|Entry||Database: EMDB / ID: 3458|
|Title||negative-stain volume of Sso DNA PolB1|
|Sample||archaeal DNA polymerase B1|
|Map data||Final map from iteration 10 onto which FSC has been calculated and displayed (Figure S4C, right). Contour level in Chimera|
|Method||single particle reconstruction, at 22.8 Å resolution|
|Authors||Abrescia NGA / Bell SD|
|Citation||Nat Commun, 2017, 8, 15075-15075|
Nat Commun, 2017, 8, 15075-15075 Yorodumi Papers
|Date||Deposition: Nov 3, 2016 / Header (metadata) release: Dec 7, 2016 / Map release: May 17, 2017 / Last update: Aug 2, 2017|
Downloads & links
|File||emd_3458.map.gz (map file in CCP4 format, 8389 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.66 Å|
CCP4 map header:
|File||emd_3458_msk_1.map ( map file in CCP4 format, 8389 KB )|
|Projections & Slices|
|Data type||Image stored as Reals|
|Annotation details||mask created using the initial reference map (Figure S4B) with soft edges.|
|Space group number||1|
-Entire archaeal DNA polymerase B1
|Entire||Name: archaeal DNA polymerase B1 / Details: This is the apo enzyme. / Number of components: 2|
|Mass||Theoretical: 101 kDa|
-Component #1: protein, archaeal DNA polymerase B1
|Protein||Name: archaeal DNA polymerase B1 / Details: This is the apo enzyme. / Recombinant expression: No|
|Mass||Theoretical: 101 kDa|
|Source (engineered)||Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 / |
-Component #2: protein, DNA polymerase B1
|Protein||Name: DNA polymerase B1 / Recombinant expression: No|
|Source (engineered)||Expression System: Archaea / Vector: pET33b|
|Sample solution||Specimen conc.: 0.01 mg/ml / pH: 7.5|
|Staining||Negatively stained EM specimens were prepared using carbon-coated grids and stained with 2% of uranyl formate solution.|
|Vitrification||Cryogen name: NONE|
-Electron microscopy imaging
|Imaging||Microscope: JEOL 2200FSC|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 30 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 60000 X (nominal), 90201 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1300 - 1700 nm / Energy filter: In-column Omega Filter / Energy window: 0-20 eV|
|Specimen Holder||Model: JEOL|
|Camera||Detector: GATAN ULTRASCAN 4000 (4k x 4k)|
|Image acquisition||Number of digital images: 108|
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 14582|
|3D reconstruction||Software: RELION|
CTF correction: phase flipping was performed using XMIPP software
Resolution: 22.8 Å / Resolution method: FSC 0.5 CUT-OFF
Details: Calculated for the converged iteration 10 in Relion using Scipion
-Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
- Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
- Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
- 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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