Experimental phase determination with selenomethionine or mercury-derivatization in serial femtosecond crystallography
Serial femtosecond crystallography (SFX) using X-ray free-electron lasers (XFELs) holds enormous potential for the structure determination of proteins for which it is difficult to produce large and high-quality crystals. SFX has been applied to various systems, but rarely to proteins that have previ...
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| Format: | Article |
| Language: | English |
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International Union of Crystallography
2017-09-01
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| Series: | IUCrJ |
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| Online Access: | http://scripts.iucr.org/cgi-bin/paper?S2052252517008557 |
| _version_ | 1818958687396429824 |
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| author | Keitaro Yamashita Naoyuki Kuwabara Takanori Nakane Tomohiro Murai Eiichi Mizohata Michihiro Sugahara Dongqing Pan Tetsuya Masuda Mamoru Suzuki Tomomi Sato Atsushi Kodan Tomohiro Yamaguchi Eriko Nango Tomoyuki Tanaka Kensuke Tono Yasumasa Joti Takashi Kameshima Takaki Hatsui Makina Yabashi Hiroshi Manya Tamao Endo Ryuichi Kato Toshiya Senda Hiroaki Kato So Iwata Hideo Ago Masaki Yamamoto Fumiaki Yumoto Toru Nakatsu |
| author_facet | Keitaro Yamashita Naoyuki Kuwabara Takanori Nakane Tomohiro Murai Eiichi Mizohata Michihiro Sugahara Dongqing Pan Tetsuya Masuda Mamoru Suzuki Tomomi Sato Atsushi Kodan Tomohiro Yamaguchi Eriko Nango Tomoyuki Tanaka Kensuke Tono Yasumasa Joti Takashi Kameshima Takaki Hatsui Makina Yabashi Hiroshi Manya Tamao Endo Ryuichi Kato Toshiya Senda Hiroaki Kato So Iwata Hideo Ago Masaki Yamamoto Fumiaki Yumoto Toru Nakatsu |
| author_sort | Keitaro Yamashita |
| collection | DOAJ |
| description | Serial femtosecond crystallography (SFX) using X-ray free-electron lasers (XFELs) holds enormous potential for the structure determination of proteins for which it is difficult to produce large and high-quality crystals. SFX has been applied to various systems, but rarely to proteins that have previously unknown structures. Consequently, the majority of previously obtained SFX structures have been solved by the molecular replacement method. To facilitate protein structure determination by SFX, it is essential to establish phasing methods that work efficiently for SFX. Here, selenomethionine derivatization and mercury soaking have been investigated for SFX experiments using the high-energy XFEL at the SPring-8 Angstrom Compact Free-Electron Laser (SACLA), Hyogo, Japan. Three successful cases are reported of single-wavelength anomalous diffraction (SAD) phasing using X-rays of less than 1 Å wavelength with reasonable numbers of diffraction patterns (13 000, 60 000 and 11 000). It is demonstrated that the combination of high-energy X-rays from an XFEL and commonly used heavy-atom incorporation techniques will enable routine de novo structural determination of biomacromolecules. |
| first_indexed | 2024-12-20T11:29:42Z |
| format | Article |
| id | doaj.art-6801e2bc89df4536aa7bf825ab1a4cbf |
| institution | Directory Open Access Journal |
| issn | 2052-2525 |
| language | English |
| last_indexed | 2024-12-20T11:29:42Z |
| publishDate | 2017-09-01 |
| publisher | International Union of Crystallography |
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| series | IUCrJ |
| spelling | doaj.art-6801e2bc89df4536aa7bf825ab1a4cbf2022-12-21T19:42:16ZengInternational Union of CrystallographyIUCrJ2052-25252017-09-014563964710.1107/S2052252517008557lz5015Experimental phase determination with selenomethionine or mercury-derivatization in serial femtosecond crystallographyKeitaro Yamashita0Naoyuki Kuwabara1Takanori Nakane2Tomohiro Murai3Eiichi Mizohata4Michihiro Sugahara5Dongqing Pan6Tetsuya Masuda7Mamoru Suzuki8Tomomi Sato9Atsushi Kodan10Tomohiro Yamaguchi11Eriko Nango12Tomoyuki Tanaka13Kensuke Tono14Yasumasa Joti15Takashi Kameshima16Takaki Hatsui17Makina Yabashi18Hiroshi Manya19Tamao Endo20Ryuichi Kato21Toshiya Senda22Hiroaki Kato23So Iwata24Hideo Ago25Masaki Yamamoto26Fumiaki Yumoto27Toru Nakatsu28RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, JapanStructural Biology Research Center, Photon Factory, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, JapanDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, JapanDepartment of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, JapanDepartment of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, JapanRIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, JapanDepartment of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, JapanRIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, JapanRIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, JapanDepartment