EMPIAR-13912 - Cryo electron tomography of yeast FIB-milled lamella after sublimation [multiple data sets in MRC format]

EMPIAR-13912

Cryo electron tomography of yeast FIB-milled lamella after sublimation [multiple data sets in MRC format]

Publication:

In-Chamber Sublimation: A Hands-On Hack to Beat Ice and Curtaining in Cryo-Electron Tomography Lamella Prep

Bondy AL, Valentin Gese G, Thersleff T, Hallberg BM

(---)

Related EMDB entry:

Deposited:

2026-09-06

Released:

2026-10-07

Last modified:

2026-10-07

Imageset size:

1.71 TB

Imageset DOI:

10.6019/EMPIAR-13912

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe

Image Sets

1. Unaligned multi-frame micrographs of FIB-milled yeast lamella, long post-milling sublimation

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

Image size:

(11520, 8184)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(1.34, 1.34)

Details:

MDOC files for each tilt-series are in the folder "MDOC".
Movie averages after WARP 1.0.9 processing (bin 1, pixel size 2.68) are in the folder "average".
Aretomo-reconstructed tomograms (10.72 A/px), tilt-series alignments (*.xf) and other aretomo output files are in the folder "aretomo".
WARP-reconstructed tomograms (16.08 A/px) are in the folder reconstruction.
Subtomograms exported by M, as well as CTF files, are in the folder "subtomo". The corresponding particle coordinates and poses after RELION 5 refinement are in the file run_data.star.

Files:

This entry cannot be downloaded from PDBj.

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. Unaligned multi-frame micrographs of FIB-milled yeast lamella, short post-milling sublimation

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

Image size:

(11520, 8184)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(1.34, 1.34)

Details:

Files:

This entry cannot be downloaded from PDBj.

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

Quick Links

Browse EMPIAR

Sample Preparation Widget

Volume Browser

Tomo Viewer Prototype

Claim entries to your ORCiD

Talks and Tutorials

EMPIAR Quick tour

Publications

Re-use study

Statistics

EMPIAR in the news

COVID-19 Data Portal

EMDB

BioImage Archive

PDBe

EMNavigator@PDBj

PDBj

Citations

Post-acquisition super resolution for cryo-electron microscopy.

Burton Smith RN, Murata K. (2026)

Structural heterogeneity of CTE Type I tau filaments with an interface-shifted polymorph

Watanabe R, Lee EB. (2026)

Ligand-induced activation of RyR1 in native membranes.

Mikirtumov V, Golusik S, Huo R, Sprink T, Balyschew N, Yang W, Diebolder C, Yuan S, Kotecha A, Kudryashev M. (2026)

QwenCryoMarker: a universal post-processing framework for contamination-aware particle cleaning.

Sun Y, Zhao J, Xu N, Wang L, Ding W, Li M. (2026)

CryoMV: Structure-Prior-Guided Modeling and Real-Particle Validation of Continuous Conformational Transitions in Cryo-EM

Li F, Dong H, Tang S, Wang X, Zhang C, Ji C, Han R, Zhang F, Wan X. (2026)

An unattended image-processing pipeline for on-the-fly quality assessment and 3D exploration in cryo-EM.

Marchán Torres D, Conesa P, Garcia A, Iceta M, Broche L, Gragera M, Linares R, Kwong HS, Chichón FJ, Svensson O, Arranz R, Effantin G, Kandiah E, Carazo JM, Sorzano COS. (2026)

AlignPCA-2D: PCA-reduced Euclidean vector alignment for 2D classification in cryo-EM.

Ramírez-Aportela E, Zarrabeitia OL, Fonseca YC, Ceska T, Subramaniam S, Carazo JM, Sorzano COS. (2026)

A variational framework with composite sparse regularization for cryo-electron tomography reconstruction.

Yu C, Xu Z, Zeng Q, Wan X, El-Messiry H, Zhang F, Han R. (2026)

Helical reconstruction of amyloids in cryoSPARC.

Schaefer JH, O'Neill RT, Donnelly JP, Powers ET, Kelly JW, Lander GC. (2026)

CryoFSL: an annotation-efficient, few-shot learning framework for robust protein particle picking in cryo-electron microscopy micrographs.

Poudel B, Gyawali R, Dhakal A, Cheng J, Xu D. (2026)

See all citations

Protein Data Bank Japan News

[2026-10-07]

308 new PDB entries have been released on 2026-10-07.