EMPIAR-10421 - Single-Particle CryoEM of Human Apoferritin Light Chain Vitrified Using Back-it-up [multiple data sets in MRCS and MRC formats]

EMPIAR-10421

Single-Particle CryoEM of Human Apoferritin Light Chain Vitrified Using Back-it-up [multiple data sets in MRCS and MRC formats]

Publication:

Through-grid wicking enables high-speed cryoEM specimen preparation

Tan YZ, Rubinstein JL

bioRxiv (2020)

DOI: 10.1101/2020.05.03.075366

Related EMDB entry:

EMD-21951

Deposited:

2020-05-13

Released:

2021-05-17

Last modified:

2021-05-17

Imageset size:

2.07 TB

Imageset DOI:

10.6019/EMPIAR-10421

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
micrographs - single frame
picked particles - multiframe - processed

Image Sets

1. Unaligned Falcon IV movie frames

Category:

micrographs - multiframe

Image format:

MRCS

No. of images or tilt series:

3168

Image size:

(4096, 4096)

Pixel type:

SIGNED 16 BIT INTEGER

Pixel spacing:

(0.816, 0.816)

Details:

3,168 movies were acquired from two grids of apoferritin prepared with BIU. The pixel size was calibrated at 0.816 Å/pixel by fitting a crystal structure of human ferritin L chain (PDB ID: 2FFX) into a preliminary 3D map. Movies were collected for 9 sec with 29 exposure fractions, a camera exposure rate of ~3 e-/pix/sec, and total specimen exposure of ~40 e-/Å^2. Note: Due to software issues, the last frames in these raw movies have errors. Please exclude the last frame (frame 30) when doing any alignments.

Files:

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2. Aligned Dose-Weighted Micrographs

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

3168

Image size:

(4096, 4096)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.816, 0.816)

Details:

Exposure fractions were aligned with MotionCor2 within Relion, using 7x7 patches and a B factor of 500 pixel^2 for global alignment and 150 pixel^2 for local alignment. There is a micrographs_ctf.star file with CTF estimation from CTFFind4. Note: Due to software issues, the last frames in these raw movies have errors. Please exclude the last frame (frame 30) when doing any alignments.

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. Final Particle Stack with Final Euler Angles and Shifts

Category:

picked particles - multiframe - processed

Image format:

MRCS

No. of images or tilt series:

Image size:

(288, 288)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.816, 0.816)

Details:

Final polished particle stack with Euler angles and shifts. Higher order CTF aberration corrections were done within CryoSPARC 2 but the resulting parameters were not able to be exported to .star format here. When using this particle stack, it is recommended to do higher order CTF aberration corrections again in CryoSPARC/Relion to obtain the best resolution.

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)

The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation.

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