A data set from flash X-ray imaging of carboxysomes

Max F. Hantke; Dirk Hasse; Tomas Ekeberg; Katja John; Martin Svenda; Duane Loh; Andrew V. Martin; Nicusor Timneanu; Daniel S.D. Larsson; Gijs Van Der Schot; Gunilla H. Carlsson; Margareta Ingelman; Jakob Andreasson; Daniel Westphal; Bianca Iwan; Charlotte Uetrecht; Johan Bielecki; Mengning Liang; Francesco Stellato; Daniel P. DePonte; Sadia Bari; Robert Hartmann; Nils Kimmel; Richard A. Kirian; M. Marvin Seibert; Kerstin Mühlig; Sebastian Schorb; Ken Ferguson; Christoph Bostedt; Sebastian Carron; John D. Bozek; Daniel Rolles; Artem Rudenko; Lutz Foucar; Sascha W. Epp; Henry N. Chapman; Anton Barty; Inger Andersson; Janos Hajdu; Filipe R.N.C. Maia

doi:10.1038/sdata.2016.61

A data set from flash X-ray imaging of carboxysomes

Max F. Hantke, Dirk Hasse, Tomas Ekeberg, Katja John, Martin Svenda, Duane Loh, Andrew V. Martin, Nicusor Timneanu, Daniel S.D. Larsson, Gijs Van Der Schot, Gunilla H. Carlsson, Margareta Ingelman, Jakob Andreasson, Daniel Westphal, Bianca Iwan, Charlotte Uetrecht, Johan Bielecki, Mengning Liang, Francesco Stellato, Daniel P. DePonteSadia Bari, Robert Hartmann, Nils Kimmel, Richard A. Kirian, M. Marvin Seibert, Kerstin Mühlig, Sebastian Schorb, Ken Ferguson, Christoph Bostedt, Sebastian Carron, John D. Bozek, Daniel Rolles, Artem Rudenko, Lutz Foucar, Sascha W. Epp, Henry N. Chapman, Anton Barty, Inger Andersson, Janos Hajdu, Filipe R.N.C. Maia

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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.

Original language	English (US)
Article number	160061
Journal	Scientific Data
Volume	3
DOIs	https://doi.org/10.1038/sdata.2016.61
State	Published - Aug 1 2016
Externally published	Yes

ASJC Scopus subject areas

Statistics and Probability
Information Systems
Education
Computer Science Applications
Statistics, Probability and Uncertainty
Library and Information Sciences

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Hantke, M. F., Hasse, D., Ekeberg, T., John, K., Svenda, M., Loh, D., Martin, A. V., Timneanu, N., Larsson, D. S. D., Van Der Schot, G., Carlsson, G. H., Ingelman, M., Andreasson, J., Westphal, D., Iwan, B., Uetrecht, C., Bielecki, J., Liang, M., Stellato, F., ... Maia, F. R. N. C. (2016). A data set from flash X-ray imaging of carboxysomes. Scientific Data, 3, Article 160061. https://doi.org/10.1038/sdata.2016.61

Hantke, MF, Hasse, D, Ekeberg, T, John, K, Svenda, M, Loh, D, Martin, AV, Timneanu, N, Larsson, DSD, Van Der Schot, G, Carlsson, GH, Ingelman, M, Andreasson, J, Westphal, D, Iwan, B, Uetrecht, C, Bielecki, J, Liang, M, Stellato, F, DePonte, DP, Bari, S, Hartmann, R, Kimmel, N, Kirian, RA, Seibert, MM, Mühlig, K, Schorb, S, Ferguson, K, Bostedt, C, Carron, S, Bozek, JD, Rolles, D, Rudenko, A, Foucar, L, Epp, SW, Chapman, HN, Barty, A, Andersson, I, Hajdu, J & Maia, FRNC 2016, 'A data set from flash X-ray imaging of carboxysomes', Scientific Data, vol. 3, 160061. https://doi.org/10.1038/sdata.2016.61

