Skip to main content

Evaluation of Electron Crystallographic Data from Images of Two-Dimensional Crystals

  • Protocol
  • First Online:
Electron Crystallography of Soluble and Membrane Proteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 955))

Abstract

In the past, various formats have been used to present data fidelity of electron crystallographic data from images of two-dimensional crystals. While each scheme provides some information about the data, not all schemes are equally useful for presenting data reliability. This brief chapter gives guidelines on how to look at datasets that are solely derived from images, and on how to summarize the data structure through graphical outputs that provide unbiased and detailed information about data quality. By the time of publication, the actual procedures described here will have been integrated into the 2dx package and therefore, these evaluation tools will be available at a “push of a button.” Because of this, the chapter focuses on brief explanations for why certain ways of presenting data make more sense than others.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 139.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 179.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Unger VM (2000) Assessment of electron crystallographic data obtained from two-dimensional crystals of biological specimens. Acta Crystallogr D Biol Crystallogr D56:1259–1269

    Article  CAS  Google Scholar 

  2. Aller SG, Unger VM (2006) Projection structure of the human copper transporter CTR1 at 6-Å resolution reveals a compact trimer with a novel channel-like architecture. Proc Natl Acad Sci USA 103:3627–3632

    Article  PubMed  CAS  Google Scholar 

  3. Valpuesta JM, Carrascosa JL, Henderson R (1994) Analysis of electron microscope images and electron diffraction patterns of thin crystals of Θ29 connectors in ice. J Mol Biol 240:281–287

    Article  PubMed  CAS  Google Scholar 

  4. Subramaniam S, Gerstein M, Oesterhelt D, Henderson R (1993) Electron diffraction analysis of structural changes in the photocycle of bacteriorhodopsin. EMBO J 12(1):1–8

    PubMed  CAS  Google Scholar 

  5. Han BG, Vonck J, Glaeser RM (1994) The bacteriorhodopsin photocycle: direct structural study of two substrates of the M-intermediate. Biophys J 67(3):1179–1186

    Article  PubMed  CAS  Google Scholar 

  6. Vonck J (1996) A three-dimensional difference map of the N intermediate in the bacteriorhodopsin photocycle: part of the F-helix tilts in the M to N transition. Biochemistry 35:5870–5878

    Article  PubMed  CAS  Google Scholar 

  7. Hendrickson FM, Burkard F, Gleaser RM (1998) Structural characterization of the L-to-M transition of the bacteriorhodopsin photocycle. Biophys J 75:1446–1454

    Article  PubMed  CAS  Google Scholar 

  8. Subramaniam S, Henderson R (1999) Electron crystallography of bacteriorhodpsin with millisecond time resolution. J Struct Biol 128:19–25

    Article  PubMed  CAS  Google Scholar 

  9. Appel M, Hizlan D, Vinothkumar KR, Ziegler C, Kühlbrandt W (2009) Conformation of NhaA, the Na/H Exchanger from Escherichia coli, in the pH-activated and ion-translocating states. J Mol Biol 386(2):351–365

    Article  PubMed  CAS  Google Scholar 

  10. Cheng A, Yeager M (2004) A graphical representation of image quality for three-dimensional structure analysis of two-dimensional crystals. Acta Crystallogr D Biol Crystallogr A60:351–354

    CAS  Google Scholar 

  11. De Feo CJ, Aller SG, Siluvai GS, Blackburn NJ, Unger VM (2009) Three-dimensional structure of the human copper transporter hCTR1. Proc Natl Acad Sci USA 106(11):4237–4242

    Article  PubMed  Google Scholar 

  12. Lindahl M, Henderson R (1997) Structure of the bacteriorhodopsin D85N/D96N double mutant showing substantial structural changes and a highly twinned, disordered lattice. Ultramicroscopy 70:95–106

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Vinzenz M. Unger .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media New York

About this protocol

Cite this protocol

Unger, V.M. (2013). Evaluation of Electron Crystallographic Data from Images of Two-Dimensional Crystals. In: Schmidt-Krey, I., Cheng, Y. (eds) Electron Crystallography of Soluble and Membrane Proteins. Methods in Molecular Biology, vol 955. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-176-9_12

Download citation

  • DOI: https://doi.org/10.1007/978-1-62703-176-9_12

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-175-2

  • Online ISBN: 978-1-62703-176-9

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics