EMD-2301 Experiments and Validation

Negative stain EM structure of TcdA1 in pore state

Single particle reconstruction
Overview of EMD-2301
Sample name: TcdA1
Organism: Photorhabdus luminescens
Related EM entries by publication: EMD-2297, EMD-2298, EMD-2299, EMD-2300

Map parameters

Recommended contour level: 0.038 (author)
Number of grid points: 112 × 112 × 112
Voxel size: 4.64 × 4.64 × 4.64 Å
Minimum density: -0.016
Maximum density: 0.158
Average density: 0.001
Standard deviation: 0.008

Sample information

Sample name: TcdA1
Protein: TcdA1

Validation information

Experimental information


Image processing

Applied symmetry: C5
Software: Sparx
Number of particles: 1936
Reconstruction protocol: Projection Matching


Microscope model: JEOL 1400
Electron source: LAB6
Nominal CS (mm): 3.40
Nominal magnification: 50000.0
Defocus max (nm): 2.00
Defocus min (nm): 1.20
Holder model: JEOL
Number of images: 80


Specimen state: particle
Specimen concentration (mg/mL): 0.02
Buffer: 50 mM CAPS, mM NaCl, 0.05% Tween-20, 5% glycerol
Staining procedure: Grids with adsorbed Protein floated on 0.07% Uranyl Formate for 45 sec.
Specimen support: glow discharged 400 mesh copper grids with thin carbon support
Apparatus: NONE
Cryogen: NONE