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Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals

View ORCID ProfileAlexander M Wolff, View ORCID ProfileIris D Young, Raymond G Sierra, Aaron S Brewster, Michael W Martynowycz, Eriko Nango, Michihiro Sugahara, Takanori Nakane, Kazutaka Ito, Andrew Aquila, Asmit Bhowmick, Justin T Biel, Sergio Carbajo, Aina E Cohen, Saul Cortez, Ana Gonzalez, Tomoya Hino, Dohyun Im, Jake D Koralek, Minoru Kubo, Tomas S Lazarou, Takashi Nomura, Shigeki Owada, Avi Samelson, Rie Tanaka, Tomoyuki Tanaka, Erin M Thompson, Henry van den Bedem, Rahel A Woldeyes, Fumiaki Yumoto, Wei Zhao, Kensuke Tono, Sébastien Boutet, So Iwata, Tamir Gonen, Nicholas K Sauter, View ORCID ProfileJames S Fraser, View ORCID ProfileMichael C Thompson
doi: https://doi.org/10.1101/767061
Alexander M Wolff
1Graduate Program in Biophysics, University of California, San Francisco, San Francisco, CA, USA
2Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
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  • ORCID record for Alexander M Wolff
Iris D Young
2Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
3Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Raymond G Sierra
4Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
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Aaron S Brewster
3Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Michael W Martynowycz
5Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, USA
6Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
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Eriko Nango
7RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
8Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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Michihiro Sugahara
7RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
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Takanori Nakane
9Department of Biological Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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Kazutaka Ito
2Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
10Laboratory for Drug Discovery, Pharmaceuticals Research Center, Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni-shi, Shizuoka 410-2321, Japan
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Andrew Aquila
4Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
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Asmit Bhowmick
3Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Justin T Biel
1Graduate Program in Biophysics, University of California, San Francisco, San Francisco, CA, USA
2Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
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Sergio Carbajo
4Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
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Aina E Cohen
11SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
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Saul Cortez
12Department of Biology, San Francisco State University, San Francisco, CA, USA
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Ana Gonzalez
11SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
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Tomoya Hino
13Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101, Koyama-cho Minami, Tottori 680-8552, Japan
14Center for Research on Green Sustainable Chemistry, Tottori University, Tottori, Japan
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Dohyun Im
8Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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Jake D Koralek
4Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
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Minoru Kubo
7RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
15Graduate School of Life Science, University of Hyogo, Ako-gun, Hyogo 678-1297, Japan
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Tomas S Lazarou
16Department of Chemistry, New York University, New York, NY, USA
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Takashi Nomura
7RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
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Shigeki Owada
7RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
22Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
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Avi Samelson
17Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
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Rie Tanaka
7RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
8Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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Tomoyuki Tanaka
7RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
8Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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Erin M Thompson
2Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
18Graduate Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, CA, USA
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Henry van den Bedem
19Bioscience Department, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
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Rahel A Woldeyes
2Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
18Graduate Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, CA, USA
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Fumiaki Yumoto
20Structural Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, Tsukuba, Ibaraki 305-0034, Japan
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Wei Zhao
21Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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Kensuke Tono
7RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
22Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
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Sébastien Boutet
4Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
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So Iwata
7RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
8Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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Tamir Gonen
5Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, USA
6Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
23Department of Physiology, University of California, Los Angeles, Los Angeles, CA
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Nicholas K Sauter
3Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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James S Fraser
2Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
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Michael C Thompson
2Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
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  • For correspondence: mct.ucsf@gmail.com
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Abstract

Innovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal electron diffraction (MicroED) have emerged as useful methods for obtaining structural information from crystals on the nanometer to micron scale. Despite the utility of these methods, their implementation can often be difficult, as they present many challenges not encountered in traditional macromolecular crystallography experiments. Here, we describe XFEL serial crystallography experiments and MicroED experiments using batch-grown microcrystals of the enzyme cyclophilin A (CypA). Our results provide a roadmap for researchers hoping to design macromolecular microcrystallography experiments, and they highlight the strengths and weaknesses of the two methods. Specifically, we focus on how the different physical conditions imposed by the sample preparation and delivery methods required for each type of experiment effect the crystal structure of the enzyme.

Footnotes

  • Synopsis The authors perform serial X-ray crystallography and microcrystal electron diffraction (MicroED) using microcrystals of the enzyme cyclophilin A. Their results highlight the strengths and weakness of the two complementary methods.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted September 12, 2019.
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Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals
Alexander M Wolff, Iris D Young, Raymond G Sierra, Aaron S Brewster, Michael W Martynowycz, Eriko Nango, Michihiro Sugahara, Takanori Nakane, Kazutaka Ito, Andrew Aquila, Asmit Bhowmick, Justin T Biel, Sergio Carbajo, Aina E Cohen, Saul Cortez, Ana Gonzalez, Tomoya Hino, Dohyun Im, Jake D Koralek, Minoru Kubo, Tomas S Lazarou, Takashi Nomura, Shigeki Owada, Avi Samelson, Rie Tanaka, Tomoyuki Tanaka, Erin M Thompson, Henry van den Bedem, Rahel A Woldeyes, Fumiaki Yumoto, Wei Zhao, Kensuke Tono, Sébastien Boutet, So Iwata, Tamir Gonen, Nicholas K Sauter, James S Fraser, Michael C Thompson
bioRxiv 767061; doi: https://doi.org/10.1101/767061
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Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals
Alexander M Wolff, Iris D Young, Raymond G Sierra, Aaron S Brewster, Michael W Martynowycz, Eriko Nango, Michihiro Sugahara, Takanori Nakane, Kazutaka Ito, Andrew Aquila, Asmit Bhowmick, Justin T Biel, Sergio Carbajo, Aina E Cohen, Saul Cortez, Ana Gonzalez, Tomoya Hino, Dohyun Im, Jake D Koralek, Minoru Kubo, Tomas S Lazarou, Takashi Nomura, Shigeki Owada, Avi Samelson, Rie Tanaka, Tomoyuki Tanaka, Erin M Thompson, Henry van den Bedem, Rahel A Woldeyes, Fumiaki Yumoto, Wei Zhao, Kensuke Tono, Sébastien Boutet, So Iwata, Tamir Gonen, Nicholas K Sauter, James S Fraser, Michael C Thompson
bioRxiv 767061; doi: https://doi.org/10.1101/767061

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