EMPIAR-10493 - Subtomogram averaging and classification of SARS-CoV-2 Spike Proteins on intact virions [multiple data sets in TIFF and MRC formats]

EMPIAR-10493

Subtomogram averaging and classification of SARS-CoV-2 Spike Proteins on intact virions [multiple data sets in TIFF and MRC formats]

Publication:

Structures and distributions of SARS-CoV-2 spike proteins on intact virions.

Ke Z, Oton J, Qu K, Cortese M, Zila V, McKeane L, Nakane T, Zivanov J, Neufeldt CJ, Cerikan B, Lu JM, Peukes J, Xiong X, Kräusslich HG, Scheres SHW, Bartenschlager R, Briggs JAG

Nature (2020)

PMID: 32805734

DOI: 10.1038/s41586-020-2665-2

Related EMDB entry:

EMD-11494 EMD-11493 EMD-11496 EMD-11495

Deposited:

2020-08-05

Released:

2020-08-19

Last modified:

2020-08-19

Imageset size:

372.39 GB

Imageset DOI:

10.6019/EMPIAR-10493

Experimental metadata:

Download xml json

Contains:

tilt series

Image Sets

1. Unaligned Frames from the microscope. Data were recorded

Category:

tilt series

Image format:

TIFF

No. of images or tilt series:

156

Image size:

(3710, 3838)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(1.532, 1.532)

Details:

156 tilt series of unconcentrated SARS-CoV-2 virions with the raw frames. The Frames collected from Titan Krios operated at 300 kV using a Gatan K2 camera. The energy filter used was 20 eV. Data collection was done in SerialEM 3.8.0 using the dose-symmetric scheme (Tilt Series Controler), 3 degrees per tilt step, +/- 60 degrees. 10 Frames were saved per each tilt image. The exposure dose per tilt image is 3.0 electrons per angstrom squared. See mdoc files for the order of the images acquired.

Please use data/gainRef/CountRef_TS_001_000_-0.0.dm4 as the gain reference.
Please see data/mdoc folder for the metadata of the 156 tilt series of unconcentrated SARS-CoV-2 virions

Files:

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2. Aligned and order sorted stack of the tilt series. This is not dose-filtered stack. Associated mdoc files are included in this folder.

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

156

Image size:

(3710, 3838)

Pixel type:

SIGNED 16 BIT INTEGER

Pixel spacing:

(1.532, 1.532)

Details:

156 tilt series of unconcentrated SARS-CoV-2 virions with aligned stacks and associated mdoc files. The stacks are sorted and not dose-filtered. Data collection was done in SerialEM 3.8.0 using the dose-symmetric scheme (Tilt Series Controler), 3 degrees per tilt step, +/- 60 degrees. The exposure dose per tilt image is 3.0 electrons per angstrom squared. Motion correction was done using alignframes command in IMOD 4.10.30 and the raw frames are in the data/Frames folder.

Files:

Archives and downloads the selected files into an uncompressed zip file.

We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

It is possible to download files by specifying the file list with rsync command, etc.

rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

Browse All Files

Files:

Archives and downloads the selected files into an uncompressed zip file.

We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

It is possible to download files by specifying the file list with rsync command, etc.

rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

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Gusach A, Lee Y, Khoshgrudi AN, Mukhaleva E, Ma N, Koers EJ, Chen Q, Edwards PC, Huang F, Kim J, Mancia F, Veprintsev DB, Vaidehi N, Weyand SN, Tate CG. (2024)

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