EMD-5606
Substrate-specific structural rearrangements of human Dicer
EMD-5606
Single-particle26.0 Å
Deposition: 10/03/2013Map released: 01/05/2013
Last modified: 19/06/2013
Concentration: 0.01
mg/mL
Buffer
pH: 7.4
Details: 20 mM HEPES, pH 7.5, 150 mM KCl, 3 mM EDTA, 1 mM DTT, and 2.5% glycerol
Details: 20 mM HEPES, pH 7.5, 150 mM KCl, 3 mM EDTA, 1 mM DTT, and 2.5% glycerol
Staining
Type:
NEGATIVE
Details: After adsorption for 1 min, we stained the samples consecutively with three droplets of 2% (w/v) uranyl formate solution, blotted off the residual stain and air-dried the sample in a hood.
Details: After adsorption for 1 min, we stained the samples consecutively with three droplets of 2% (w/v) uranyl formate solution, blotted off the residual stain and air-dried the sample in a hood.
Grid
Details: Glow-discharged holey carbon grids with a thin layer of carbon over the holes
Microscope: FEI TECNAI 12
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: LAB6
Acceleration voltage: 120 kV
Nominal CS: 5.2 mm
Nominal defocus: 0.4 µm - 1.5 µm
Nominal magnification: 50000.0
Specimen holder model: OTHER
Alignment procedure: LEGACY (Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification, Electron beam tilt params: )
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: LAB6
Acceleration voltage: 120 kV
Nominal CS: 5.2 mm
Nominal defocus: 0.4 µm - 1.5 µm
Nominal magnification: 50000.0
Specimen holder model: OTHER
Alignment procedure: LEGACY (Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification, Electron beam tilt params: )
Image Recording
[1]
Detector category:
CCD
Detector model: GENERIC TVIPS (4k x 4k)
Number of real images: 400
Average electron dose per image: 20 e/Å2
Detector model: GENERIC TVIPS (4k x 4k)
Number of real images: 400
Average electron dose per image: 20 e/Å2
Final
reconstruction
Resolution: 26.0
Å
(
BY AUTHOR)
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 10000
Algorithm: OTHER
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 10000
Algorithm: OTHER
⌯ Applied Symmetry
Point group:
C1
Software
[1]
| Name | Version | Details |
|---|---|---|
| EMAN2/SPARX, multi-model | - | - |
CTF correction
Details:Each micrograph
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Negative stain EM reconstruction of Dicer-PACT in the open conformation
Details: ::::EMDATABANK.org::::EMD-5606::::
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Negative stain EM reconstruction of Dicer-PACT in the open conformation
Details: ::::EMDATABANK.org::::EMD-5606::::
⬡ Geometry
| X | Y | Z | |
|---|---|---|---|
| Dimensions | 80 | 80 | 80 |
| Origin | 0 | 0 | 0 |
| Spacing | 80 | 80 | 80 |
| Voxel size | 4.36 Å | 4.36 Å | 4.36 Å |
Contour list
| Primary | Level | Source |
|---|---|---|
| True | 4.83 | AUTHOR |