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Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers

Nature Methods volume 11, pages 545–548 (2014)Cite this article

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A Corrigendum to this article was published on 30 June 2015

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Abstract

X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and without radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract meaningful high-resolution signals from fewer diffraction measurements.

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Figure 1: Thermolysin structure determination at 2.1 Å resolution.
Figure 2: Calibration and validation.

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  • 03 June 2015

    In the version of this article initially published, the authors claimed that with the tool cctbx.xfel, weak diffraction signals can be measured using fewer crystal specimens than are needed for the previously available program CrystFEL. However, there is not enough evidence to support this claim. The inaccurate statements have been corrected in the HTML and PDF versions of the article.

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Acknowledgements

This work was supported by US National Institutes of Health (NIH) grants GM095887 and GM102520 and Director, Office of Science, US Department of Energy (DOE) under contract DE-AC02-05CH11231 for data-processing methods (N.K.S.); Director, DOE Office of Science, Office of Basic Energy Sciences (OBES), Chemical Sciences, Geosciences and Biosciences Division (CSGB) under contract DE-AC02-05CH11231 (J.Y. and V.K.Y.); NIH grant GM055302 (V.K.Y.); and NIH grant P41GM103393 (U.B.). Sample injection was supported by LCLS (M.J.B. and D.W.S.) and the Atomic, Molecular and Optical Science program, CSGB Division, OBES, DOE (M.J.B.), and through the SLAC National Accelerator Laboratory Directed Research and Development program (M.J.B. and H.L.). J.M. was supported by the Artificial Leaf Project Umeå (K&A Wallenberg Foundation), the Solar Fuels Strong Research Environment Umeå (Umeå University), Vetenskapsrådet and Swedish Energy Agency (Energimyndigheten). Experiments were carried out at the LCLS at SLAC, an Office of Science User Facility operated for the DOE by Stanford University. We thank A. Perazzo, M. Dubrovin, I. Ofte, and A. Salnikov for collaboration on data analysis, and C. Kenney for expertise related to the CSPAD detector.

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Author notes

  1. Richard J Gildea

    Present address: Present address: Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, UK.,

Authors and Affiliations

  1. Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA

    Johan Hattne, Nathaniel Echols, Rosalie Tran, Jan Kern, Richard J Gildea, Aaron S Brewster, Benedikt Lassalle-Kaiser, Alyssa Lampe, Guangye Han, Sheraz Gul, Petrus H Zwart, Ralf W Grosse-Kunstleve, Junko Yano, Vittal K Yachandra, Paul D Adams & Nicholas K Sauter

  2. Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California, USA

    Roberto Alonso-Mori, Despina Milathianaki, Alan R Fry, Alan Miahnahri, William E White, Donald W Schafer, M Marvin Seibert, Jason E Koglin, Michael J Bogan, Marc Messerschmidt, Garth J Williams, Sébastien Boutet & Uwe Bergmann

  3. Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität, Berlin, Germany

    Carina Glöckner, Julia Hellmich, Dörte DiFiore & Athina Zouni

  4. Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California, USA

    Hartawan Laksmono, Raymond G Sierra & Michael J Bogan

  5. Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA

    Dimosthenis Sokaras, Tsu-Chien Weng, Jonas Sellberg & Matthew J Latimer

  6. Department of Physics, AlbaNova, Stockholm University, Stockholm, Sweden

    Jonas Sellberg

  7. European Synchrotron Radiation Facility, Grenoble, France

    Pieter Glatzel

  8. Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, Umeå, Sweden

    Johannes Messinger

  9. Institut für Biologie, Humboldt Universität zu Berlin, Berlin, Germany

    Athina Zouni

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  1. Johan Hattne
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Contributions

J. Hattne, J.K., J.Y., U.B., V.K.Y., P.D.A. and N.K.S. conceived of the new data-processing methods and analyzed the data; J. Hattne, N.E., R.J.G., A.S.B., R.W.G.-K., P.H.Z., M.M., P.D.A. and N.K.S. wrote the data-processing software; U.B., J.Y., V.K.Y., J.K., R.A.-M., J.M., A.Z., N.K.S., G.J.W., S.B., A.R.F., A.M., D.M., D.W.S., W.E.W. and M.J.B. designed the experiment; R.T., C.G., J. Hellmich, D.D., A.L., G.H., J.K. and A.Z. prepared samples; S.B., J.E.K., M.M., M.M.S., G.J.W. operated the CXI instrument; M.J.B., H.L., R.G.S., J.K., J.M., B.L.-K., S.G., R.T., C.G., J. Hellmich, J.S., D.W.S., A.M. and G.J.W. developed, tested and ran the sample delivery system; R.A.-M., U.B., M.J.B., S.B., N.E., R.J.G., P.G., C.G.,S.G., G.H., J.Hattne., J.Hellmich, J.K., J.E.K., H.L., A.L., B.L.-K., D.M., M.M., J.M., N.K.S., M.M.S., J.S., R.G.S., D.S., R.T., T.-C.W., G.J.W., V.K.Y., J.Y. and A.Z. performed the LCLS experiment; J. Hattne, N.E., J.K., J.Y., U.B., V.K.Y., P.D.A. and N.K.S. wrote the manuscript with input from all authors.

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Correspondence to Nicholas K Sauter.

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Hattne, J., Echols, N., Tran, R. et al. Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers. Nat Methods 11, 545–548 (2014). https://doi.org/10.1038/nmeth.2887

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