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- EMDB-9261: Electron cryotomogram of Bdellovibrio bacteriovorus acquired by c... -

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Basic information

Entry
Database: EMDB / ID: EMD-9261
TitleElectron cryotomogram of Bdellovibrio bacteriovorus acquired by continuous tilting
Map dataTomographic reconstruction of Bdellovibrio bacteriovorus cell. Binned 4 times.
Sample
  • Cell: Bdellovibrio bacteriovorus
Biological speciesBdellovibrio bacteriovorus (bacteria)
Methodelectron tomography / cryo EM
AuthorsChreifi G / Chen S / Metskas LA / Kaplan M / Jensen GJ
CitationJournal: J Struct Biol / Year: 2019
Title: Rapid tilt-series acquisition for electron cryotomography.
Authors: Georges Chreifi / Songye Chen / Lauren Ann Metskas / Mohammed Kaplan / Grant J Jensen /
Abstract: Using a new Titan Krios stage equipped with a single-axis holder, we developed two methods to accelerate the collection of tilt-series. We demonstrate a continuous-tilting method that can record a ...Using a new Titan Krios stage equipped with a single-axis holder, we developed two methods to accelerate the collection of tilt-series. We demonstrate a continuous-tilting method that can record a tilt-series in seconds, but with loss of details finer than ∼4 nm. We also demonstrate a fast-incremental method that can record a tilt-series several-fold faster than current methods and with similar resolution. We characterize the utility of both methods in real biological electron cryotomography workflows. We identify opportunities for further improvements in hardware and software and speculate on the impact such advances could have on structural biology.
History
DepositionOct 25, 2018-
Header (metadata) releaseNov 21, 2018-
Map releaseJan 30, 2019-
UpdateMar 13, 2019-
Current statusMar 13, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Movie viewer
Supplemental images

emd_9261.png

Downloads & links

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Map

FileDownload / File: emd_9261.map.gz / Format: CCP4 / Size: 1019.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTomographic reconstruction of Bdellovibrio bacteriovorus cell. Binned 4 times.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
17.28 Å/pix.
x 300 pix.
= 5184. Å		17.28 Å/pix.
x 928 pix.
= 16035.841 Å		17.28 Å/pix.
x 960 pix.
= 16588.801 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 17.28 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-0.2578049 - 0.1690594
Average (Standard dev.)0.037843894 (±0.008837259)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-300
Dimensions928960300
Spacing960928300
CellA: 16588.8 Å / B: 16035.841 Å / C: 5184.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z17.28000104166717.28000107758617.28
M x/y/z960928300
origin x/y/z0.0000.0000.000
length x/y/z16588.80116035.8415184.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS00-300
NC/NR/NS960928300
D min/max/mean-0.2580.1690.038

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Supplemental data

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Sample components

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Entire : Bdellovibrio bacteriovorus

EntireName: Bdellovibrio bacteriovorus (bacteria)
Components
  • Cell: Bdellovibrio bacteriovorus

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Supramolecule #1: Bdellovibrio bacteriovorus

SupramoleculeName: Bdellovibrio bacteriovorus / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Bdellovibrio bacteriovorus (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.8
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 296 K / Instrument: FEI VITROBOT MARK IV
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Ted Pella / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 0.08 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: SIMULTANEOUS ITERATIVE (SIRT) / Software - Name: TOMO3D (ver. 2.0) / Number images used: 1260

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