EMPIAR-13217 - Structure of a headful DNA-packaging bacterial virus at 2.89 Angstrom resolution by electron cryo-microscopy [multiple data sets in MRC format]

EMPIAR-13217

Structure of a headful DNA-packaging bacterial virus at 2.89 Angstrom resolution by electron cryo-microscopy [multiple data sets in MRC format]

Publication:

Structure of a headful DNA-packaging bacterial virus at 2.9 Å resolution by electron cryo-microscopy

Zhao H, Li K, Jiang W, Tang L

Proceedings of the National Academy of Sciences of the United States of America 114 (2017) 3601-3606

PMID: 28320961

DOI: 10.1073/pnas.1615025114

Related EMDB entry:

EMD-8314

Deposited:

2026-01-15

Released:

2026-01-26

Last modified:

2026-01-26

Imageset size:

1.14 TB

Imageset DOI:

10.6019/EMPIAR-13217

Experimental metadata:

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Compressed by PDBj:

Image formats and pixel types shown below are those of the original, non-compressed files.

Movies in this entry (data/gpc/Frames/*.mrc) were compressed to TIFF by EMPIAR Japan to save space and bandwidth.
The compression is lossless in that all pixel intensities remain exactly the same after decompression.
However, some metadata in the MRC header were lost.
The original files before compressio0n are available from EMPIAR EBI.

PDBj discovered that `data/Leginon/rawdata` and `data/gpc/Leginon` contained exactly same files.
`data/Frames` and `data/gpc/Frames` are also the same. Therefore, `data/gpc` was removed.

Original size:   3,910,994,633 kilobytes
Compressed size:   658,901,792 kilobytes

Contains:

micrographs - multiframe
micrographs - single frame

Image Sets

1. unaligned multi-frame micrographs

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

2009

Image size:

(7420, 7676)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.84, 0.84)

Details:

Coordinates of picked particles are in the folder boxdb-2009 in the eman2 convention and in boxdb-2009-for-relion in the relion convention.

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2. single-frame micrographs aligned and averaged by Leginon, bin1

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

2009

Image size:

(7420, 7676)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.84, 0.84)

Details:

---

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3. single-frame micrographs aligned and averaged by Leginon, bin2

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

2009

Image size:

(3710, 3838)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(1.68, 1.68)

Details:

---

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4. Leginon grid target images

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

Image size:

(927, 959)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(None, None)

Details:

---

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5. Leginon square target images

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

Image size:

(927, 959)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(None, None)

Details:

---

Files:

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

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6. Leginon hole target images

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

242

Image size:

(927, 959)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(None, None)

Details:

---

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7. dose estimation image during Leginon data collection

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

Image size:

(3696, 3696)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(None, None)

Details:

---

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Citations

CryoSift: an accessible and automated CNN-driven tool for cryo-EM 2D class selection.

Schäfer JH, Calza A, Hom K, Damodar P, Peng R, Bogdanović N, Lander GC, Stagg SM, Cianfrocco MA. (2025)

IsoNet2 determines cellular structures at submolecular resolution without averaging

--- (2026)

GTpick: A deep neural network for Cryo-EM particle detection.

Ni S, Yang C, Liu Y, Zhang Y, Shi Y, Qian A, Kong R, Chang S. (2025)

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)

Comparing cryo-EM methods and molecular dynamics simulation to investigate heterogeneity in ligand-bound TRPV1.

Astore MA, Silva-Sánchez D, Blackwell R, Cossio P, Hanson SM. (2025)

DiameTR: A cryo-EM tool for diameter sorting of tubular samples.

Peng R, Elkhaligy H, Grant T, Stagg SM. (2025)

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

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

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