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- EMDB-7422: Single-Molecule 3D Image of Half IgG1 (No. 005) -

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Basic information

Entry
Database: EMDB / ID: 7422
TitleSingle-Molecule 3D Image of Half IgG1 (No. 005)
Map dataSingle-Molecule 3D Image of Half IgG1 (No. 005)
SampleHalf IgG1:
Sourceunidentified (others)
Methodelectron tomography / negative staining / 12.26 Å resolution
AuthorsLei D / Liu J / Liu H / Lei M / Ren G
CitationJournal: To Be Published
Title: Single Molecule 3D Image of a Hole-Hole Homodimer Species Generated in the Production of a Bispecific Recombinant IgG1
Authors: Lei D / Liu J / Liu H / Lei M / Ren G
DateDeposition: Jan 25, 2018 / Header (metadata) release: Feb 28, 2018 / Map release: Jan 30, 2019 / Last update: Jan 30, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7422.png

Downloads & links

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Map

Fileemd_7422.map.gz (map file in CCP4 format, 8389 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
2.96 Å/pix.
= 378.88 Å		128 pix
2.96 Å/pix.
= 378.88 Å		128 pix
2.96 Å/pix.
= 378.88 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.96 Å
Density

Histogram

Histogram (log scale)
Contour Level:0.2 (movie #1):
Minimum - Maximum-0.24137859 - 1.9371517
Average (Standard dev.)0.002295061 (0.041113857)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin0.043.00.0
Limit127.0170.0127.0
Spacing128128128
CellA=B=C: 378.88 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.962.962.96
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z378.880378.880378.880
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS4300
NC/NR/NS128128128
D min/max/mean-0.2411.9370.002

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Supplemental data

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Sample components

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Entire Half IgG1

EntireName: Half IgG1 / Number of components: 1

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Component #1: protein, Half IgG1

ProteinName: Half IgG1 / Recombinant expression: No
SourceSpecies: unidentified (others)
Source (engineered)Expression System: Cricetulus griseus (Chinese hamster) / Cell of expression system: ovary

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: negative staining
Sample solutionBuffer solution: Dulbecco's phosphate buffered saline (DPBS)
pH: 7
StainingThe grid was stained with 1% (w/v) uranyl formate
VitrificationCryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: ZEISS LIBRA120PLUS
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 70.55 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 80000.0 X (nominal) / Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Energy filter: In-column Omega Filter
Specimen HolderModel: OTHER
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Image processing

ProcessingMethod: electron tomography / Number of sections: 61
Details: X-ray speckles in images were removed before CTF correction.
3D reconstructionAlgorithm: FOURIER SPACE / Resolution: 12.26 Å / Resolution method: FSC 0.5 CUT-OFF
Details: The 3D reconstruction was performed by using Individual-Particle Electron Tomography (IPET). The obtained 3D map was Gaussian low-pass filtered to 2 nm. Image of the 3D map was taken in Chimera with the 'hide dust' function activated.
FSC plot
(resolution estimation)

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