Article
Multidisciplinary Sciences
P. Mehrabi, R. Buecker, G. Bourenkov, H. M. Ginn, D. von Stetten, H. M. Mueller-Werkmeister, A. Kuo, T. Morizumi, B. T. Eger, W-L Ou, S. Oghbaey, A. Sarracini, J. E. Besaw, O. Pare-Labrosse, S. Meier, H. Schikora, F. Tellkamp, A. Marx, D. A. Sherrell, D. Axford, R. L. Owen, O. P. Ernst, E. F. Pai, E. C. Schulz, R. J. D. Miller
Summary: This study systematically compared crystallographic diffraction data collected by SFX and SSX methods for myoglobin and fluoroacetate dehalogenase, finding that approximately 5000 room-temperature diffraction images are sufficient for reasonable data statistics regardless of the radiation source. The data suggest that the quality of diffraction data obtained from these samples is more related to the properties of the crystals rather than the radiation source.
Article
Multidisciplinary Sciences
Thomas R. M. Barends, Benjamin Stauch, Vadim Cherezov, Ilme Schlichting
Summary: This article introduces the basic principles of X-ray free-electron lasers and serial crystallography, providing assistance for structural biology groups in planning and conducting SFX experiments. The main content includes microcrystal growth and characterization, sample delivery and data processing techniques, experimental preparation and operation at different stages, as well as the possibilities of SFX in various application areas.
NATURE REVIEWS METHODS PRIMERS
(2022)
Article
Chemistry, Multidisciplinary
Hongjie Li, Yoshiki Nakajima, Takashi Nomura, Michihiro Sugahara, Shinichiro Yonekura, Siu Kit Chan, Takanori Nakane, Takahiro Yamane, Yasufumi Umena, Mamoru Suzuki, Tetsuya Masuda, Taiki Motomura, Hisashi Naitow, Yoshinori Matsuura, Tetsunari Kimura, Kensuke Tono, Shigeki Owada, Yasumasa Joti, Rie Tanaka, Eriko Nango, Fusamichi Akita, Minoru Kubo, So Iwata, Jian-Ren Shen, Michihiro Suga
Summary: The study successfully captured the structural dynamics of light-sensitive proteins during the S-1 to S-2 transition using pump-probe time-resolved serial femtosecond crystallography (TR-SFX), while also avoiding the influence of light contamination, revealing key structural changes important for the water-splitting reaction.
Article
Optics
Jaehyun Park, Ki Hyun Nam
Summary: Serial femtosecond crystallography (SFX) using an X-ray free electron laser (XFEL) is able to determine room-temperature structures without causing radiation damage. In this study, various sample delivery methods for SFX at the PAL-XFEL NCI experimental station are reported, which will benefit PAL-XFEL users in accessing the SFX system for their experiments.
Article
Chemistry, Multidisciplinary
J. Mia Lahey-Rudolph, Robert Schonherr, Miriam Barthelmess, Pontus Fischer, Carolin Seuring, Armin Wagner, Alke Meents, Lars Redecke
Summary: This study presents an efficient approach for high-resolution structure elucidation using serial femtosecond in cellulo diffraction of micrometre-sized crystals of the protein HEX-1 on a fixed target. Compared with liquid-jet injection systems, the increased hit rates and reduced background scattering allowed for the elucidation of the HEX-1 structure. The results demonstrate that fixed-target SFX using micro-patterned silicon chips is ideally suited for efficient in cellulo diffraction data collection and offers huge potential for straightforward structure elucidation of proteins that form intracellular crystals at both XFELs and synchrotron sources.
Article
Biochemistry & Molecular Biology
Robert Buecker, Pascal Hogan-Lamarre, R. J. Dwayne Miller
Summary: Serial electron diffraction (SerialED) is a novel technique that applies the snapshot data-collection mode to three-dimensional electron diffraction, leading to minimal radiation damage and high automation. However, new data processing techniques are required to address challenges specific to SerialED.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Crystallography
Oleksii Turkot, Fabio Dall'Antonia, Richard J. Bean, Juncheng E, Hans Fangohr, Danilo E. Ferreira de Lima, Sravya Kantamneni, Henry J. Kirkwood, Faisal H. M. Koua, Adrian P. Mancuso, Diogo V. M. Melo, Adam Round, Michael Schuh, Egor Sobolev, Raphael de Wijn, James J. Wrigley, Luca Gelisio
Summary: Researchers have developed a semi-automated pipeline called EXtra-Xwiz to streamline and accelerate the analysis of serial femtosecond crystallography (SFX) data, which is crucial for experiments with high data complexity like the European XFEL.
