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


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.

Data availability

All diffraction data have been deposited in the figshare depository and are accessible at 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. 26 are available online.


  1. Jaskolski, M., Dauter, Z. & Wlodawer, A. A brief history of macromolecular crystallography, illustrated by a family tree and its Nobel fruits. FEBS. J. 281, 3985–4009 (2014).

    Article  CAS  Google Scholar 

  2. Duke, E. M. H. & Johnson, L. N. Macromolecular crystallography at synchrotron radiation sources: current status and future developments. Proc. R. Soc. Lond. A Math. Phys. Eng. Sci. 466, 3421–3452 (2010).

    Article  CAS  Google Scholar 

  3. Gruner, S. M., Eikenberry, E. F. & Tate, M. W. in International Tables for Crystallography 2nd edn, Vol. F (eds Rossmann, M. G., Himmel, D. M. & Arnold, E.) 177–182 (International Union of Crystallography, Chester, UK, 2012).

  4. von Seggern, H. Photostimulable x-ray storage phosphors: a review of present understanding. Brazilian Journal of Physics 29, 254–268 (1999).

    Article  Google Scholar 

  5. Howard, A. J. et al. The use of an imaging proportional counter in macromolecular crystallography. J. Appl. Crystallogr. 20, 383–387 (1987).

    Article  CAS  Google Scholar 

  6. Arndt, U. W. X‐ray television area detectors. Synchrotron Radiat. News 3, 17–22 (1990).

    Article  Google Scholar 

  7. Gruner, S. M., Tate, M. W. & Eikenberry, E. F. Charge-coupled device area x-ray detectors. Rev. Sci. Instrum. 73, 2815–2842 (2002).

    Article  CAS  Google Scholar 

  8. Graafsma, H. in Semiconductor Radiation Detection Systems (ed Iniewski, K.) 217–236 (CRC Press, Boca Raton, FL, 2010).

  9. Waterman, D. & Evans, G. Estimation of errors in diffraction data measured by CCD area detectors. J. Appl. Crystallogr. 43, 1356–1371 (2010).

    Article  CAS  Google Scholar 

  10. Dauter, Z. Data-collection strategies. Acta Crystallogr. D Biol. Crystallogr. 55, 1703–1717 (1999).

    Article  CAS  Google Scholar 

  11. Broennimann, Ch. et al. The PILATUS 1M detector. J. Synchrotron. Radiat. 13, 120–130 (2006).

    Article  CAS  Google Scholar 

  12. Mueller, M., Wang, M. & Schulze-Briese, C. Optimal fine φ-slicing for single-photon-counting pixel detectors. Acta Crystallogr. D Biol. Crystallogr. 68, 42–56 (2012).

    Article  CAS  Google Scholar 

  13. Dinapoli, R. et al. EIGER: next generation single photon counting detector for X-ray applications. Nucl. Instrum. Methods. Phys. Res. A 650, 79–83 (2011).

    Article  CAS  Google Scholar 

  14. Casanas, A. et al. EIGER detector: application in macromolecular crystallography. Acta Crystallogr. D Struct. Biol. 72, 1036–1048 (2016).

    Article  CAS  Google Scholar 

  15. Wojdyla, J. A. et al. Fast two-dimensional grid and transmission X-ray microscopy scanning methods for visualizing and characterizing protein crystals. J. Appl. Crystallogr. 49, 944–952 (2016).

    Article  CAS  Google Scholar 

  16. Diederichs, K. & Wang, M. in Protein Crystallography: Methods and Protocols (eds Wlodawer, A., Dauter, Z. & Jaskolski, M.) 239–272 (Humana Press, New York, 2017).

  17. Ballabriga, R. et al. The Medipix3RX: a high resolution, zero dead-time pixel detector readout chip allowing spectroscopic imaging. J. Instrum. 8, C02016 (2013).

    Article  Google Scholar 

  18. Sobott, B. A. et al. Success and failure of dead-time models as applied to hybrid pixel detectors in high-flux applications. J. Synchrotron. Radiat. 20, 347–354 (2013).

    Article  CAS  Google Scholar 

  19. Loeliger, T. et al. in 2012 IEEE Nuclear Science Symposium and Medical Imaging Conference Record (NSS/MIC) (ed Yu, B.) 610–615 (IEEE, New York, 2012).

  20. Eriksson, M., van der Veen, J. F. & Quitmann, C. Diffraction-limited storage rings—a window to the science of tomorrow. J. Synchrotron. Radiat. 21, 837–842 (2014).

    Article  CAS  Google Scholar 

  21. Denes, P. & Schmitt, B. Pixel detectors for diffraction-limited storage rings. J. Synchrotron. Radiat. 21, 1006–1010 (2014).

    Article  Google Scholar 

  22. Graafsma, H., Becker, J. & Gruner, S. M. in Synchrotron Light Sources and Free-Electron Lasers (eds Jaeschke, E. et al.) 1029–1054 (Springer, Cham, 2016).

  23. Tate, M. W. et al. A medium-format, mixed-mode pixel array detector for kilohertz X-ray imaging. J. Phys. Conf. Ser. 425, 062004 (2013).

    Article  Google Scholar 

  24. Mozzanica, A. et al. Characterization results of the JUNGFRAU full scale readout ASIC. J. Instrum. 11, C02047 (2016).

    Article  Google Scholar 

  25. Chapman, H. N. et al. Femtosecond X-ray protein nanocrystallography. Nature 470, 73–77 (2011).

    Article  CAS  Google Scholar 

  26. Redford, S. et al. First full dynamic range calibration of the JUNGFRAU photon detector. J. Instrum. 13, C01027 (2018).

