EMD-6272
Single particle cryo-EM structure of rotavirus VP6 at 2.6 Angstroms resolution
EMD-6272
Single-particle2.6 Å
Deposition: 19/02/2015Map released: 04/03/2015
Last modified: 17/02/2016
Concentration: 2.5
mg/mL
Grid
Details: C-Flat 1.2/1.3
Vitrification
Cryogen name: ETHANE
Chamber humidity: 80%
Chamber temperature: 120 K
Instrument: FEI VITROBOT MARK II
Method: Blot for 4-6 seconds.
Chamber humidity: 80%
Chamber temperature: 120 K
Instrument: FEI VITROBOT MARK II
Method: Blot for 4-6 seconds.
Microscope: FEI TITAN KRIOS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.7 mm
Nominal defocus: 0.4 µm - 2.0 µm
Nominal magnification: 29000.0
Calibrated magnification: 48876.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Alignment procedure: LEGACY (Astigmatism: Corrected at 29,000 times magnification, Electron beam tilt params: )
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.7 mm
Nominal defocus: 0.4 µm - 2.0 µm
Nominal magnification: 29000.0
Calibrated magnification: 48876.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Alignment procedure: LEGACY (Astigmatism: Corrected at 29,000 times magnification, Electron beam tilt params: )
Image Recording
[1]
Detector category:
CCD
Detector model: GATAN K2 (4k x 4k)
Number of real images: 531
Average electron dose per image: 100 e/Å2
Details: 130-frame movies, 0.1 seconds per frame, 100e/A2 total dose. Super resolution.
Detector model: GATAN K2 (4k x 4k)
Number of real images: 531
Average electron dose per image: 100 e/Å2
Details: 130-frame movies, 0.1 seconds per frame, 100e/A2 total dose. Super resolution.
Details: Additional 13-fold averaging was performed on top of the I symmetry.
Final
reconstruction
Resolution: 2.6
Å
(
BY AUTHOR)
Resolution method: OTHER
Number of images used: 4000
Algorithm: OTHER
Details: Final map is a 13-fold average of VP6 trimers from the asymmetric unit of the reconstruction of the whole capsid. Data at resolutions higher than 15A were not used for alignments.
Resolution method: OTHER
Number of images used: 4000
Algorithm: OTHER
Details: Final map is a 13-fold average of VP6 trimers from the asymmetric unit of the reconstruction of the whole capsid. Data at resolutions higher than 15A were not used for alignments.
⌯ Applied Symmetry
Point group:
I
Software
[1]
| Name | Version | Details |
|---|---|---|
| TIGRIS, IMAGIC, FREALIGN | - | - |
CTF correction
Details: Each Particle
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Unsharpened reconstruction of rotavirus VP6
Details: ::::EMDATABANK.org::::EMD-6272::::
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Unsharpened reconstruction of rotavirus VP6
Details: ::::EMDATABANK.org::::EMD-6272::::
⬡ Geometry
| X | Y | Z | |
|---|---|---|---|
| Origin | -54 | -54 | -54 |
| Dimensions (px) | 108 | 108 | 108 |
| Dimensions (Å) | 110.484 | 110.484 | 110.484 |
| Voxel size (Å) | 1.023 | 1.023 | 1.023 |
Contour list
| Primary | Level | Source |
|---|---|---|
| True | 0.0198 | AUTHOR |