IDEAS home Printed from https://ideas.repec.org/a/nat/nature/v496y2013i7446d10.1038_nature12070.html
   My bibliography  Save this article

Accurate assessment of mass, models and resolution by small-angle scattering

Author

Listed:
  • Robert P. Rambo

    (Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA)

  • John A. Tainer

    (Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
    The Skaggs Institute for Chemical Biology, The Scripps Research Institute)

Abstract

Modern small-angle scattering (SAS) experiments with X-rays or neutrons provide a comprehensive, resolution-limited observation of the thermodynamic state. However, methods for evaluating mass and validating SAS-based models and resolution have been inadequate. Here we define the volume of correlation, Vc, a SAS invariant derived from the scattered intensities that is specific to the structural state of the particle, but independent of concentration and the requirements of a compact, folded particle. We show that Vc defines a ratio, QR, that determines the molecular mass of proteins or RNA ranging from 10 to 1,000 kilodaltons. Furthermore, we propose a statistically robust method for assessing model-data agreements (χ2free) akin to cross-validation. Our approach prevents over-fitting of the SAS data and can be used with a newly defined metric, RSAS, for quantitative evaluation of resolution. Together, these metrics (Vc, QR, χ2free and RSAS) provide analytical tools for unbiased and accurate macromolecular structural characterizations in solution.

Suggested Citation

  • Robert P. Rambo & John A. Tainer, 2013. "Accurate assessment of mass, models and resolution by small-angle scattering," Nature, Nature, vol. 496(7446), pages 477-481, April.
    • Handle: RePEc:nat:nature:v:496:y:2013:i:7446:d:10.1038_nature12070
    DOI: 10.1038/nature12070
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/nature12070
    File Function: Abstract
    Download Restriction: Access to the full text of the articles in this series is restricted.
    File URL: https://libkey.io/10.1038/nature12070?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Re’em Moskovitz & Tossapol Pholcharee & Sophia M. DonVito & Bora Guloglu & Edward Lowe & Franziska Mohring & Robert W. Moon & Matthew K. Higgins, 2023. "Structural basis for DARC binding in reticulocyte invasion by Plasmodium vivax," Nature Communications, Nature, vol. 14(1), pages 1-9, December.
    2. Jienyu Ding & Yun-Tzai Lee & Yuba Bhandari & Charles D. Schwieters & Lixin Fan & Ping Yu & Sergey G. Tarosov & Jason R. Stagno & Buyong Ma & Ruth Nussinov & Alan Rein & Jinwei Zhang & Yun-Xing Wang, 2023. "Visualizing RNA conformational and architectural heterogeneity in solution," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    3. Amika Kikuchi & Hiroki Onoda & Kosuke Yamaguchi & Satomi Kori & Shun Matsuzawa & Yoshie Chiba & Shota Tanimoto & Sae Yoshimi & Hiroki Sato & Atsushi Yamagata & Mikako Shirouzu & Naruhiko Adachi & Jafa, 2022. "Structural basis for activation of DNMT1," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    4. Yufan Zhang & Zhonghe Xu & Yu Xiao & Haodong Jiang & Xiaobing Zuo & Xing Li & Xianyang Fang, 2024. "Structural mechanisms for binding and activation of a contact-quenched fluorophore by RhoBAST," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    5. Jan Felix & Ladislav Bumba & Clarissa Liesche & Angélique Fraudeau & Fabrice Rébeillé & Jessica Y. El Khoury & Karine Huard & Benoit Gallet & Christine Moriscot & Jean-Philippe Kleman & Yoan Duhoo & M, 2022. "The AAA+ ATPase RavA and its binding partner ViaA modulate E. coli aminoglycoside sensitivity through interaction with the inner membrane," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    6. Johnny Lisboa & Cassilda Pereira & Rute D. Pinto & Inês S. Rodrigues & Liliana M. G. Pereira & Bruno Pinheiro & Pedro Oliveira & Pedro José Barbosa Pereira & Jorge E. Azevedo & Dominique Durand & Rola, 2023. "Unconventional structure and mechanisms for membrane interaction and translocation of the NF-κB-targeting toxin AIP56," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    7. Xiang Chen & Yan Wang & Zhonghe Xu & Meng-Li Cheng & Qing-Qing Ma & Rui-Ting Li & Zheng-Jian Wang & Hui Zhao & Xiaobing Zuo & Xiao-Feng Li & Xianyang Fang & Cheng-Feng Qin, 2023. "Zika virus RNA structure controls its unique neurotropism by bipartite binding to Musashi-1," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    8. Abhishek Jamwal & Florent Colomb & Henry J. McSorley & Matthew K. Higgins, 2024. "Structural basis for IL-33 recognition and its antagonism by the helminth effector protein HpARI2," Nature Communications, Nature, vol. 15(1), pages 1-9, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:nature:v:496:y:2013:i:7446:d:10.1038_nature12070. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.