|Entry||Database: EMDB / ID: 1048|
|Title||Three-dimensional structure of bacteriophage T4 baseplate.|
|Sample||Bacteriophage T4 baseplate-tail tube assembly|
|Source||Enterobacteria phage T4 / virus / bacteriophage T4|
|Map data||map contains the baseplate and the proximal part of the tail tube|
|Method||single particle reconstruction, at 12 Å resolution|
|Authors||Kostyuchenko VA / Leiman PG / Chipman PR / Kanamaru S / vanRaaij MJ / Arisaka F / Mesyanzhinov VV / Rossmann MG|
|Citation||Nat. Struct. Biol., 2003, 10, 688-693|
|Validation Report||PDB-ID: 1pdf|
About validation report
|Date||Deposition: May 19, 2003 / Header (metadata) release: May 19, 2003 / Map release: Sep 19, 2003 / Last update: Oct 24, 2012|
Downloads & links
|File||emd_1048.map.gz (map file in CCP4 format, 29414 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 2.97872 Å|
CCP4 map header:
-Entire Bacteriophage T4 baseplate-tail tube assembly
|Entire||Name: Bacteriophage T4 baseplate-tail tube assembly / Number of components: 1 / Oligomeric State: the complex has sixfold symmetry|
-Component #1: protein, baseplate-tail tube complex
|Protein||Name: baseplate-tail tube complex / Recombinant expression: Yes|
|Source||Species: Enterobacteria phage T4 / virus / bacteriophage T4 / Strain: T4 18-,23-|
|Source (engineered)||Expression System: Escherichia coli be / bacteria / image: Escherichia coli|
|Source (natural)||Organelle: baseplate and tail tube|
|Sample solution||Specimen conc.: 5 mg/ml / Buffer solution: water / pH: 7|
|Support film||holey carbon|
|Vitrification||Cryogen name: ETHANE / Method: Blot for 2 seconds before plunging|
-Electron microscopy imaging
|Imaging||Microscope: FEI/PHILIPS CM300FEG/T / Date: Jan 30, 2001|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 45000 X (nominal), 47000 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200 - 5000 nm|
|Specimen Holder||Holder: 626 Single Tilt Cryotransfer System / Model: GATAN LIQUID NITROGEN|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 15 / Scanner: ZEISS SCAI / Sampling size: 14 microns / Bit depth: 8|
Details: images were scanned at 7 micron per pixel and averaged 2x2 to give 14 micron per pixel
|Processing||Method: single particle reconstruction / Number of projections: 945 / Applied symmetry: C6 (6 fold cyclic)|
|3D reconstruction||Algorithm: model based projection matching / Software: SPIDER / CTF correction: each particle|
Details: modified SPIDER version was used to allow reconstruction of the whole baseplate-tail tube assembly
Resolution: 12 Å / Resolution method: FSC 0.5
-Atomic model buiding
|Modeling #1||Software: Situs 2.0, Colores / Refinement protocol: rigid body / Target criteria: correlation coefficient / Refinement space: REAL / Details: Protocol: laplacian filtered real space|
|Modeling #2||Software: Situs 2.0, Colores / Refinement protocol: rigid body / Target criteria: correlation coefficient / Refinement space: REAL / Details: Protocol: laplacian filtered real space|
|Modeling #3||Software: Situs 2.0, Colores / Refinement protocol: rigid body / Target criteria: correlation coefficient / Refinement space: REAL / Details: Protocol: laplacian filtered real space|
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External links: The 2017 Nobel Prize in Chemistry - Press Release
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