|Entry||Database: EMDB / ID: 1457|
|Title||A test-bed for optimizing high-resolution single particle reconstructions.|
|Map data||This is a single particle reconstruction of GroEL|
|Source||Escherichia coli (E. coli)|
|Method||single particle reconstruction / cryo EM / negative staining / 5.4 Å resolution|
|Authors||Stagg SM / Lander GC / Quispe J / Voss NR / Cheng A / Bradlow H / Bradlow S / Carragher B / Potter CS|
|Citation||Journal: 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
|Date||Deposition: Nov 9, 2007 / Header (metadata) release: Nov 9, 2007 / Map release: Jun 24, 2008 / Last update: May 26, 2011|
|Structure viewer||EM map: |
Downloads & links
|File||emd_1457.map.gz (map file in CCP4 format, 14831 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.63 Å|
CCP4 map header:
|Entire||Name: GroEL / Oligomeric State: D7 14-mer / Number of components: 1|
|Mass||Theoretical: 800 kDa / Experimental: 800 kDa|
-Component #1: protein, GroEL
|Protein||Name: GroEL / a.k.a: GroEL / Oligomeric Details: homotetradecamer / Recombinant expression: Yes / Number of Copies: 14|
|Mass||Theoretical: 800 kDa / Experimental: 800 kDa|
|Source||Species: Escherichia coli (E. coli)|
|Source (natural)||Location in cell: cytosol / Cell: E. coli|
|Specimen||Specimen state: particle / Method: negative staining, cryo EM|
|Sample solution||Specimen conc.: 4 mg/ml|
Buffer solution: 100mM Hepes, 10mM Mg(OAc)2, 10mM KOAc, 2mM DTT
|Support film||Protochips C-flat grid: holey carbon with 2um holes and 2um spacing 400 mesh copper grid|
|Vitrification||Instrument: 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.
-Electron microscopy imaging
Model: Tecnai F20 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F20 / Date: Jul 12, 2006|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 13 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 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 Holder||Holder: Side entry liquid nitrogen-cooled cryo specimen holder|
Model: GATAN LIQUID NITROGEN / Temperature: 102 K
|Camera||Detector: GATAN ULTRASCAN 4000 (4k x 4k)|
|Processing||Method: single particle reconstruction / Number of class averages: 1294 / Number of projections: 55351 / Applied symmetry: D7 (2*7 fold dihedral)|
|3D reconstruction||Algorithm: 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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