EMD-5603 Experiments and Validation

Substrate-specific structural rearrangements of human Dicer

Single particle reconstruction
Overview of EMD-5603
Sample name: Human Dicer in complex with pre-let7
Organism: Homo sapiens
Related EM entries by publication: EMD-5605, EMD-5604, EMD-5606, EMD-5601, EMD-5602

Map parameters

Minimum density: -3.641
Maximum density: 15.154
Average density: 0.00
Standard deviation: 1.00
Recommended contour level: 2.95 (author)

Sample information

Sample name: Human Dicer in complex with pre-let7
Nucleic acid: pre-let7
Protein: Endoribonuclease Dicer

Validation information

Experimental information

 

Image processing

Applied symmetry: C1
Software: EMAN2/SPARX
Number of particles: 4100
Reconstruction protocol: back projection
CTF correction: each micrograph

Imaging

Session
Microscope model: JEOL 3100FFC
Electron source: FIELD EMISSION GUN
Electron dose (e/A**2): 20.0
Energy filter: JEOL
Energy window (eV): 0.00
Nominal CS (mm): 3.70
Nominal magnification: 60000.0
Defocus max (nm): 0.00
Defocus min (nm): 0.00
Holder model: JEOL
Acquisition
Number of images: 800

Specimen

Preparation
Specimen state: particle
Specimen concentration (mg/mL): 0.05
Buffer: 20 mM HEPES, pH 7.5, 150 mM KCl, 3 mM EDTA, 1 mM DTT, and 2.5% glycerol
Specimen support: glow-discharged Quantifoil R 1.2/1.3 MO 200 mesh holey carbon grids
Vitrification
Apparatus: FEI VITROBOT MARK IV
Cryogen: ETHANE
Humidity: 100
Protocol: The samples were automatically blotted for 4-5 s at -2.5 mm offset before plunging.