Article
Chemistry, Multidisciplinary
Raphael de Wijn, Diogo V. M. Melo, Faisal H. M. Koua, Adrian P. Mancuso
Summary: This perspective review discusses emerging techniques and future opportunities for time-resolved serial femtosecond crystallography experiments using high repetition rate XFEL sources. The efficient use of these sources for pump-probe experiments and mix-and-inject experiments is highlighted. The development of photocaged compounds is also being explored to expand the application of time-resolved serial femtosecond crystallography.
APPLIED SCIENCES-BASEL
(2022)
Article
Biology
Juliane John, Oskar Aurelius, Vivek Srinivas, Patricia Saura, In-Sik Kim, Asmit Bhowmick, Philipp S. Simon, Medhanjali Dasgupta, Cindy Pham, Sheraz Gul, Kyle D. Sutherlin, Pierre Aller, Agata Butryn, Allen M. Orville, Mun Hon Cheah, Shigeki Owada, Kensuke Tono, Franklin D. Fuller, Alexander Batyuk, Aaron S. Brewster, Nicholas K. Sauter, Vittal K. Yachandra, Junko Yano, Ville Ri Kaila, Jan Kern, Hugo Lebrette, Martin Hogbom
Summary: Redox reactions play a central role in biochemistry and are controlled by protein structural changes. In this study, the authors utilized femtosecond crystallography to examine the structural rearrangements and crosstalk within the Bacillus cereus ribonucleotide reductase R2b-NrdI complex. They found that the flavin in the complex is under steric strain, which likely affects its redox properties and promotes superoxide generation. The redox state of the flavin also controls a binding site that is linked to the channel responsible for transporting superoxide species. These findings have important implications for understanding the control of reactive oxygen species and radical generation in protein R2b.
Article
Chemistry, Multidisciplinary
Keondo Lee, Donghyeon Lee, Jaehyun Park, Jong-Lam Lee, Wan Kyun Chung, Yunje Cho, Ki Hyun Nam
Summary: This study introduces an upgraded inject-and-transfer system that improves beamtime efficiency for serial femtosecond crystallography. It is reported that the widely used viscous solution for protein crystallization can be stably deposited on a hydrophobic surface without any special treatment. Additionally, the development of an inject-and-diffuse method for time-resolved studies with liquid applications in the system is presented.
APPLIED SCIENCES-BASEL
(2022)
Article
Crystallography
Ki Hyun Nam
Summary: Cryocrystallography is a widely used method for determining the crystal structure of macromolecules. This study introduces a method for processing multicrystal diffraction data using a serial crystallography program, which allows for the integration of diffraction patterns from multiple crystals in a single image.
Article
Crystallography
Omur Guven, Mehmet Gul, Esra Ayan, J. Austin Johnson, Baris Cakilkaya, Gozde Usta, Fatma Betul Ertem, Nurettin Tokay, Busra Yuksel, Oktay Gocenler, Cengizhan Buyukdag, Sabine Botha, Gihan Ketawala, Zhen Su, Brandon Hayes, Frederic Poitevin, Alexander Batyuk, Chun Hong Yoon, Christopher Kupitz, Serdar Durdagi, Raymond G. Sierra, Hasan DeMirci
Summary: Global investigation into COVID-19 since early 2020 aiming to characterize the virus and develop vaccines. Drug repurposing studies conducted with a focus on in silico drug screening for efficiency. Utilization of advanced technology for high-throughput drug screening with X-ray Free-Electron Laser (XFEL) for remote data collection at ambient temperature.
Article
Biochemical Research Methods
Kyprianos Hadjidemetriou, Nicolas Coquelle, Thomas R. M. Barends, Elke De Zitter, Ilme Schlichting, Jacques-Philippe Colletier, Martin Weik
Summary: By combining various techniques, researchers have elucidated the catalytic mechanism of fatty-acid photodecarboxylase, which converts free fatty acids into hydrocarbon compounds. The study faced challenges and further experiments are needed to identify the photoproducts and their movements during the catalytic cycle.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Sam Horrell, Danny Axford, Nicholas E. Devenish, Ali Ebrahim, Michael A. Hough, Darren A. Sherrell, Selina L. S. Storm, Ivo Tews, Jonathan A. R. Worrall, Robin L. Owen
Summary: The user manual for fixed target data collection at I24, Diamond Light Source provides detailed step-by-step instructions, figures, and videos to assist users in smooth data collection with serial data collection technique.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2021)
Review
Biochemistry & Molecular Biology
Sabine Botha, Petra Fromme
Summary: Serial femtosecond crystallography (SFX) is a revolutionary method that allows the collection of X-ray diffraction data from tiny crystals at room temperature, enabling high temporal resolution studies of macromolecules. The global COVID-19 pandemic in 2020 had a significant impact on SFX research, leading to a shift in focus towards studying the SARS-CoV-2 virus.
