EMPIAR-10013 - Structure of β-galactosidase at 3.2-Å resolution obtained by cryo-electron microscopy [multiple data sets in MRC and DM4 formats]

EMPIAR-10013

Structure of β-galactosidase at 3.2-Å resolution obtained by cryo-electron microscopy [multiple data sets in MRC and DM4 formats]

Publication:

Structure of beta-galactosidase at 3.2-A resolution obtained by cryo-electron microscopy

Bartesaghi A, Matthies D, Banerjee S, Merk A, Subramaniam S

Pnas 111 (2014) 11709-11714

PMID: 25071206

DOI: doi:10.1073/pnas.1402809111

Related EMDB entry:

EMD-5995

Deposited:

2014-07-23

Released:

2014-08-07

Last modified:

2014-08-07

Imageset size:

442.52 GB

Imageset DOI:

10.6019/EMPIAR-10013

Experimental metadata:

Download xml json

Version history:

2015-07-01

REL

Directory structure reorganized. Entry has now full set of micrographs including frame alignment shifts, particle locations and defoci.

Contains:

micrographs - multiframe

Image Sets

1. Full set of multi-frame micrographs

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

509

Image size:

(7420, 7676)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.6375, 0.6375)

Details:

Full set of multiframe micrographs related to the dataset:10012. Related PDB: 3J7H.
Please note that the number of frames varies between [5, 10, 25 and 38]!
Although the image files are in MRC format, they have been compressed to save space. They can be uncompresssed using for example: for f in *.tbz; do tar -xjf $f -C mrc/ ; done
Image files are numbered: BGal_000000_frames.tbz to BGal_000508_frames.tbz
Frame alignment shifts in IMOD's transform format: BGal_000000.xf to BGal_000508.xf
Picked particle locations in EMAN's boxer format: BGal_000000.box to BGal_000508.box
Defocus per image in Angstroms: BGal_defocus.txt
Additional details:
Cs : 2.7
Anisotropic magnification (if known) ? : N/A
frame rate : 2.5 to .33 frames/s
dose per frame : 1.2 to 9 e-/A^2
alignment method/software : 10.1073/pnas.1402809111
which frame used for alignment reference: middle frame
particle selection software : 10.1073/pnas.1402809111

Files:

選択したファイルを無圧縮zipファイルにアーカイブ化してダウンロードします。

ダウンロードするファイル数やサイズによっては、膨大な時間がかかります。また、この機能は不安定で正常に動作しない可能性があり、ダウンロードされたファイルのチェックサムは検証されません。

rsync、aspera、globus 等の利用をおすすめします。

選択したファイルのリストをダウンロードします。

rsyncコマンド等でファイルリストを指定してダウンロードすることが可能です。

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

2. Sample set of multi-frame micrographs

Category:

micrographs - multiframe

Image format:

DM4

No. of images or tilt series:

Image size:

(7420, 7676)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.6375, 0.6375)

Details:

Selection of 5 multiframe micrographs related to the dataset:10012. Related PDB: 3J7H.

Files:

選択したファイルを無圧縮zipファイルにアーカイブ化してダウンロードします。

rsync、aspera、globus 等の利用をおすすめします。

選択したファイルのリストをダウンロードします。

rsyncコマンド等でファイルリストを指定してダウンロードすることが可能です。

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

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)

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)

prismPYP: Power-spectrum and image domain learning for self-supervised micrograph evaluation.

He L, Bartesaghi A. (2026)

CryoSIP: unleashing protein high-resolution Cryo-EM via semantic-instance collaborative picking.

Deng Y, Wang S, Xiang M, Li Y, Zhuo L, Cao D, Fu X, Zou Q. (2026)

Unbend, correction of local beam-induced sample motion in cryo-EM images using a 3D spline model.

Kong L, Zottig X, Elferich J, Grigorieff N. (2026)

Chart builder: an interactive tool for user driven data visualization in the electron microscopy data bank.

Fonseca N, Duraisamy AK, Wang Z, Somasundharam S, Tayebinia M, de Oliveira LC, Ma M, Turner J, Patwardhan A, Kleywegt GJ, Hartley M, Morris KL. (2026)

CryoVirusDB: An Annotated Dataset for AI-Based Virus Particle Identification in Cryo-EM Micrographs.

Gyawali R, Dhakal A, Wang L, Cheng J. (2026)

Dual site targeting of the bacterial 70S ribosome by tetracyclines.

Devarkar SC, Lomakin IB, Wang J, Grada A, Bunick CG. (2026)

Deep-learning methods for contrast enhancement and artifact reduction in cryo-electron tomography: a systematic analysis of the state of the art and proposed improvements.

Jones HN, Deshmukh A, Pande K. (2026)

CryoGS: High-Quality Cryo-EM Homogeneous Reconstruction by Gaussian Splatting

Zeng B, Liu S, Cheng S, Xu G, Fan H. (2026)

See all citations

Protein Data Bank Japan News

[2026-06-17]

324件のPDBエントリーが新たに公開されました。（2026-06-17付）