EMD-5623 Experiments and Validation

3D reconstruction of archaeal 20S proteasome

Single particle reconstruction
Overview of EMD-5623
Sample name: Thermoplasma acidophilum 20S proteasome
Organism: Thermoplasma acidophilum
Fitted atomic model: 3j9i

Map parameters

Recommended contour level: 0.25 (author)
Number of grid points: 256 × 256 × 256
Voxel size: 1.22 × 1.22 × 1.22 Å
Minimum density: -0.555
Maximum density: 1.20
Average density: -0.008
Standard deviation: 0.049

Sample information

Sample name: Thermoplasma acidophilum 20S proteasome
Protein: 20S proteasome

Validation information

Experimental information

 

Image processing

Applied symmetry: D7
Software: FREALIGN
Number of particles: 126729
CTF correction: each particle

Fitting

Initial atomic model: 1PMA
Fitting software: Chimera, MDFF
Fitting protocol: flexible
Refinement space: REAL

Imaging

Session
Microscope model: FEI POLARA 300
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 20.0
Nominal CS (mm): 2.00
Nominal magnification: 31000.0
Defocus max (nm): 1,900.00
Defocus min (nm): 800.00
Tilt max (degrees): 0.00
Tilt min (degrees): 0.00
Holder model: SIDE ENTRY, EUCENTRIC
Details: Images were recorded in dose-fractionated format using K2 Summit operated in counting and super-resolution mode. Motion correction was performed for each image.
Acquisition
Number of images: 600

Specimen

Preparation
Specimen state: particle
Specimen support: Quantifoil grid
Vitrification
Apparatus: FEI VITROBOT MARK III
Cryogen: ETHANE
Humidity: 100