EMPIAR-10169 - CryoET of apoferritin single particle with spot-to-plunge time of 100ms [multiple data sets in MRC and DYNAMO TBL AND OMD FILES formats]

EMPIAR-10169

CryoET of apoferritin single particle with spot-to-plunge time of 100ms [multiple data sets in MRC and DYNAMO TBL AND OMD FILES formats]

Publication:

Reducing effects of particle adsorption to the air-water interface in cryoEM

Noble AJ, Wei H, Dandey VP, Zhang Z, Potter CS, Carragher B

BioRxiv (---)

DOI: 10.1101/288340

Related EMDB entry:

EMD-7623

Deposited:

2018-03-23

Released:

2018-04-05

Last modified:

2018-04-05

Imageset size:

119.33 GB

Imageset DOI:

10.6019/EMPIAR-10169

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
micrographs - single frame
particle picking
tilt series

Image Sets

1. K2 tilt-series frames

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

Image size:

(3710, 3838)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(2.16423, 2.16423)

Details:

~8 e-/px/s dose rate on the camera
Gain and dark references included
Includes tilt-series from the same session (apoferritin at 400ms spot-to-plunge time and insulin-bound insulin receptor at 600ms spot-to-plunge time)

Files:

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

Depending on the number and size of files to be downloaded, this can take an enormous amount of time. Also, this feature is unstable and may not work properly, and checksums of downloaded files are not verified.

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)

2. Whole-frame aligned tilt images along with all other magnification images from the collection

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

Image size:

(3710, 3838)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(2.16423, 2.16423)

Details:

Whole-frame aligned tilt images using Motioncor2.
Includes tilt-series from the same session (apoferritin at 400ms spot-to-plunge time and insulin-bound insulin receptor at 600ms spot-to-plunge time).

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)

3. Manual particle picking in Dynamo

Category:

particle picking

Image format:

DYNAMO TBL AND OMD FILES

No. of images or tilt series:

Image size:

(None, None)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(None, None)

Details:

Binned by 4 manual particle picking of the series0001 tomogram using Dynamo. Manual picking was performed to accurately distinguish between particles adsorbed to the air-water interfaces, non-adsorbed particles, and particles over or adsorbed to carbon.

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)

4. Appion-Protomo tilt-series alignments

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(3710, 3838)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(2.16423, 2.16423)

Details:

Includes a full tilt-series alignment run for all 100ms spot-to-plunge time apoferritin tilt-series.
To view properly, navigate to the protomo_alignments folder in Appion-Protomo.
The export/ directory contains SerialEM-formatted unaligned tilt-series stacks, mdoc files, and tilt files. This allows for easy upload to Appion-Protomo.

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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