6I5A

Tobacco Mosaic Virus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Capabilities of the Falcon III detector for single-particle structure determination.

Song, B.Lenhart, J.Flegler, V.J.Makbul, C.Rasmussen, T.Bottcher, B.

(2019) Ultramicroscopy 203: 145-154

  • DOI: https://doi.org/10.1016/j.ultramic.2019.01.002
  • Primary Citation of Related Structures:  
    6I5A

  • PubMed Abstract: 

    Direct electron detectors are an essential asset for the resolution revolution in electron cryo microscopy of biological objects. The direct detectors provide two modes of data acquisition; the counting mode in which single electrons are counted, and the integrating mode in which the signal that arises from the incident electrons is integrated. While counting mode leads to far higher detective quantum efficiency at all spatial frequencies, the integrating mode enables faster data acquisition at higher exposure rates. For optimal throughput at best possible resolution it is important to understand when the better performance in counting mode becomes essential for solving a structure and when the lower detective quantum efficiency in integrating mode can be compensated by increasing the number of particles in the data set. Here, we provide a case study of the Falcon III camera, which has counting mode capability at exposure rates of <0.9 e - /Px² and integrating mode capability at exposure rates above 10 e - /Px². We found that counting mode gives better resolution for medium sized complexes such as the β-galactosidase (465 kDa) (2.2 Å, 97% of Nyquist vs. 2.4 Å, 89% of Nyquist) with data sets of similar size. However, for larger particles such as Hepatitis B virus capsid like particles (4.8 MDa) we did not find any resolution gain in counting mode.


  • Organizational Affiliation

    Julius-Maximilians-Universität Würzburg, Josef Schneider Straße 2, 97080 Würzburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein159Tobacco mosaic virus (vulgare)Mutation(s): 0 
UniProt
Find proteins for P69687 (Tobacco mosaic virus (strain vulgare))
Explore P69687 
Go to UniProtKB:  P69687
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69687
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTWarp8.0
RECONSTRUCTIONRELION3.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermany359471283

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2019-05-01
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Other
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references