@article{14822784a86f474d8f120683a38c7b92,

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.",

author = "Hantke, {Max F.} and Dirk Hasse and Tomas Ekeberg and Katja John and Martin Svenda and Duane Loh and Martin, {Andrew V.} and Nicusor Timneanu and Larsson, {Daniel S.D.} and {Van Der Schot}, Gijs and Carlsson, {Gunilla H.} and Margareta Ingelman and Jakob Andreasson and Daniel Westphal and Bianca Iwan and Charlotte Uetrecht and Johan Bielecki and Mengning Liang and Francesco Stellato and DePonte, {Daniel P.} and Sadia Bari and Robert Hartmann and Nils Kimmel and Kirian, {Richard A.} and Seibert, {M. Marvin} and Kerstin M{\"u}hlig and Sebastian Schorb and Ken Ferguson and Christoph Bostedt and Sebastian Carron and Bozek, {John D.} and Daniel Rolles and Artem Rudenko and Lutz Foucar and Epp, {Sascha W.} and Chapman, {Henry N.} and Anton Barty and Inger Andersson and Janos Hajdu and Maia, {Filipe R.N.C.}",

note = "Funding Information: This work was supported by the Swedish Research Council, the Knut and Alice Wallenberg Foundation, the Swedish Foundation for Strategic Research, the European Research Council, the Ro.ntgen-A.ngstro.m Cluster, Stiftelsen Olle Engkvist Byggma.stare, the Ministry of Education, Youth and Sports of the Czech Republic (ELI-Beamlines Registered No. CZ.1.05/1.1.00/02.0061), the Academy of Sciences of the Czech Republic (M100101210), and EMBO ALTF 1531.2010. Portions of this research were carried out at the Linac Coherent Light Source, a national user facility operated by Stanford University on behalf of the US Department of Energy, Office of Basic Energy Sciences. The authors thank the scientific and technical staff of the LCLS for support. The authors thank the CAMP collaboration for giving access to their experimental set-up and for supporting the experiment at the LCLS. The authors also acknowledge the Max Planck Society for funding the development and operation of the CAMP instrument.",

year = "2016",

month = aug,

day = "1",

doi = "10.1038/sdata.2016.61",

language = "English (US)",

volume = "3",

journal = "Scientific Data",

issn = "2052-4463",

publisher = "Nature Publishing Group",

}

TY - JOUR

T1 - A data set from flash X-ray imaging of carboxysomes

AU - Hantke, Max F.

AU - Hasse, Dirk

AU - Ekeberg, Tomas

AU - John, Katja

AU - Svenda, Martin

AU - Loh, Duane

AU - Martin, Andrew V.

AU - Timneanu, Nicusor

AU - Larsson, Daniel S.D.

AU - Van Der Schot, Gijs

AU - Carlsson, Gunilla H.

AU - Ingelman, Margareta

AU - Andreasson, Jakob

AU - Westphal, Daniel

AU - Iwan, Bianca

AU - Uetrecht, Charlotte

AU - Bielecki, Johan

AU - Liang, Mengning

AU - Stellato, Francesco

AU - DePonte, Daniel P.

AU - Bari, Sadia

AU - Hartmann, Robert

AU - Kimmel, Nils

AU - Kirian, Richard A.

AU - Seibert, M. Marvin

AU - Mühlig, Kerstin

AU - Schorb, Sebastian

AU - Ferguson, Ken

AU - Bostedt, Christoph

AU - Carron, Sebastian

AU - Bozek, John D.

AU - Rolles, Daniel

AU - Rudenko, Artem

AU - Foucar, Lutz

AU - Epp, Sascha W.

AU - Chapman, Henry N.

AU - Barty, Anton

AU - Andersson, Inger

AU - Hajdu, Janos

AU - Maia, Filipe R.N.C.

N1 - Funding Information: This work was supported by the Swedish Research Council, the Knut and Alice Wallenberg Foundation, the Swedish Foundation for Strategic Research, the European Research Council, the Ro.ntgen-A.ngstro.m Cluster, Stiftelsen Olle Engkvist Byggma.stare, the Ministry of Education, Youth and Sports of the Czech Republic (ELI-Beamlines Registered No. CZ.1.05/1.1.00/02.0061), the Academy of Sciences of the Czech Republic (M100101210), and EMBO ALTF 1531.2010. Portions of this research were carried out at the Linac Coherent Light Source, a national user facility operated by Stanford University on behalf of the US Department of Energy, Office of Basic Energy Sciences. The authors thank the scientific and technical staff of the LCLS for support. The authors thank the CAMP collaboration for giving access to their experimental set-up and for supporting the experiment at the LCLS. The authors also acknowledge the Max Planck Society for funding the development and operation of the CAMP instrument.

PY - 2016/8/1

Y1 - 2016/8/1

N2 - 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.

AB - 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.

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UR - http://www.scopus.com/inward/citedby.url?scp=84982731506&partnerID=8YFLogxK

U2 - 10.1038/sdata.2016.61

DO - 10.1038/sdata.2016.61

M3 - Article

C2 - 27479842

AN - SCOPUS:84982731506

SN - 2052-4463

VL - 3

JO - Scientific Data

JF - Scientific Data

M1 - 160061

ER -

A data set from flash X-ray imaging of carboxysomes

Abstract

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