdk8 kinase module

Single particle reconstruction
Overview of EMD-5588
Sample name: Cdk8 kinase module of yeast Mediator complex
Organism: Saccharomyces cerevisiae
Related EM entry by publication: EMD-5589

Map parameters

Recommended contour level: 0.001 (emdb)
Number of grid points: 144 × 144 × 144
Voxel size: 2.10 × 2.10 × 2.10 Å
Minimum density: -0.016
Maximum density: 0.038
Average density: 0.00
Standard deviation: 0.002

Sample information

Sample name: Cdk8 kinase module of yeast Mediator complex
Proteins: Med12, Med13, Cdk8, CycC

Validation information

Experimental information

 

Image processing

Applied symmetry: C1
Software: SPARX, SPIDER
Number of particles: 70000
Reconstruction protocol: projection matching
CTF correction: Each particle

Imaging

Session
Microscope model: FEI TECNAI F20
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 15.0
Nominal CS (mm): 1.20
Nominal magnification: 60000.0
Defocus max (nm): 4,000.00
Defocus min (nm): 1,500.00
Holder model: GATAN LIQUID NITROGEN
Acquisition
Number of images: 154
Scanner model: NIKON SUPER COOLSCAN 9000
Sampling interval (μm): 6.3499999999999996

Specimen

Preparation
Specimen state: particle
Specimen concentration (mg/mL): 0.02
Buffer: 20mM HEPES, 200mM potassium acetate, 5mM beta-mercaptoethanol
Specimen support: 300 mesh Cu/Rh grids with continuous carbon, glow discharged in amylamine atmosphere
Vitrification
Apparatus: HOMEMADE PLUNGER
Cryogen: ETHANE
Humidity: 95