Combining Electron Microscopic with X-Ray Crystallographic Structures

Combining Electron Microscopic with X-Ray Crystallographic Structures Analgorithm has been developed for placing three-dimensional atomic structures into appropriately scaled cryoelectron microscopy maps. The first stage in this process is to conduct a three-dimensional angular search in which the center of gravity of an X-ray crystallographically determined structure is placed on a selected position in the cryoelectron microscopy map. The quality of the fit is measured by the sum of the density at each atomic position. The second stage is to refine the three angles and three translational parameters for the best (usually 25 to 100) fits. Useful criteria for this refinement include the sum of densities at atomic sites, the lack of atoms in negative or low density, the absence of atomic clashes between symmetry-related positions of the atomic structure, and the distances between identifiable features in the map and their positions on the fitted atomic structure. These refinements generally lead to a convergence of the originally chosen, top scoring fits to just a few (about 3 to 8) acceptable possibilities. Usually, the best remaining fit is clearly superior to any of the others. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Journal of Structural Biology Elsevier

Combining Electron Microscopic with X-Ray Crystallographic Structures

Loading next page...
 
/lp/elsevier/combining-electron-microscopic-with-x-ray-crystallographic-structures-A0Hw6ssVbz
Publisher
Elsevier
Copyright
Copyright © 2001 Elsevier Science (USA)
ISSN
1047-8477
eISSN
1095-8657
DOI
10.1006/jsbi.2002.4435
Publisher site
See Article on Publisher Site

Abstract

Analgorithm has been developed for placing three-dimensional atomic structures into appropriately scaled cryoelectron microscopy maps. The first stage in this process is to conduct a three-dimensional angular search in which the center of gravity of an X-ray crystallographically determined structure is placed on a selected position in the cryoelectron microscopy map. The quality of the fit is measured by the sum of the density at each atomic position. The second stage is to refine the three angles and three translational parameters for the best (usually 25 to 100) fits. Useful criteria for this refinement include the sum of densities at atomic sites, the lack of atoms in negative or low density, the absence of atomic clashes between symmetry-related positions of the atomic structure, and the distances between identifiable features in the map and their positions on the fitted atomic structure. These refinements generally lead to a convergence of the originally chosen, top scoring fits to just a few (about 3 to 8) acceptable possibilities. Usually, the best remaining fit is clearly superior to any of the others.

Journal

Journal of Structural BiologyElsevier

Published: Dec 1, 2001

References

  • Low resolution meets high: Towards a resolution continuum from cells to atoms
    Baker, T.S.; Johnson, J.E.
  • Improved methods for building protein models in electron density maps and the location of errors in these models
    Jones, T.A.; Zou, J.Y.; Cowan, S.W.; Kjeldgaard, M.
  • Structural studies of two rhinovirus serotypes complexed with fragments of their cellular receptor
    Kolatkar, P.R.; Bella, J.; Olson, N.H.; Bator, C.M.; Baker, T.S.; Rossmann, M.G.
  • Docking structures of domains into maps from cryo-electron microscopy using local correlation
    Roseman, A.M.
  • Fitting atomic models into electron microscopy maps
    Rossmann, M.G.
  • Quantitative fitting of atomic models into observed densities derived by electron microscopy
    Volkmann, N.; Hanein, D.
  • Situs: A package for docking crystal structures into low-resolution maps from electron microscopy
    Wriggers, W.; Milligan, R.A.; McCammon, J.A.

You’re reading a free preview. Subscribe to read the entire article.


DeepDyve is your
personal research library

It’s your single place to instantly
discover and read the research
that matters to you.

Enjoy affordable access to
over 18 million articles from more than
15,000 peer-reviewed journals.

All for just $49/month

Explore the DeepDyve Library

Search

Query the DeepDyve database, plus search all of PubMed and Google Scholar seamlessly

Organize

Save any article or search result from DeepDyve, PubMed, and Google Scholar... all in one place.

Access

Get unlimited, online access to over 18 million full-text articles from more than 15,000 scientific journals.

Your journals are on DeepDyve

Read from thousands of the leading scholarly journals from SpringerNature, Elsevier, Wiley-Blackwell, Oxford University Press and more.

All the latest content is available, no embargo periods.

See the journals in your area

DeepDyve

Freelancer

DeepDyve

Pro

Price

FREE

$49/month
$360/year

Save searches from
Google Scholar,
PubMed

Create folders to
organize your research

Export folders, citations

Read DeepDyve articles

Abstract access only

Unlimited access to over
18 million full-text articles

Print

20 pages / month

PDF Discount

20% off