EMD-2347 Experiments and Validation

cryo-EM structure of the NavCt voltage-gated sodium channel

Electron crystallography
Overview of EMD-2347
Sample name: voltage-gated sodium channel
Organism: Caldalkalibacillus thermarum
Fitted atomic model: 4bgn

Map parameters

Recommended contour level: 1.30 (emdb)
Number of grid points: 55 × 55 × 81
Voxel size: 2.09 × 2.09 × 2.22 Å
Minimum density: -5.027
Maximum density: 6.82
Average density: 0.003
Standard deviation: 0.993

Sample information

Sample name: voltage-gated sodium channel
Protein: voltage-gated sodium channel

Validation information

Experimental information

 

Image processing

Software: MRC
CTF correction: Each micrographs

Fitting

Initial atomic model: 3RVY
Fitting software: CNS
Refinement space: REAL

Imaging

Session
Microscope model: JEOL KYOTO-3000SFF
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 20.0
Nominal CS (mm): 1.60
Nominal magnification: 40000.0
Defocus max (nm): 3,820.00
Defocus min (nm): 910.00
Tilt max (degrees): 60.00
Tilt min (degrees): 0.00
Holder model: JEOL
Acquisition
Number of images: 77
Scanner model: ZEISS SCAI
Sampling interval (μm): 7.0

Specimen

Preparation
Specimen state: twoDArray
Specimen concentration (mg/mL): 4.00
Buffer: 50mM glycine-NaOH pH9.0, 200mM NaCl, 4mM MgCl2, 5% glycerol, 5% methyl-2,4-pentanediol, 1.5mM NaN3
Specimen support: molybdenum EM grid
Crystal grow: Crystals grown by dialysis
Aggregation parameters (crystal parameters)
Plane group: P 4
Unit cell length A (Å): 115.0
Unit cell length B (Å): 115.0
Unit cell angle gamma (degrees): 90.0
Vitrification
Apparatus: LEICA KF80
Cryogen: NITROGEN