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A data set from flash X-ray imaging of carboxysomes
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
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2016 (English)In: Scientific Data, ISSN 1012-0602, E-ISSN 2052-4463, Vol. 3, 160061Article in journal (Refereed) Published
Resource type
Text
Abstract [en]

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.

Place, publisher, year, edition, pages
2016. Vol. 3, 160061
National Category
Biophysics
Identifiers
URN: urn:nbn:se:uu:diva-300202DOI: 10.1038/sdata.2016.61ISI: 000390225400006OAI: oai:DiVA.org:uu-300202DiVA: diva2:951092
Note

Data Descriptor

Available from: 2016-08-05 Created: 2016-08-05 Last updated: 2017-02-07Bibliographically approved
In thesis
1. Coherent Diffractive Imaging with X-ray Lasers
Open this publication in new window or tab >>Coherent Diffractive Imaging with X-ray Lasers
2016 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The newly emerging technology of X-ray free-electron lasers (XFELs) has the potential to revolutionise molecular imaging. XFELs generate very intense X-ray pulses and predictions suggest that they may be used for structure determination to atomic resolution even for single molecules. XFELs produce femtosecond pulses that outrun processes of radiation damage and permit the study of structures at room temperature and of structural dynamics.

While the first demonstrations of flash X-ray diffractive imaging (FXI) on biological particles were encouraging, they also revealed technical challenges. In this work we demonstrated how some of these challenges can be overcome. We exemplified, with heterogeneous cell organelles, how tens of thousands of FXI diffraction patterns can be collected, sorted, and analysed in an automatic data processing pipeline. We improved  image resolution and reduced problems with missing data. We validated, described, and deposited the experimental data in the Coherent X-ray Imaging Data Bank.

We demonstrated that aerosol injection can be used to collect FXI data at high hit ratios and with low background. We reduced problems with non-volatile sample contaminants by decreasing aerosol droplet sizes from ~1000 nm to ~150 nm. We achieved this by adapting an electrospray aerosoliser to the Uppsala sample injector. Mie scattering imaging was used as a diagnostic tool to measure positions, sizes, and velocities of individual injected particles.

XFEL experiments generate large amounts of data at high rates. Preparation, execution, and data analysis of these experiments benefits from specialised software. In this work we present new open-source software tools that facilitates prediction, online-monitoring, display, and pre-processing of XFEL diffraction data.

We hope that this work is a valuable contribution in the quest of transitioning FXI from its first experimental demonstration into a technique that fulfills its potentials.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2016. 84 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1451
Keyword
coherent diffractive X-ray imaging, lensless imaging, coherent X-ray diffractive imaging, flash diffractive imaging, single particle imaging, aerosol injection, electrospray injection, substrate-free sample delivery, carboxysome, phase retrieval, X-ray diffraction software, X-ray free-electron laser, XFEL, FEL, CXI, CDI, CXDI, FXI
National Category
Biophysics Atom and Molecular Physics and Optics Structural Biology
Identifiers
urn:nbn:se:uu:diva-306609 (URN)978-91-554-9748-4 (ISBN)
Public defence
2016-12-19, E10:1307-E10:1309, Biomedical Centre, Husargatan 3, Uppsala, 09:30 (English)
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Supervisors
Available from: 2016-11-29 Created: 2016-10-30 Last updated: 2016-12-28

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Hantke, Max F.Hasse, DirkEkeberg, TomasSvenda, MartinTimneanu, NicusorLarsson, Daniel S.D.van der Schot, GijsCarlsson, Gunilla H.Ingelman, MargaretaAndreasson, JakobWestphal, DanielBielecki, JohanSeibert, M. MarvinMühlig, KerstinAndersson, IngerHajdu, JanosMaia, Filipe R.N.C.
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