EMD-2048
Cryo-EM structure of the UPF-EJC complex
EMD-2048
Single-particle16.0 Å
Deposition: 13/03/2012Map released: 10/04/2012
Last modified: 30/03/2016
Concentration: 0.175
mg/mL
Buffer
pH: 7.5
Details: 50 mM K-phosphate,150 mM NaCl, 3 mM MgCl2, 20% sucrose, 0.1% glutaraldehyde
Details: 50 mM K-phosphate,150 mM NaCl, 3 mM MgCl2, 20% sucrose, 0.1% glutaraldehyde
Grid
Details: Quantifoil grids (R2/2) with thin carbon film on top
Vitrification
Cryogen name: ETHANE
Chamber humidity: 95%
Instrument: FEI VITROBOT MARK III
Method: Manual Application (3.5 microliters) Humidifier Off During Process Blot offset: -2 mm Blot Total: 2 Blot Time: 2 s Wait Time: 30 s Drain Time: 1 s
Chamber humidity: 95%
Instrument: FEI VITROBOT MARK III
Method: Manual Application (3.5 microliters) Humidifier Off During Process Blot offset: -2 mm Blot Total: 2 Blot Time: 2 s Wait Time: 30 s Drain Time: 1 s
Microscope: JEOL 2200FS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 200 kV
Nominal CS: 2.0 mm
Nominal defocus: 1.112 µm - 4.0 µm
Nominal magnification: 50000.0
Calibrated magnification: 69494.0
Specimen holder model: GATAN LIQUID NITROGEN
Specimen holder details: Eucentric. 626 cryo-holder (Gatan Inc., Warrendale, PA, USA)
Alignment procedure: LEGACY (Astigmatism: Objective lens astigmatism was corrected calculating the Fourier Transform of the CCD frames. Phase flipping, Electron beam tilt params: )
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 200 kV
Nominal CS: 2.0 mm
Nominal defocus: 1.112 µm - 4.0 µm
Nominal magnification: 50000.0
Calibrated magnification: 69494.0
Specimen holder model: GATAN LIQUID NITROGEN
Specimen holder details: Eucentric. 626 cryo-holder (Gatan Inc., Warrendale, PA, USA)
Alignment procedure: LEGACY (Astigmatism: Objective lens astigmatism was corrected calculating the Fourier Transform of the CCD frames. Phase flipping, Electron beam tilt params: )
Temperature
Minimum: 83
K
Average: 91.5 K
Maximum: 100 K
Average: 91.5 K
Maximum: 100 K
Specialist optics
Energy filter
Image Recording
[1]
Detector category:
CCD
Detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Sampling interval: 15 µm
Average electron dose per image: 15 e/Å2
Bits per pixel: 16.0
Details: 0.22 nm per pixel, final sampling
Detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Sampling interval: 15 µm
Average electron dose per image: 15 e/Å2
Bits per pixel: 16.0
Details: 0.22 nm per pixel, final sampling
Final
reconstruction
Resolution: 16.0
Å
(
BY AUTHOR)
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 85000
Algorithm: OTHER
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 85000
Algorithm: OTHER
⌯ Applied Symmetry
Point group:
C1
Software
[1]
| Name | Version | Details |
|---|---|---|
| EMAN, XMIPP, SPIDER, BSOFT | - | - |
CTF correction
Details:Each CCD Frame using BSOFT
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Cryo-EM reconstruction of the nonsense-mediated mRNA decay (NMD) complex containing proteins UPF1, UPF2, UPF3 and the Exon Junction Complex (EJC).
Details: ::::EMDATABANK.org::::EMD-2048::::
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Cryo-EM reconstruction of the nonsense-mediated mRNA decay (NMD) complex containing proteins UPF1, UPF2, UPF3 and the Exon Junction Complex (EJC).
Details: ::::EMDATABANK.org::::EMD-2048::::
⬡ Geometry
| X | Y | Z | |
|---|---|---|---|
| Dimensions | 136 | 136 | 136 |
| Origin | 0 | 0 | 0 |
| Spacing | 136 | 136 | 136 |
| Voxel size | 2.2 Å | 2.2 Å | 2.2 Å |
Contour list
| Primary | Level | Source |
|---|---|---|
| True | 2.4 | AUTHOR |