EMD-5389

Single-particle
25.0 Å
EMD-5389 Deposition: 06/02/2012
Map released: 03/04/2013
Last modified: 10/04/2013
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-5389

An RNA Degradation Machine Sculpted by Ro Autoantigen and Noncoding RNA

EMD-5389

Single-particle
25.0 Å
EMD-5389 Deposition: 06/02/2012
Map released: 03/04/2013
Last modified: 10/04/2013
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
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
Staining
Type: NEGATIVE
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
Vitrification
Cryogen name: NONE
Instrument: OTHER
Microscopy [1]
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: )
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
Image processing [1]
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:
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
Map
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::::
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