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Ab initio electron density determination directly from solution scattering data

Nature Methods volume 15, pages 191193 (2018) | Download Citation

Abstract

Using a novel iterative structure factor retrieval algorithm, here I show that electron density can be directly calculated from solution scattering data without modeling. The algorithm was validated with experimental data from 12 different biological macromolecules. This approach avoids many of the assumptions limiting the resolution and accuracy of modeling algorithms by explicitly calculating electron density. This algorithm can be applied to a wide variety of molecular systems.

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Acknowledgements

The author is grateful to W. Bauer, J. Chen, R. Kirian, E. Lattman, E. Snell and J. Spence for discussions and review of the manuscript. Financial support was provided by the BioXFEL NSF Science and Technology Center (NSF 1231306).

Author information

Affiliations

  1. Department of Structural Biology, University at Buffalo, State University of New York, New York, USA.

    • Thomas D Grant
  2. Hauptman-Woodward Medical Research Institute, Buffalo, New York, USA.

    • Thomas D Grant

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Competing interests

The author declares no competing financial interests.

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Correspondence to Thomas D Grant.

Integrated supplementary information

Supplementary information

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    Supplementary Text and Figures

    Supplementary Figures 1–10, Supplementary Tables 1–3 and Supplementary Notes 1–5

  2. 2.

    Life Sciences Reporting Summary

  3. 3.

    Supplementary Protocol

    DENSS installation and usage instructions

Videos

  1. 1.

    Convergence process of electron density reconstruction from SAXS data

    This video shows the convergence process for a single ab initio electron density reconstruction from SAXS data using the software DENSS for sample 11. Electron density is displayed as a volume object colored according to density. The top right graph shows the fit of the calculated scattering profile (red circles) to the smooth (black line) and raw (black circles) experimental data. After convergence is achieved, the known high-resolution atomic coordinates are superimposed to the density, shown in cartoon representation.

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DOI

https://doi.org/10.1038/nmeth.4581