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Title: A data set from flash X-ray imaging of carboxysomes

Abstract

Ultra-intense femtosecond X-ray pulses from X-ray lasers permit structural studies on single particles and biomolecules without crystals. We present a large data set on inherently heterogeneous, polyhedral carboxysome particles. Carboxysomes are cell organelles that vary in size and facilitate up to 40% of Earth’s carbon fixation by cyanobacteria and certain proteobacteria. Variation in size hinders crystallization. Carboxysomes appear icosahedral in the electron microscope. A protein shell encapsulates a large number of Rubisco molecules in paracrystalline arrays inside the organelle. We used carboxysomes with a mean diameter of 115 ±26 nm from Halothiobacillus neapolitanus. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min. Every diffraction pattern is a unique structure measurement and high-throughput imaging allows sampling the space of structural variability. The different structures can be separated and phased directly from the diffraction data and open a way for accurate, high-throughput studies on structures and structural heterogeneity in biology and elsewhere.

Authors:
 [1];  [1];  [1];  [1];  [1];  [2];  [3];  [4];  [1];  [1];  [1];  [1];  [5];  [1];  [1];  [1];  [1];  [6];  [7];  [8] more »;  [9];  [10];  [11];  [6];  [12];  [1];  [8];  [8];  [8];  [8];  [8];  [13];  [14];  [15];  [16];  [6];  [6];  [1];  [17];  [18] « less
+ Show Author Affiliations
  1. Uppsala Univ. (Sweden). Dept. of Cell and Molecular Biology, Lab. of Molecular Biophysics
  2. National University of Singapore (Singapore). Centre for BioImaging Sciences
  3. Univ. of Melbourne (Australia). ARC Centre of Excellence for Advanced Molecular Imaging. School of Physics
  4. Uppsala Univ. (Sweden). Dept. of Cell and Molecular Biology, Lab. of Molecular Biophysics; Uppsala Univ. (Sweden). Dept. of Physics and Astronomy
  5. Uppsala Univ. (Sweden). Dept. of Cell and Molecular Biology, Lab. of Molecular Biophysics; Academy of Sciences of the Czech Republic, Prague (Czech Republic). Inst. of Physics. ELI beamlines
  6. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany). Center for Free-Electron Laser Science
  7. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany). Center for Free-Electron Laser Science; Tor Vergata Univ. of Rome (Italy). Physics Dept. INFN
  8. SLAC National Accelerator Lab., Menlo Park, CA (United States). Linac Coherent Light Source (LCLS)
  9. European X-ray Free-Electron Laser (XFEL), Hamburg (Germany); Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)
  10. PNSensor GmbH, München (Germany)
  11. Max Planck Inst. fuer Extraterrestrische Physik, Garching (Germany)
  12. Uppsala Univ. (Sweden). Dept. of Cell and Molecular Biology, Lab. of Molecular Biophysics; SLAC National Accelerator Lab., Menlo Park, CA (United States). Linac Coherent Light Source (LCLS)
  13. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany). Center for Free-Electron Laser Science; Kansas State Univ., Manhattan, KS (United States). J.R. Macdonald Lab. Dept. of Physics; Max Planck Inst. for Medical Research, Heidelberg (Germany); Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Hamburg (Germany)
  14. Kansas State Univ., Manhattan, KS (United States). J.R. Macdonald Lab. Dept. of Physics; Max Planck Inst. for Medical Research, Heidelberg (Germany); Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Hamburg (Germany); Max Planck Inst. fuer Kernphysik, Heidelberg (Germany)
  15. Kansas State Univ., Manhattan, KS (United States). J.R. Macdonald Lab. Dept. of Physics; Max Planck Inst. for Medical Research, Heidelberg (Germany)
  16. Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Hamburg (Germany); Max Planck Inst. fuer Kernphysik, Heidelberg (Germany); Max Planck Inst. for the Structure and Dynamics of Matter, Hamburg (Germany)
  17. Uppsala Univ. (Sweden). Dept. of Cell and Molecular Biology, Lab. of Molecular Biophysics; European X-ray Free-Electron Laser (XFEL), Hamburg (Germany)
  18. Uppsala Univ. (Sweden). Dept. of Cell and Molecular Biology, Lab. of Molecular Biophysics; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Rocky Mountain Oilfield Testing Center (RMOTC), Casper, WY (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
OSTI Identifier:
1624548
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Data
Additional Journal Information:
Journal Volume: 3; Journal Issue: 1; Journal ID: ISSN 2052-4463
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Science & Technology - Other Topics

