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Time-resolved crystallography using the Hadamard transform

Nature Methods volume 11, pages 1131–1134 (2014)Cite this article

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A Corrigendum to this article was published on 29 January 2015

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Abstract

We describe a method for performing time-resolved X-ray crystallographic experiments based on the Hadamard transform, in which time resolution is defined by the underlying periodicity of the probe pulse sequence, and signal/noise is greatly improved over that for the fastest pump-probe experiments depending on a single pulse. This approach should be applicable on standard synchrotron beamlines and will enable high-resolution measurements of protein and small-molecule structural dynamics. It is also applicable to other time-resolved measurements where a probe can be encoded, such as pump-probe spectroscopy.

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Figure 1: Comparison of classical pump-probe and HATRX methods.
Figure 2: Difference electron density maps showing the comparison of control and HATRX data for thaumatin.
Figure 3: Experimental design used to demonstrate HATRX.

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Change history

  • 08 January 2015

    In the version of this article initially published, the Figure 2 legend misidentified the control data as on the left and the HATRX data as on the right. The error has been corrected in the HTML and PDF versions of the article.

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Acknowledgements

B.A.Y. is supported by the Wellcome Trust 4-year PhD program “The Molecular Basis of Biological Mechanisms” 089312/Z/09/Z. This work was also supported by the EPSRC Award “Dynamic Structural Science at the Research Complex at Harwell” EP/I01974X/1 and by BBSRC Award BB/H001905/1. Diffraction data were collected on beamline I24 at Diamond Light Source under proposal nt5810. We thank Diamond Light Source and the staff of I24 for beamtime and support and D. Waterman (CCP4) for the SUMSUB code. We also thank P. Raithby, C. Wilson, J. Trincao, J. Christensen, M. Hamilton, E. Snell, T. Burnley, C. Wood and C. Ballard for useful discussions and critical reading of the manuscript.

Author information

Author notes

  1. Briony A Yorke, Godfrey S Beddard & Arwen R Pearson

    Present address: Current addresses: Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Hamburg, Germany (B.A.Y., A.R.P.); School of Chemistry, University of Edinburgh, Edinburgh, Scotland, UK (G.S.B.).,

Authors and Affiliations

  1. Astbury Centre for Structural Molecular Biology, The University of Leeds, Leeds, UK

    Briony A Yorke & Arwen R Pearson

  2. School of Chemistry, The University of Leeds, Leeds, UK

    Godfrey S Beddard

  3. Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK

    Robin L Owen

Authors
  1. Briony A Yorke
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  2. Godfrey S Beddard
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  3. Robin L Owen
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Contributions

G.S.B. and B.A.Y. originally proposed the application of the Hadamard transform to time-resolved experiments. B.A.Y., R.L.O. and A.R.P. devised the proof-of-principle crystallographic experiment and collected the data. B.A.Y., R.L.O., G.S.B. and A.R.P. all processed data, wrote software and jointly wrote the manuscript.

Corresponding authors

Correspondence to Godfrey S Beddard, Robin L Owen or Arwen R Pearson.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–4 and Supplementary Tables 4 and 5. (PDF 10730 kb)

Supplementary Table 1

Scaling statistics for the reference data (XLSX 102 kb)

Supplementary Table 2

Scaling statistics for the n = 3 HATRX data (XLSX 93 kb)

Supplementary Table 3

Weighted R factors (W rel) by resolution shell14 for the comparison of the reference data (R) at each time point with the HATRX data. (XLSX 56 kb)

Supplementary Software 1

This script takes a user defined set of images from multiple crystals and produces an integrated list of reflections using XDS. These data can then be scaled, merged and converted to structure factors using the CCP4 software suite. (TXT 10 kb)

Supplementary Software 2

This script takes a plain text file (with the format H K L F1 SIGF1 F2 SIGF2 ... Fn SIGFn), calculates the S-matrix and carries out the HATRX transform. It outputs a plain text file in the same format as the input data. (TXT 3 kb)

Supplementary Software 3

This script converts the output of 2_HATRX.py into a CCP4 format mtz file ready for further analysis using any standard crystallographic software package. (TXT 0 kb)

Supplementary Software 4

This script uses the sumsub routine to create HATRX encoded images from a series of CBF format images. It was used to create the HATRX images here to show proof of principle of the method. When the HATRX data are generated by detector or beam encoding this step is not required. (TXT 3 kb)

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Yorke, B., Beddard, G., Owen, R. et al. Time-resolved crystallography using the Hadamard transform. Nat Methods 11, 1131–1134 (2014). https://doi.org/10.1038/nmeth.3139

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