EMPIAR-10171 - CryoET of apoferritin with 0.5 mM TCEP single particle with spot-to-plunge time of 170ms [multiple data sets in MRC and DYNAMO TBL AND OMD FILES formats]

EMPIAR-10171

CryoET of apoferritin with 0.5 mM TCEP single particle with spot-to-plunge time of 170ms [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-7627

Deposited:

2018-04-03

Released:

2018-04-05

Last modified:

2018-04-05

Imageset size:

33.96 GB

Imageset DOI:

10.6019/EMPIAR-10171

Experimental metadata:

Download xml json

Contains:

tilt series
particle picking

Image Sets

1. Tilt-series image stacks

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(3712, 4984)

Pixel type:

SIGNED 16 BIT INTEGER

Pixel spacing:

(2.34, 2.34)

Details:

Not frame-aligned.
.mdoc files included.

Files:

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2. 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:

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3. Appion-Protomo tilt-series alignments

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(3712, 4984)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(2.34, 2.34)

Details:

Includes a full tilt-series alignment run for each tilt-series. To view properly, navigate to the protomo_alignments folder in 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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Citations

High-resolution ab initio reconstruction enables cryo-EM structure determination of small particles

Kim K, Li H, Clarke OB. (2025)

CLEM-Reg: an automated point cloud-based registration algorithm for volume correlative light and electron microscopy.

Krentzel D, Elphick M, Domart MC, Peddie CJ, Laine RF, Shand C, Henriques R, Collinson LM, Jones ML. (2025)

CryoEMNet driven symmetry-aware molecular reconstruction through deep learning enhanced electron microscopy.

Arora S, Pan SH, Kumar S, Singh SK, Chauhan U, Alhalabi W, Arya V, Alsulami BS, Hsu CH, Chui KT, Gupta BB. (2025)

PERC: a suite of software tools for the curation of cryoEM data with application to simulation, modeling and machine learning.

Costa-Gomes B, Greer J, Juraschko N, Parkhurst J, Mirecka J, Famili M, Rangel-Smith C, Strickson O, Lowe A, Basham M, Burnley T. (2025)

Self-supervised learning for generalizable particle picking in cryo-EM micrographs.

Zamanos A, Koromilas P, Bouritsas G, Kastritis PL, Panagakis Y. (2025)

Laser flash melting cryo-EM samples to overcome preferred orientation.

Straub MS, Harder OF, Mowry NJ, Barrass SV, Hruby J, Drabbels M, Lorenz UJ. (2025)

In situ structure determination of conformationally flexible targets using nextPYP.

Liu HF, Zhou Y, Huang Q, Martin J, Bartesaghi A. (2025)

EMICSS: added-value annotations for EMDB entries.

Duraisamy AK, Fonseca N, Kleywegt GJ, Patwardhan A, Morris KL. (2025)

Global conformations of <i>Pichia pastoris</i> complex I are distinguished by the binding of a unique interdomain bridging subunit.

Lee CS, Grba DN, Wright JJ, Ivanov BS, Hirst J. (2025)

Overcoming Preferred Orientation in Cryo-EM With Ultrasonic Excitation During Vitrification

Williams HM, Curtis WA, Haubner M, Hruby J, Drabbels M, Lorenz UJ. (2025)

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