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- EMDB-8613: 3D-reconstruction of O3-33 from a grid prepared with a single rou... -

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Basic information

Database: EMDB / ID: 8613
Title3D-reconstruction of O3-33 from a grid prepared with a single round of blotting
Map data3D-reconstruction of O3-33
Methodsingle particle reconstruction, at 7.8 Å resolution
AuthorsSnijder J / Borst AJ / Dosey A / Walls AC / Burrell A / Reddy V / Kollman J / Veesler D
CitationJ. Struct. Biol., 2017, 198, 38-42

J. Struct. Biol., 2017, 198, 38-42 StrPapers
Vitrification after multiple rounds of sample application and blotting improves particle density on cryo-electron microscopy grids.
Joost Snijder / Andrew J Borst / Annie Dosey / Alexandra C Walls / Anika Burrell / Vijay S Reddy / Justin M Kollman / David Veesler

DateDeposition: Feb 23, 2017 / Header (metadata) release: Mar 15, 2017 / Map release: Mar 15, 2017 / Last update: May 3, 2017

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.12
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.12
  • Imaged by UCSF CHIMERA
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_8613.map.gz (map file in CCP4 format, 8389 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
2.5 Å/pix.
= 320. Å
128 pix
2.5 Å/pix.
= 320. Å
128 pix
2.5 Å/pix.
= 320. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.5 Å
Contour Level:0.12 (by author), 0.12 (movie #1):
Minimum - Maximum-0.05387538 - 0.2440007
Average (Standard dev.)0.0020366071 (0.016570222)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 320 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.52.52.5
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z320.000320.000320.000
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0540.2440.002

Supplemental data

Sample components

Entire O3-33

EntireName: O3-33 / Number of components: 2
MassTheoretical: 480 kDa

Component #1: protein, O3-33

ProteinName: O3-33 / Recombinant expression: No
MassTheoretical: 480 kDa
SourceSpecies: Unidentified
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

Component #2: protein, Computationally designed octahedral protein cage O3-33

ProteinName: Computationally designed octahedral protein cage O3-33
Recombinant expression: No
Source (engineered)Expression System: Unidentified

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 1 mg/ml / pH: 8
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 40000 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD
CameraDetector: GATAN K2 (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 100

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: O (octahedral) / Number of projections: 6000
3D reconstructionAlgorithm: FOURIER SPACE / Software: Relion / Resolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF

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