EMD-1232
Structure of the Sec13-31 COPII coat cage.
EMD-1232
Single-particle30.0 Å
Deposition: 26/05/2006Map released: 05/06/2006
Last modified: 22/07/2011
Concentration: 0.9
mg/mL
Buffer
pH: 6.5
Details: 50mM MES pH 6.5, 225mM KOAc, 1mM MgCl2
Details: 50mM MES pH 6.5, 225mM KOAc, 1mM MgCl2
Grid
Details: Quantifoil 2/2, 400 mesh copper grid
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 93 K
Instrument: OTHER
Method: Temperature of chamber was 4 degrees C. 0 seconds drain time. Single blot. 0 mm offset. 4 ul sample applied to grid. Blot for 3.0 seconds before plunging.
Details: Vitrification instrument: FEI Vitrobot. Grid plasma cleaned for 30s with Fischione 1020 plasma cleaner using 75-25 Argon-Oxygen mix.
Chamber humidity: 100%
Chamber temperature: 93 K
Instrument: OTHER
Method: Temperature of chamber was 4 degrees C. 0 seconds drain time. Single blot. 0 mm offset. 4 ul sample applied to grid. Blot for 3.0 seconds before plunging.
Details: Vitrification instrument: FEI Vitrobot. Grid plasma cleaned for 30s with Fischione 1020 plasma cleaner using 75-25 Argon-Oxygen mix.
Microscope: FEI TECNAI 20
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 200 kV
Nominal CS: 2 mm
Nominal defocus: 0.8 µm - 2.5 µm
Nominal magnification: 50000.0
Specimen holder model: GATAN LIQUID NITROGEN
Specimen holder details: Side entry liquid nitrogen-cooled cryo specimen holder.
Alignment procedure: LEGACY (Astigmatism: objective lens astigmatism was corrected at 50,000X magnification, Electron beam tilt params: )
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 200 kV
Nominal CS: 2 mm
Nominal defocus: 0.8 µm - 2.5 µm
Nominal magnification: 50000.0
Specimen holder model: GATAN LIQUID NITROGEN
Specimen holder details: Side entry liquid nitrogen-cooled cryo specimen holder.
Alignment procedure: LEGACY (Astigmatism: objective lens astigmatism was corrected at 50,000X magnification, Electron beam tilt params: )
Temperature
Average: 94
K
Image Recording
[1]
Detector category:
CCD
Detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Average electron dose per image: 20 e/Å2
Bits per pixel: 16.0
Detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Average electron dose per image: 20 e/Å2
Bits per pixel: 16.0
Details: The images were acquired using the Leginon automated data aquisition system. The particles were automatically selected using the Selexon package. The CTF was automatically estimated using the ACE package
Final
reconstruction
Resolution: 30.0
Å
(
BY AUTHOR)
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 9777
Algorithm: OTHER
Details:
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 9777
Algorithm: OTHER
Details:
⌯ Applied Symmetry
Point group:
O
Software
[1]
| Name | Version | Details |
|---|---|---|
| EMAN | - | - |
Final 2D classification
Number of classes:
92
CTF correction
Details: Phase correction for each particle.
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: This is a 30 angstrom resolution map of the self-assembing Sec13/31 cage.
Details: ::::EMDATABANK.org::::EMD-1232::::
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: This is a 30 angstrom resolution map of the self-assembing Sec13/31 cage.
Details: ::::EMDATABANK.org::::EMD-1232::::
⬡ Geometry
| X | Y | Z | |
|---|---|---|---|
| Origin | -96 | -96 | -96 |
| Dimensions (px) | 192 | 192 | 192 |
| Dimensions (Å) | 868.992 | 868.992 | 868.992 |
| Voxel size (Å) | 4.526 | 4.526 | 4.526 |
Contour list
| Primary | Level | Source |
|---|---|---|
| True | 5.0 | EMDB |