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- EMDB-1457: A test-bed for optimizing high-resolution single particle reconst... -

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Basic information

Entry
Database: EMDB / ID: 1457
TitleA test-bed for optimizing high-resolution single particle reconstructions.
Map dataThis is a single particle reconstruction of GroEL
SampleGroEL:
SourceEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / negative staining / 5.4 Å resolution
AuthorsStagg SM / Lander GC / Quispe J / Voss NR / Cheng A / Bradlow H / Bradlow S / Carragher B / Potter CS
CitationJournal: J. Struct. Biol. / Year: 2008
Title: A test-bed for optimizing high-resolution single particle reconstructions.
Authors: Scott M Stagg / Gabriel C Lander / Joel Quispe / Neil R Voss / Anchi Cheng / Henry Bradlow / Steven Bradlow / Bridget Carragher / Clinton S Potter
DateDeposition: Nov 9, 2007 / Header (metadata) release: Nov 9, 2007 / Map release: Jun 24, 2008 / Last update: May 26, 2011

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_1457.map.gz (map file in CCP4 format, 14831 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
156 pix
1.63 Å/pix.
= 254.28 Å
156 pix
1.63 Å/pix.
= 254.28 Å
156 pix
1.63 Å/pix.
= 254.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.63 Å
Density
Contour Level:2.55, 4 (movie #1):
Minimum - Maximum-7.09001 - 10.484
Average (Standard dev.)0.0530646 (1.33817)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions156156156
Origin-78-78-78
Limit777777
Spacing156156156
CellA=B=C: 254.28 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.631.631.63
M x/y/z156156156
origin x/y/z0.0000.0000.000
length x/y/z254.280254.280254.280
α/β/γ90.00090.00090.000
start NX/NY/NZ-60-60-59
NX/NY/NZ120120120
MAP C/R/S123
start NC/NR/NS-78-78-78
NC/NR/NS156156156
D min/max/mean-7.09010.4840.053

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Supplemental data

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Sample components

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Entire GroEL

EntireName: GroEL / Oligomeric State: D7 14-mer / Number of components: 1
MassTheoretical: 800 kDa / Experimental: 800 kDa

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Component #1: protein, GroEL

ProteinName: GroEL / a.k.a: GroEL / Oligomeric Details: homotetradecamer / Recombinant expression: Yes / Number of Copies: 14
MassTheoretical: 800 kDa / Experimental: 800 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (natural)Location in cell: cytosol / Cell: E. coli

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: negative staining, cryo EM
Sample solutionSpecimen conc.: 4 mg/ml
Buffer solution: 100mM Hepes, 10mM Mg(OAc)2, 10mM KOAc, 2mM DTT
pH: 7.5
Support filmProtochips C-flat grid: holey carbon with 2um holes and 2um spacing 400 mesh copper grid
Stainingnot stained
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 93 K / Humidity: 100 %
Method: Temperature of chamber was 4 degrees C. 0 seconds drain time. Single blot. 0 mm offset. 4 ul sample applied to grid. Blot for 3.5 seconds before plunging.
Details: Vitrification instrument: Vitrobot. Grid plasma cleaned for 20s with Fischione 1020 plasma cleaner using 75% Argon 25% Oxygen mix.

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20 / Date: Jul 12, 2006
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 13 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 100000 X (nominal), 100000 X (calibrated)
Astigmatism: objective lens astigmatism was corrected automatically using Leginon
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 3000 nm
Specimen HolderHolder: Side entry liquid nitrogen-cooled cryo specimen holder
Model: GATAN LIQUID NITROGEN / Temperature: 102 K
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of class averages: 1294 / Number of projections: 55351 / Applied symmetry: D7 (2*7 fold dihedral)
3D reconstructionAlgorithm: single particle reconstruction / Software: EMAN / CTF correction: Phase correction for each particle. / Resolution: 5.4 Å / Resolution method: FSC 0.5

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