Selenium single-wavelength anomalous diffraction de novo phasing using an X-ray-free electron laser

Hunter, Mark S.; Yoon, Chun Hong; DeMi̇rci̇, Hasan; Sierra, Raymond G.; Dao, E. Han; Ahmadi, Radman; Akşit, Fulya; Aquila, Andrew; Çi̇ftçi̇, Halilibrahim; Guillet, Serge; Hayes, Matt J.; Lane, Thomas J; Liang, Meng; Lundström, Ulf; Koglin, Jason E.; Mgbam, Paul; Rao, Yashas; Zhang, Lindsey; Wakatsuki, Soichi; Holton, James M.; Boutet, Sébastien

doi:10.1038/ncomms13388

Cited by 41 publications

(25 citation statements)

References 35 publications

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“…For the de novo phasing of macromolecules, many studies report having achieved experimental phasing in SFX using heavy-atom derivatives of protein crystals 9,22,[35][36][37][38][47][48][49][50] . We recently performed the de novo structural determination of proteinase K from Pr-derivatised crystals (sized 4 μm-7 μm) using a cellulose matrix 22 .…”

Section: Discussionmentioning

confidence: 99%

Viscosity-adjustable grease matrices for serial nanocrystallography

Sugahara

Motomura

Suzuki

et al. 2020

Sci Rep

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or saturation cutoff. We merged measured diffraction intensities by process_hkl in the CrystFEL suite 68 with scaling (-scale option). We determined the structures of proteinase K by difference Fourier synthesis using a search model (PDB: 5b1d). For the Pr-derivatised proteinase K, we carried out substructure search, phasing and phase improvement using the SHELX C, D and E programmes 43. We fed the auto-traced model from SHELXE into Buccaneer 45 from the CCP4 suite 69. We performed manual model revision and structure refinement using Coot 70 and PHENIX 71 , respectively. In Table 1, we summarise details of the data collection and refinement statistics.

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Section: Discussionmentioning

confidence: 99%

Viscosity-adjustable grease matrices for serial nanocrystallography

Sugahara

Motomura

Suzuki

et al. 2020

Sci Rep

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“…The preparation of the crystals of selenobiotinyl-streptavidin (Se-B SA) co-crystals was described previously 2 . X-ray diffraction data were acquired at the Coherent X-ray Imaging (CXI) instrument of the LCLS 4 .…”

Section: Methodsmentioning

confidence: 99%

Se-SAD serial femtosecond crystallography datasets from selenobiotinyl-streptavidin

et al. 2017

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We provide a detailed description of selenobiotinyl-streptavidin (Se-B SA) co-crystal datasets recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS) for selenium single-wavelength anomalous diffraction (Se-SAD) structure determination. Se-B SA was chosen as the model system for its high affinity between biotin and streptavidin where the sulfur atom in the biotin molecule (C10H16N2O3S) is substituted with selenium. The dataset was collected at three different transmissions (100, 50, and 10%) using a serial sample chamber setup which allows for two sample chambers, a front chamber and a back chamber, to operate simultaneously. Diffraction patterns from Se-B SA were recorded to a resolution of 1.9 Å. The dataset is publicly available through the Coherent X-ray Imaging Data Bank (CXIDB) and also on LCLS compute nodes as a resource for research and algorithm development.

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“…In the most favorable case, one could phase from only 3000 indexed images by praseodymium SAD phasing (Sugahara et al 2017). Selenium SAD phasing was also successful at the LCLS (Hunter et al 2016).…”

Section: Experimental Phasing By Sfxmentioning

confidence: 99%

Serial femtosecond crystallography at the SACLA: breakthrough to dynamic structural biology

et al. 2017

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X-ray crystallography visualizes the world at the atomic level. It has been used as the most powerful technique for observing the three-dimensional structures of biological macromolecules and has pioneered structural biology. To determine a crystal structure with high resolution, it was traditionally required to prepare large crystals (> 200 μm). Later, synchrotron radiation facilities, such as SPring-8, that produce powerful X-rays were built. They enabled users to obtain good quality X-ray diffraction images even with smaller crystals (ca. 200-50 μm). In recent years, one of the most important technological innovations in structural biology has been the development of X-ray free electron lasers (XFELs). The SPring-8 Angstrom Compact free electron LAser (SACLA) in Japan generates the XFEL beam by accelerating electrons to relativistic speeds and directing them through in-vacuum, short-period undulators. Since user operation started in 2012, we have been involved in the development of serial femtosecond crystallography (SFX) measurement systems using XFEL at the SACLA. The SACLA generates X-rays a billion times brighter than SPring-8. The extremely bright XFEL pulses enable data collection with microcrystals (ca. 50-1 μm). Although many molecular analysis techniques exist, SFX is the only technique that can visualize radiation-damage-free structures of biological macromolecules at room temperature in atomic resolution and fast time resolution. Here, we review the achievements of the SACLA-SFX Project in the past 5 years. In particular, we focus on: (1) the measurement system for SFX; (2) experimental phasing by SFX; (3) enzyme chemistry based on damage-free room-temperature structures; and (4) molecular movie taken by time-resolved SFX.

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Selenium single-wavelength anomalous diffraction de novo phasing using an X-ray-free electron laser

Cited by 41 publications

References 35 publications

Viscosity-adjustable grease matrices for serial nanocrystallography

Viscosity-adjustable grease matrices for serial nanocrystallography

Se-SAD serial femtosecond crystallography datasets from selenobiotinyl-streptavidin

Serial femtosecond crystallography at the SACLA: breakthrough to dynamic structural biology

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