EMD-2280 Experiments and Validation

Negative stain EM structure of the HOPS tethering complex (conformation 1)

Single particle reconstruction
Overview of EMD-2280
Sample name: vacuole protein sorting (HOPS) tethering complex containing Vps11, Vps16, Vps18, Vps33, Vp39, Vps41
Organism: Saccharomyces cerevisiae

Map parameters

Minimum density: -0.027
Maximum density: 0.075
Average density: 0.00
Standard deviation: 0.004
Recommended contour level: 0.018 (author)

Sample information

Sample name: vacuole protein sorting (HOPS) tethering complex containing Vps11, Vps16, Vps18, Vps33, Vp39, Vps41
Proteins: vacuolar protein sorting-associated protein 41, vacuolar protein sorting-associated protein 39, vacuolar protein sorting-associated protein 33, vacuolar protein sorting-associated protein 18, vacuolar protein sorting-associated protein 11, vacuolar protein sorting-associated protein 16

Validation information

Experimental information

 

Image processing

Applied symmetry: C1
Software: SPARX
Number of particles: 2979
Reconstruction protocol: Projection matching

Imaging

Session
Microscope model: JEOL 1400
Electron source: LAB6
Electron dose (e/A**2): 4.5
Nominal CS (mm): 3.40
Nominal magnification: 50000.0
Defocus max (nm): 1.70
Defocus min (nm): 1.30
Holder model: JEOL
Acquisition
Number of images: 920
Scanner model: OTHER
Sampling interval (μm): 10.5

Specimen

Preparation
Specimen state: particle
Buffer: 1 M NaCl, 50 mM Hepes/NaOH, 10% glycerol
Staining procedure: Grids with adsorbed Protein floated on 0.07% Uranyl Formate for 1-3h at 4C.
Specimen support: glow discharged 400 mesh copper grids with thin carbon support
Vitrification
Apparatus: NONE
Cryogen: NONE