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- EMDB-1587: ab initio 3D reconstruction of GroEL using 3DESS (3D alignment by... -

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Entry
Database: EMDB / ID: 1587
Titleab initio 3D reconstruction of GroEL using 3DESS (3D alignment by differential Evolution with Spectral Self-adaptation), which is a new high-resolution single-particle orientation refinement method based on spectrally self-adapting common lines
KeywordsGroEL / common lines / spectral self-adaptation
SampleGroEL data provided by National Resource for Automated Molecular Microscopy
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataab initio 3D reconstruction of GroEL using 3DESS
Methodsingle particle reconstruction, at 7 Å resolution
AuthorsElmlund D / Elmlund H
CitationJ. Struct. Biol., 2009, 167, 83-94

J. Struct. Biol., 2009, 167, 83-94 Yorodumi Papers
High-resolution single-particle orientation refinement based on spectrally self-adapting common lines.
Dominika Elmlund / Hans Elmlund

DateDeposition: Dec 15, 2008 / Header (metadata) release: Dec 15, 2008 / Map release: Apr 1, 2009 / Last update: Oct 24, 2012

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.013
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-1oel
  • Surface level: 0.013
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-1oel
  • Surface level: 0.013
  • Imaged by UCSF CHIMERA
  • Download
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Map

Fileemd_1587.map.gz (map file in CCP4 format, 10720 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
140 pix
1.63 Å/pix.
= 228.2 Å
140 pix
1.63 Å/pix.
= 228.2 Å
140 pix
1.63 Å/pix.
= 228.2 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.63 Å
Density
Contour Level:0.00689, 0.013 (movie #1):
Minimum - Maximum-0.0491726 - 0.0902491
Average (Standard dev.)0.000727468 (0.00502245)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions140140140
Origin-70-70-70
Limit696969
Spacing140140140
CellA=B=C: 228.2 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.631.631.63
M x/y/z140140140
origin x/y/z0.0000.0000.000
length x/y/z228.200228.200228.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-100-100-99
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-70-70-70
NC/NR/NS140140140
D min/max/mean-0.0490.0900.001

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Supplemental data

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Sample components

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Entire GroEL data provided by National Resource for Automated Molecular ...

EntireName: GroEL data provided by National Resource for Automated Molecular Microscopy
Details: All sample details described in Stagg, S. M. et al. A test-bed for optimizing high-resolution single particle reconstructions, JSB 2008, 163(1), 29-39
Number of components: 1 / Oligomeric State: 14-meric and d7 symmetric GroEL

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Component #1: cellular-component, GroEL

Cellular-componentName: GroEL / a.k.a: GroEL / Recombinant expression: Yes
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Experimental details

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Sample preparation

Specimen stateparticle
VitrificationInstrument: NONE / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Details: All imaging details described in Stagg, S. M. et al. A test-bed for optimizing high-resolution single particle reconstructions, JSB 2008, 163(1), 29-39
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN

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Image acquisition

Image acquisitionDetails: All image processing details described in Stagg, S. M. et al. A test-bed for optimizing high-resolution single particle

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Image processing

ProcessingMethod: single particle reconstruction
Details: All experimental details described in Stagg, S. M. et al. A test-bed for optimizing high-resolution single particle reconstructions, JSB 2008, 163(1), 29-39
Applied symmetry: D7 (2*7 fold dihedral)
3D reconstructionAlgorithm: cross-common lines / Software: Evol-Align / CTF correction: each micrograph, phase flipping only / Resolution: 7 Å / Resolution method: FSC 0.5

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