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Fast and accurate data collection for macromolecular crystallography using the JUNGFRAU detector

Nature Methods volume 15, pages 799–804 (2018)Cite this article

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Abstract

The accuracy of X-ray diffraction data is directly related to how the X-ray detector records photons. Here we describe the application of a direct-detection charge-integrating pixel-array detector (JUNGFRAU) in macromolecular crystallography (MX). JUNGFRAU features a uniform response on the subpixel level, linear behavior toward high photon rates, and low-noise performance across the whole dynamic range. We demonstrate that these features allow accurate MX data to be recorded at unprecedented speed. We also demonstrate improvements over previous-generation detectors in terms of data quality, using native single-wavelength anomalous diffraction (SAD) phasing, for thaumatin, lysozyme, and aminopeptidase N. Our results suggest that the JUNGFRAU detector will substantially improve the performance of synchrotron MX beamlines and equip them for future synchrotron light sources.

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Fig. 1: Demonstration of the dynamic gain-switching of the JUNGFRAU detector.
Fig. 2: Comparison of data quality between JF1M and E1M data from routine MX applications.
Fig. 3: Comparison of measurements with different photon rates acquired with the JUNGFRAU detector.
Fig. 4: Comparison of 6-keV thaumatin crystal data measured with JF1M and E1M detectors (two threshold settings for E1M).
Fig. 5: Sub-pixel uniformity characterization of the JUNGFRAU and EIGER detectors.
Fig. 6: Fast native-SAD phasing with an unattenuated beam at both 6 keV and 12.4 keV with JF1M.

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Data availability

All diffraction data have been deposited in the figshare depository and are accessible at https://doi.org/10.6084/m9.figshare.6087368. Diffraction data and refined models for native-SAD structures have been deposited in the Protein Data Bank as PDB 6G89 (thaumatin), 6G8A (lysozyme), and 6G8B (PepN). Source data for Figs. 2–6 are available online.

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Acknowledgements

The project was funded by the Paul Scherrer Institute. We thank C. Tarnus, C. Schmitt, and S. Albrecht for the preparation of PepN crystals.

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Authors and Affiliations

  1. Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland

    Filip Leonarski, Sophie Redford, Aldo Mozzanica, Carlos Lopez-Cuenca, Ezequiel Panepucci, Karol Nass, Dmitry Ozerov, Laura Vera, Vincent Olieric, Dominik Buntschu, Roman Schneider, Gemma Tinti, Erik Froejdh, Oliver Bunk, Bernd Schmitt & Meitian Wang

  2. Fachbereich Biologie, Universität Konstanz, Konstanz, Germany

    Kay Diederichs

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Contributions

M.W., O.B., and B.S. conceived the research; S.R., A.M., and C.L.-C. built and calibrated the JF1M detector; A.M., D.B., and R.S. installed JF1M and E1M detectors at beamline X06SA; F.L., A.M., and E.P. developed diffraction-data collection software; L.V. and V.O. prepared samples; F.L., S.R., A.M., E.P., and M.W. collected data; F.L., S.R., K.N., D.O., G.T., E.F., K.D., and M.W. analyzed data; and F.L., S.R., O.B., and M.W. wrote the manuscript with contributions from all other authors.

Corresponding authors

Correspondence to Bernd Schmitt or Meitian Wang.

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Integrated supplementary information

Supplementary Figure 1

Experimental setup with a JUNGFRAU 1M detector at the X06SA beamline, SLS.

Supplementary Figure 2 Spatial profile of Bragg spots from a thaumatin crystal (Thau2).

One diffraction image and reflection profiles of six reflections from different resolution shells and regions of the E1M detector are shown. To obtain full reflections, the image presented here corresponds to 1.76o rotation of the crystal (sum of 20 frames). Reflections are about single pixel wide horizontally but elongated vertically.

Supplementary Figure 3 Comparison of 6-keV data from a thaumatin crystal measured with JUNGFRAU and EIGER detectors (two threshold settings for EIGER).

The <I/σ>mrgd values are plotted as a function of resolution.

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Supplementary Figs. 1–3 and Supplementary Tables 1–6

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Leonarski, F., Redford, S., Mozzanica, A. et al. Fast and accurate data collection for macromolecular crystallography using the JUNGFRAU detector. Nat Methods 15, 799–804 (2018). https://doi.org/10.1038/s41592-018-0143-7

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