of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, JapanInstitute for Integrated Cell-Material Sciences, Kyoto University, Yoshida Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501, JapanDepartment of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, JapanRIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, JapanRIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, JapanJapan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, JapanJapan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, JapanJapan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, JapanRIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, JapanRIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, JapanMolecular Glycobiology, Research Team for Mechanism of Aging, Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo 173-0015, JapanMolecular Glycobiology, Research Team for Mechanism of Aging, Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo 173-0015, JapanStructural Biology Research Center, Photon Factory, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, JapanStructural Biology Research Center, Photon Factory, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, JapanRIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, JapanRIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, JapanRIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, JapanRIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, JapanStructural Biology Research Center, Photon Factory, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, JapanRIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, JapanSerial femtosecond crystallography (SFX) using X-ray free-electron lasers (XFELs) holds enormous potential for the structure determination of proteins for which it is difficult to produce large and high-quality crystals. SFX has been applied to various systems, but rarely to proteins that have previously unknown structures. Consequently, the majority of previously obtained SFX structures have been solved by the molecular replacement method. To facilitate protein structure determination by SFX, it is essential to establish phasing methods that work efficiently for SFX. Here, selenomethionine derivatization and mercury soaking have been investigated for SFX experiments using the high-energy XFEL at the SPring-8 Angstrom Compact Free-Electron Laser (SACLA), Hyogo, Japan. Three successful cases are reported of single-wavelength anomalous diffraction (SAD) phasing using X-rays of less than 1 Å wavelength with reasonable numbers of diffraction patterns (13 000, 60 000 and 11 000). It is demonstrated that the combination of high-energy X-rays from an XFEL and commonly used heavy-atom incorporation techniques will enable routine de novo structural determination of biomacromolecules.http://scripts.iucr.org/cgi-bin/paper?S2052252517008557serial femtosecond crystallographySAD phasingXFELsselenomethionine derivatizationmercury soaking |
| spellingShingle | Keitaro Yamashita Naoyuki Kuwabara Takanori Nakane Tomohiro Murai Eiichi Mizohata Michihiro Sugahara Dongqing Pan Tetsuya Masuda Mamoru Suzuki Tomomi Sato Atsushi Kodan Tomohiro Yamaguchi Eriko Nango Tomoyuki Tanaka Kensuke Tono Yasumasa Joti Takashi Kameshima Takaki Hatsui Makina Yabashi Hiroshi Manya Tamao Endo Ryuichi Kato Toshiya Senda Hiroaki Kato So Iwata Hideo Ago Masaki Yamamoto Fumiaki Yumoto Toru Nakatsu Experimental phase determination with selenomethionine or mercury-derivatization in serial femtosecond crystallography IUCrJ serial femtosecond crystallography SAD phasing XFELs selenomethionine derivatization mercury soaking |
| title | Experimental phase determination with selenomethionine or mercury-derivatization in serial femtosecond crystallography |
| title_full | Experimental phase determination with selenomethionine or mercury-derivatization in serial femtosecond crystallography |
| title_fullStr | Experimental phase determination with selenomethionine or mercury-derivatization in serial femtosecond crystallography |
| title_full_unstemmed | Experimental phase determination with selenomethionine or mercury-derivatization in serial femtosecond crystallography |
| title_short | Experimental phase determination with selenomethionine or mercury-derivatization in serial femtosecond crystallography |
| title_sort | experimental phase determination with selenomethionine or mercury derivatization in serial femtosecond crystallography |
| topic | serial femtosecond crystallography SAD phasing XFELs selenomethionine derivatization mercury soaking |
| url | http://scripts.iucr.org/cgi-bin/paper?S2052252517008557 |
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