Structure Determination from Single-Molecule X‑ray Scattering Images Using Stochastic Gradient Ascent

Scattering experiments using ultrashort X-ray free electron laser pulses have opened a new path for structure determination of a wide variety of specimens, including nanocrystals and entire viruses, approaching atomistic spatial and femtoseconds time resolution. However, random and unknown sample or...

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Published inJournal of chemical theory and computation Vol. 21; no. 16; pp. 8227 - 8234
Main Authors Schultze, Steffen, Luke, D. Russell, Grubmüller, Helmut
Format Journal Article
LanguageEnglish
Published United States American Chemical Society 26.08.2025
Subjects
Biomolecular Systems
Biomolecules
Electron density
Free electron lasers
X-ray scattering
Online AccessGet full text
ISSN1549-9618
1549-9626
1549-9626
DOI10.1021/acs.jctc.5c00748

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Abstract Scattering experiments using ultrashort X-ray free electron laser pulses have opened a new path for structure determination of a wide variety of specimens, including nanocrystals and entire viruses, approaching atomistic spatial and femtoseconds time resolution. However, random and unknown sample orientations as well as low signal-to-noise ratios have so far prevented a successful application to smaller specimens like single biomolecules. We here present resolution-annealed stochastic gradient ascent (RASTA), a new approach for direct atomistic electron density determination, which utilizes our recently developed rigorous Bayesian treatment of single-particle X-ray scattering. We demonstrate electron density determination at 2 Å resolution of various small proteins from synthetic scattering images with as low as 15 photons per image.
AbstractList Scattering experiments using ultrashort X-ray free electron laser pulses have opened a new path for structure determination of a wide variety of specimens, including nanocrystals and entire viruses, approaching atomistic spatial and femtoseconds time resolution. However, random and unknown sample orientations as well as low signal-to-noise ratios have so far prevented a successful application to smaller specimens like single biomolecules. We here present resolution-annealed stochastic gradient ascent (RASTA), a new approach for direct atomistic electron density determination, which utilizes our recently developed rigorous Bayesian treatment of single-particle X-ray scattering. We demonstrate electron density determination at 2 Å resolution of various small proteins from synthetic scattering images with as low as 15 photons per image.
Scattering experiments using ultrashort X-ray free electron laser pulses have opened a new path for structure determination of a wide variety of specimens, including nanocrystals and entire viruses, approaching atomistic spatial and femtoseconds time resolution. However, random and unknown sample orientations as well as low signal-to-noise ratios have so far prevented a successful application to smaller specimens like single biomolecules. We here present resolution-annealed stochastic gradient ascent (RASTA), a new approach for direct atomistic electron density determination, which utilizes our recently developed rigorous Bayesian treatment of single-particle X-ray scattering. We demonstrate electron density determination at 2 Å resolution of various small proteins from synthetic scattering images with as low as 15 photons per image.Scattering experiments using ultrashort X-ray free electron laser pulses have opened a new path for structure determination of a wide variety of specimens, including nanocrystals and entire viruses, approaching atomistic spatial and femtoseconds time resolution. However, random and unknown sample orientations as well as low signal-to-noise ratios have so far prevented a successful application to smaller specimens like single biomolecules. We here present resolution-annealed stochastic gradient ascent (RASTA), a new approach for direct atomistic electron density determination, which utilizes our recently developed rigorous Bayesian treatment of single-particle X-ray scattering. We demonstrate electron density determination at 2 Å resolution of various small proteins from synthetic scattering images with as low as 15 photons per image.
Scattering experiments using ultrashort X-ray free electron laser pulses have opened a new path for structure determination of a wide variety of specimens, including nanocrystals and entire viruses, approaching atomistic spatial and femtoseconds time resolution. However, random and unknown sample orientations as well as low signal-to-noise ratios have so far prevented a successful application to smaller specimens like single biomolecules. We here present resolution-annealed stochastic gradient ascent (RASTA), a new approach for direct atomistic electron density determination, which utilizes our recently developed rigorous Bayesian treatment of single-particle X-ray scattering. We demonstrate electron density determination at 2 Å resolution of various small proteins from synthetic scattering images with as low as 15 photons per image.
Author Grubmüller, Helmut
Schultze, Steffen
Luke, D. Russell
AuthorAffiliation Institute for Numerical and Applied Mathematics
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Snippet Scattering experiments using ultrashort X-ray free electron laser pulses have opened a new path for structure determination of a wide variety of specimens,...
Scattering experiments using ultrashort X-ray free electron laser pulses have opened a new path for structure determination of a wide variety of specimens,...
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SubjectTerms Biomolecular Systems
Biomolecules
Electron density
Free electron lasers
X-ray scattering
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Title Structure Determination from Single-Molecule X‑ray Scattering Images Using Stochastic Gradient Ascent
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