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- EMDB-6801: Near-atomic resolution reconstruction of over-focused apoferritin -

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Basic information

Entry
Database: EMDB / ID: 6801
TitleNear-atomic resolution reconstruction of over-focused apoferritin
SampleNear-atomic resolution reconstruction of over-focused apoferritin
SourceHomo sapiens / human
Map data
Methodsingle particle reconstruction, at 3.2 Å resolution
AuthorsFan X / Zhao LY
CitationStructure, 2017, 25, 1623-1630.e3

Structure, 2017, 25, 1623-1630.e3 Yorodumi Papers
Near-Atomic Resolution Structure Determination in Over-Focus with Volta Phase Plate by Cs-Corrected Cryo-EM.
Xiao Fan / Lingyun Zhao / Chuan Liu / Jin-Can Zhang / Kelong Fan / Xiyun Yan / Hai-Lin Peng / Jianlin Lei / Hong-Wei Wang

DateDeposition: Jul 21, 2017 / Header (metadata) release: Nov 22, 2017 / Map release: Nov 22, 2017 / Last update: Nov 22, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.08
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_6801.map.gz (map file in CCP4 format, 55297 KB)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
240 pix
0.88 Å/pix.
= 211.2 Å
240 pix
0.88 Å/pix.
= 211.2 Å
240 pix
0.88 Å/pix.
= 211.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 0.88 Å
Density
Contour Level:0.08 (by author), 0.08 (movie #1):
Minimum - Maximum-0.17084123 - 0.3486837
Average (Standard dev.)0.000896646 (0.02381075)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions240240240
Origin000
Limit239239239
Spacing240240240
CellA=B=C: 211.2 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.880.880.88
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z211.200211.200211.200
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.1710.3490.001

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Supplemental data

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Sample components

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Entire Near-atomic resolution reconstruction of over-focused apoferritin

EntireName: Near-atomic resolution reconstruction of over-focused apoferritin
Number of components: 1

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Component #1: protein, Near-atomic resolution reconstruction of over-focused ap...

ProteinName: Near-atomic resolution reconstruction of over-focused apoferritin
Recombinant expression: No
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Escherichia coli bl21(de3) / bacteria / image: Escherichia coli
Strain: BL21(DE3)

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 1 mg/ml / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 283 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 0.001 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionSampling size: 14 microns

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 51722
3D reconstructionSoftware: RELION / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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