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- EMDB-7627: Apoferritin 0.5 mM TCEP with spot-to-plunge time of 170ms -

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Basic information

Entry
Database: EMDB / ID: EMD-7627
TitleApoferritin 0.5 mM TCEP with spot-to-plunge time of 170ms
Map dataApoferritin 0.5 mM TCEP with spot-to-plunge time of 170ms
Sample
  • Complex: Apoferritin
Biological speciesTabanus atratus (black horsefly)
Methodelectron tomography / cryo EM
AuthorsNoble AJ / Wei H / Dandey VP / Zhang Z / Potter CS / Carragher B
CitationJournal: Nat Methods / Year: 2018
Title: Reducing effects of particle adsorption to the air-water interface in cryo-EM.
Authors: Alex J Noble / Hui Wei / Venkata P Dandey / Zhening Zhang / Yong Zi Tan / Clinton S Potter / Bridget Carragher /
Abstract: Most protein particles prepared in vitreous ice for single-particle cryo-electron microscopy (cryo-EM) are adsorbed to air-water or substrate-water interfaces, which can cause the particles to adopt ...Most protein particles prepared in vitreous ice for single-particle cryo-electron microscopy (cryo-EM) are adsorbed to air-water or substrate-water interfaces, which can cause the particles to adopt preferred orientations. By using a rapid plunge-freezing robot and nanowire grids, we were able to reduce some of the deleterious effects of the air-water interface by decreasing the dwell time of particles in thin liquid films. We demonstrated this by using single-particle cryo-EM and cryo-electron tomography (cryo-ET) to examine hemagglutinin, insulin receptor complex, and apoferritin.
History
DepositionMar 26, 2018-
Header (metadata) releaseApr 4, 2018-
Map releaseApr 4, 2018-
UpdateOct 17, 2018-
Current statusOct 17, 2018Processing 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_7627.png

Downloads & links

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Map

FileDownload / File: emd_7627.map.gz / Format: CCP4 / Size: 1.5 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationApoferritin 0.5 mM TCEP with spot-to-plunge time of 170ms
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.34 Å/pix.
x 300 pix.
= 702. Å		2.34 Å/pix.
x 1320 pix.
= 3088.8 Å		2.34 Å/pix.
x 1030 pix.
= 2410.2 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: 2.34 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-0.05555154 - 0.11568687
Average (Standard dev.)0.023998505 (±0.0065333275)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-128
Dimensions13201030300
Spacing10301320300
CellA: 2410.2 Å / B: 3088.7998 Å / C: 702.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.342.342.34
M x/y/z10301320300
origin x/y/z0.0000.0000.000
length x/y/z2410.2003088.800702.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS00-128
NC/NR/NS10301320300
D min/max/mean-0.0560.1160.024

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Supplemental data

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Sample components

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Entire : Apoferritin

EntireName: Apoferritin
Components
  • Complex: Apoferritin

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Supramolecule #1: Apoferritin

SupramoleculeName: Apoferritin / type: complex / ID: 1 / Parent: 0 / Details: with 0.5 mM TCEP
Source (natural)Organism: Tabanus atratus (black horsefly)
Recombinant expressionOrganism: unidentified (others)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

Concentration15 mg/mL
BufferpH: 0.0001
GridModel: Homemade
VitrificationCryogen name: ETHANE / Instrument: OTHER
Details: The value given for _emd_vitrification.instrument is SPOTITON. This is not in a list of allowed values set(['LEICA EM CPC', 'GATAN CRYOPLUNGE 3', 'LEICA PLUNGER', 'FEI VITROBOT MARK II', ...Details: The value given for _emd_vitrification.instrument is SPOTITON. This is not in a list of allowed values set(['LEICA EM CPC', 'GATAN CRYOPLUNGE 3', 'LEICA PLUNGER', 'FEI VITROBOT MARK II', 'HOMEMADE PLUNGER', 'REICHERT-JUNG PLUNGER', 'FEI VITROBOT MARK I', 'LEICA KF80', 'FEI VITROBOT MARK III', 'LEICA EM GP', 'OTHER', 'FEI VITROBOT MARK IV']) so OTHER is written into the XML file.
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Detector mode: INTEGRATING / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: SIMULTANEOUS ITERATIVE (SIRT) / Software - Name: TOMO3D / Software - details: SIRT, 30 iterations / Number images used: 30

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