EMD-5389
An RNA Degradation Machine Sculpted by Ro Autoantigen and Noncoding RNA
EMD-5389
Single-particle25.0 Å
Deposition: 06/02/2012
Map released: 03/04/2013
Last modified: 10/04/2013
Concentration: 0.1
mg/mL
Buffer
pH: 7.5
Details: 20 mM HEPES, 50 mM NaCl, 2 mM beta-mercaptoethanol, 1 mM MgCl2, 1 mM MnCl2, 1 mM Petabloc
Details: 20 mM HEPES, 50 mM NaCl, 2 mM beta-mercaptoethanol, 1 mM MgCl2, 1 mM MnCl2, 1 mM Petabloc
Staining
Type:
NEGATIVE
Details: Grids with adsorbed protein were stained consecutively with 3 droplets of 2% w/v uranyl acetate for 10 seconds each.
Details: Grids with adsorbed protein were stained consecutively with 3 droplets of 2% w/v uranyl acetate for 10 seconds each.
Grid
Details: Homemade 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: 2.3 mm
Nominal defocus: 0.8 µm - 1.2 µm
Nominal magnification: 49000.0
Specimen holder model: OTHER
Alignment procedure: LEGACY (Astigmatism: object lens astigmatism was corrected at 42,000 magnification, Electron beam tilt params: )
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: LAB6
Acceleration voltage: 120 kV
Nominal CS: 2.3 mm
Nominal defocus: 0.8 µm - 1.2 µm
Nominal magnification: 49000.0
Specimen holder model: OTHER
Alignment procedure: LEGACY (Astigmatism: object lens astigmatism was corrected at 42,000 magnification, Electron beam tilt params: )
Image Recording
[1]
Detector category:
CCD
Detector model: TVIPS TEMCAM-F416 (4k x 4k)
Number of real images: 40
Average electron dose per image: 20 e/Å2
Detector model: TVIPS TEMCAM-F416 (4k x 4k)
Number of real images: 40
Average electron dose per image: 20 e/Å2
Details: The particles were selected manually using boxer in EMAN.
Final
reconstruction
Resolution: 25.0
Å
(
BY AUTHOR)
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 9000
Algorithm: OTHER
Details:
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 9000
Algorithm: OTHER
Details:
⌯ Applied Symmetry
Point group:
C1
Software
[1]
Name | Version | Details |
---|---|---|
LEGINON, EMAN2, SPARX | - | - |
Final 2D classification
Number of classes:
50
CTF correction
Details:Each particle in IMAGIC
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Negative stain single particle reconstruction of GraFix-prepared Rsr/Y RNA/PNPase complex
Details: ::::EMDATABANK.org::::EMD-5389::::
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Negative stain single particle reconstruction of GraFix-prepared Rsr/Y RNA/PNPase complex
Details: ::::EMDATABANK.org::::EMD-5389::::
⬡ Geometry
X | Y | Z | |
---|---|---|---|
Dimensions | 72 | 72 | 72 |
Origin | 0 | 0 | 0 |
Spacing | 72 | 72 | 72 |
Voxel size | 4.36 Å | 4.36 Å | 4.36 Å |
Contour list
Primary | Level | Source |
---|---|---|
True | 3.67 | AUTHOR |