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Related Concept Videos

X-ray Diffraction of Biological Samples01:10

X-ray Diffraction of Biological Samples

X-ray diffraction or XRD is an analytical tool that utilizes X-rays to study ordered structures such as crystalline organic and inorganic samples, polycrystalline materials, proteins, carbohydrates, and drugs.
According to Bragg's law, when X-rays strike the sample positioned on a stage, the rays are  scattered by the electron clouds around the sample atoms. The  X-ray diffraction or scattering is caused by constructive interference of the X-ray waves that reflect off the internal crystal...
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Related Experiment Video

Updated: Jun 4, 2026

Small and Wide Angle X-Ray Scattering Studies of Biological Macromolecules in Solution
12:53

Small and Wide Angle X-Ray Scattering Studies of Biological Macromolecules in Solution

Published on: January 8, 2013

SoftWAXS: a computational tool for modeling wide-angle X-ray solution scattering from biomolecules.

Jaydeep Bardhan, Sanghyun Park, Lee Makowski

    Journal of Applied Crystallography
    |February 23, 2011
    PubMed
    Summary

    This study introduces SoftWAXS, a computational tool for estimating wide-angle X-ray solution scattering (WAXS) from proteins. The program offers accurate calculations by explicitly modeling the solute-solvent and hydration layers, improving WAXS data analysis.

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    Biochemical and Structural Characterization of the Carbohydrate Transport Substrate-binding-protein SP0092
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    Last Updated: Jun 4, 2026

    Small and Wide Angle X-Ray Scattering Studies of Biological Macromolecules in Solution
    12:53

    Small and Wide Angle X-Ray Scattering Studies of Biological Macromolecules in Solution

    Published on: January 8, 2013

    Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae
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    Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae

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    Biochemical and Structural Characterization of the Carbohydrate Transport Substrate-binding-protein SP0092
    08:53

    Biochemical and Structural Characterization of the Carbohydrate Transport Substrate-binding-protein SP0092

    Published on: October 2, 2017

    Area of Science:

    • Biophysics
    • Computational Biology
    • Structural Biology

    Background:

    • Wide-angle X-ray solution scattering (WAXS) is crucial for determining protein structures in solution.
    • Accurate computational modeling of WAXS is essential for interpreting experimental data.
    • Existing models for excluded volume and solvent representation have limitations.

    Purpose of the Study:

    • To develop and analyze a computational approach for estimating protein WAXS patterns.
    • To implement this approach in a user-friendly program called SoftWAXS.
    • To assess the accuracy and efficiency of SoftWAXS for various models and proteins.

    Main Methods:

    • Developed a computational method incorporating numerical spherical averaging.
    • Explicitly represented the solute-solvent boundary and hydration layer.
    • Computed Fourier transforms of excluded volume and hydration layer directly and accurately.

    Main Results:

    • SoftWAXS demonstrated accuracy and efficiency on model problems and proteins.
    • The explicit hydration layer model differed significantly from Gaussian-based excluded volume models.
    • Comparison with molecular dynamics highlighted limitations of time-averaged solvent profiles.

    Conclusions:

    • The developed SoftWAXS approach provides accurate WAXS estimations.
    • Sophisticated solvent treatments are necessary for predictive, high-resolution WAXS calculations.
    • This method facilitates future investigations into hydration shell electron density treatments.