    Article  Google Scholar 

  27. Liu, Q. et al. Structures from anomalous diffraction of native biological macromolecules. Science 336, 1033–1037 (2012).

    Article  CAS  Google Scholar 

  28. Weinert, T. et al. Fast native-SAD phasing for routine macromolecular structure determination. Nat. Methods 12, 131–133 (2015).

    Article  CAS  Google Scholar 

  29. Terwilliger, T. C. et al. Can I solve my structure by SAD phasing? Anomalous signal in SAD phasing. Acta Crystallogr. D Struct. Biol. 72, 346–358 (2016).

    Article  CAS  Google Scholar 

  30. Sheldrick, G. M. Experimental phasing with SHELXC/D/E: combining chain tracing with density modification. Acta Crystallogr. D Biol. Crystallogr. 66, 479–485 (2010).

    Article  CAS  Google Scholar 

  31. Skubák, P. & Pannu, N. S. Automatic protein structure solution from weak X-ray data. Nat. Commun. 4, 2777 (2013).

    Article  Google Scholar 

  32. Garman, E. F. Radiation damage in macromolecular crystallography: what is it and why should we care? Acta Crystallogr. D Biol. Crystallogr. 66, 339–351 (2010).

    Article  CAS  Google Scholar 

  33. Neutze, R. & Moffat, K. Time-resolved structural studies at synchrotrons and X-ray free electron lasers: opportunities and challenges. Curr. Opin. Struct. Biol. 22, 651–659 (2012).

    Article  CAS  Google Scholar 

  34. Gati, C. et al. Serial crystallography on in vivo grown microcrystals using synchrotron radiation. IUCrJ 1, 87–94 (2014).

    Article  CAS  Google Scholar 

  35. Weinert, T. et al. Serial millisecond crystallography for routine room-temperature structure determination at synchrotrons. Nat. Commun. 8, 542 (2017).

    Article  Google Scholar 

  36. Beyerlein, K. R. et al. Mix-and-diffuse serial synchrotron crystallography. IUCrJ 4, 769–777 (2017).

    Article  CAS  Google Scholar 

  37. Gruner, S. M. & Lattman, E. E. Biostructural science inspired by next-generation X-ray sources. Annu. Rev. Biophys. 44, 33–51 (2015).

    Article  CAS  Google Scholar 

  38. Meents, A. et al. Pink-beam serial crystallography. Nat. Commun. 8, 1281 (2017).

    Article  CAS  Google Scholar 

  39. Barty, A. et al. Cheetah: software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data. J. Appl. Crystallogr. 47, 1118–1131 (2014).

    Article  CAS  Google Scholar 

  40. Mariani, V. et al. OnDA: online data analysis and feedback for serial X-ray imaging. J. Appl. Crystallogr. 49, 1073–1080 (2016).

    Article  CAS  Google Scholar 

  41. Zeldin, O. B. et al. Data Exploration Toolkit for serial diffraction experiments. Acta Crystallogr. D Biol. Crystallogr. 71, 352–356 (2015).

    Article  CAS  Google Scholar 

  42. Wojdyla, J. A. et al. DA+ data acquisition and analysis software at the Swiss Light Source macromolecular crystallography beamlines. J. Synchrotron. Radiat. 25, 293–303 (2018).

    Article  CAS  Google Scholar 

  43. Redford, S. et al. Calibration status and plans for the charge integrating JUNGFRAU pixel detector for SwissFEL. J. Instrum. 11, C11013 (2016).

    Article  Google Scholar 

  44. Bernstein, H. J. & Hammersley, A. P. in International Tables for Crystallography Vol. G (eds Hall, S. R. & McMahon, B.) 37–43 (International Union of Crystallography, Chester, UK, 2006).

  45. Peng, G. et al. Insight into the remarkable affinity and selectivity of the aminobenzosuberone scaffold for the M1 aminopeptidases family based on structure analysis. Proteins 85, 1413–1421 (2017).

    Article  CAS  Google Scholar 

  46. Paithankar, K. S., Owen, R. L. & Garman, E. F. Absorbed dose calculations for macromolecular crystals: improvements to RADDOSE. J. Synchrotron. Radiat. 16, 152–162 (2009).

    Article  CAS  Google Scholar 

  47. Kabsch, W. XDS. Acta Crystallogr. D Biol. Crystallogr. 66, 125–132 (2010).

    Article  CAS  Google Scholar 

  48. Pape, T. & Schneider, T. R. HKL2MAP: a graphical user interface for macromolecular phasing withSHELXprograms. J. Appl. Crystallogr. 37, 843–844 (2004).

    Article  CAS  Google Scholar 

  49. Thorn, A. & Sheldrick, G. M. ANODE: anomalous and heavy-atom density calculation. J. Appl. Crystallogr. 44, 1285–1287 (2011).

    Article  CAS  Google Scholar 

  50. Afonine, P. V. et al. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr. D Biol. Crystallogr. 68, 352–367 (2012).

    Article  CAS  Google Scholar 

  51. Diederichs, K. & Karplus, P. A. Improved R-factors for diffraction data analysis in macromolecular crystallography. Nat. Struct. Biol. 4, 269–275 (1997).

    Article  CAS  Google Scholar 

  52. Johnson, I. et al. Eiger: a single-photon counting x-ray detector. J. Instrum. 9, C05032 (2014).

    Article  Google Scholar 

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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



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.

Supplementary information

Supplementary Text and Figures

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).

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