Citation Formats

Hantke, Max F., Hasse, Dirk, Ekeberg, Tomas, John, Katja, Svenda, Martin, Loh, Duane, Martin, Andrew V., Timneanu, Nicusor, Larsson, Daniel S. D., van der Schot, Gijs, Carlsson, Gunilla H., Ingelman, Margareta, Andreasson, Jakob, Westphal, Daniel, Iwan, Bianca, Uetrecht, Charlotte, Bielecki, Johan, Liang, Mengning, Stellato, Francesco, DePonte, Daniel P., Bari, Sadia, Hartmann, Robert, Kimmel, Nils, Kirian, Richard A., Seibert, M. Marvin, Mühlig, Kerstin, Schorb, Sebastian, Ferguson, Ken, Bostedt, Christoph, Carron, Sebastian, Bozek, John D., Rolles, Daniel, Rudenko, Artem, Foucar, Lutz, Epp, Sascha W., Chapman, Henry N., Barty, Anton, Andersson, Inger, Hajdu, Janos, and Maia, Filipe R. N. C. A data set from flash X-ray imaging of carboxysomes. United States: N. p., 2016. Web. doi:10.1038/sdata.2016.61.
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Hantke, Max F., Hasse, Dirk, Ekeberg, Tomas, John, Katja, Svenda, Martin, Loh, Duane, Martin, Andrew V., Timneanu, Nicusor, Larsson, Daniel S. D., van der Schot, Gijs, Carlsson, Gunilla H., Ingelman, Margareta, Andreasson, Jakob, Westphal, Daniel, Iwan, Bianca, Uetrecht, Charlotte, Bielecki, Johan, Liang, Mengning, Stellato, Francesco, DePonte, Daniel P., Bari, Sadia, Hartmann, Robert, Kimmel, Nils, Kirian, Richard A., Seibert, M. Marvin, Mühlig, Kerstin, Schorb, Sebastian, Ferguson, Ken, Bostedt, Christoph, Carron, Sebastian, Bozek, John D., Rolles, Daniel, Rudenko, Artem, Foucar, Lutz, Epp, Sascha W., Chapman, Henry N., Barty, Anton, Andersson, Inger, Hajdu, Janos, & Maia, Filipe R. N. C. A data set from flash X-ray imaging of carboxysomes. United States. https://doi.org/10.1038/sdata.2016.61
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Hantke, Max F., Hasse, Dirk, Ekeberg, Tomas, John, Katja, Svenda, Martin, Loh, Duane, Martin, Andrew V., Timneanu, Nicusor, Larsson, Daniel S. D., van der Schot, Gijs, Carlsson, Gunilla H., Ingelman, Margareta, Andreasson, Jakob, Westphal, Daniel, Iwan, Bianca, Uetrecht, Charlotte, Bielecki, Johan, Liang, Mengning, Stellato, Francesco, DePonte, Daniel P., Bari, Sadia, Hartmann, Robert, Kimmel, Nils, Kirian, Richard A., Seibert, M. Marvin, Mühlig, Kerstin, Schorb, Sebastian, Ferguson, Ken, Bostedt, Christoph, Carron, Sebastian, Bozek, John D., Rolles, Daniel, Rudenko, Artem, Foucar, Lutz, Epp, Sascha W., Chapman, Henry N., Barty, Anton, Andersson, Inger, Hajdu, Janos, and Maia, Filipe R. N. C. Mon . "A data set from flash X-ray imaging of carboxysomes". United States. https://doi.org/10.1038/sdata.2016.61. https://www.osti.gov/servlets/purl/1624548.
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@article{osti_1624548,
title = {A data set from flash X-ray imaging of carboxysomes},
author = {Hantke, Max F. and Hasse, Dirk and Ekeberg, Tomas and John, Katja and Svenda, Martin and Loh, Duane and Martin, Andrew V. and Timneanu, Nicusor and Larsson, Daniel S. D. and van der Schot, Gijs and Carlsson, Gunilla H. and Ingelman, Margareta and Andreasson, Jakob and Westphal, Daniel and Iwan, Bianca and Uetrecht, Charlotte and Bielecki, Johan and Liang, Mengning and Stellato, Francesco and DePonte, Daniel P. and Bari, Sadia and Hartmann, Robert and Kimmel, Nils and Kirian, Richard A. and Seibert, M. Marvin and Mühlig, Kerstin and Schorb, Sebastian and Ferguson, Ken and Bostedt, Christoph and Carron, Sebastian and Bozek, John D. and Rolles, Daniel and Rudenko, Artem and Foucar, Lutz and Epp, Sascha W. and Chapman, Henry N. and Barty, Anton and Andersson, Inger and Hajdu, Janos and Maia, Filipe R. N. C.},
abstractNote = {Ultra-intense femtosecond X-ray pulses from X-ray lasers permit structural studies on single particles and biomolecules without crystals. We present a large data set on inherently heterogeneous, polyhedral carboxysome particles. Carboxysomes are cell organelles that vary in size and facilitate up to 40% of Earth’s carbon fixation by cyanobacteria and certain proteobacteria. Variation in size hinders crystallization. Carboxysomes appear icosahedral in the electron microscope. A protein shell encapsulates a large number of Rubisco molecules in paracrystalline arrays inside the organelle. We used carboxysomes with a mean diameter of 115 ±26 nm from Halothiobacillus neapolitanus. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min. Every diffraction pattern is a unique structure measurement and high-throughput imaging allows sampling the space of structural variability. The different structures can be separated and phased directly from the diffraction data and open a way for accurate, high-throughput studies on structures and structural heterogeneity in biology and elsewhere.},
doi = {10.1038/sdata.2016.61},
journal = {Scientific Data},
number = 1,
volume = 3,
place = {United States},
year = {Mon Aug 01 00:00:00 EDT 2016},
month = {Mon Aug 01 00:00:00 EDT 2016}
}
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