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
Chemistry, Multidisciplinary
Karol Nass, Camila Bacellar, Claudio Cirelli, Florian Dworkowski, Yaroslav Gevorkov, Daniel James, Philip J. M. Johnson, Demet Kekilli, Gregor Knopp, Isabelle Martiel, Dmitry Ozerov, Alexandra Tolstikova, Laura Vera, Tobias Weinert, Oleksandr Yefanov, Joerg Standfuss, Sven Reiche, Christopher J. Milne
Summary: This study demonstrates the use of large-bandwidth X-ray pulses at Swiss X-ray free-electron laser in serial femtosecond crystallography (SFX) to improve the partiality of Bragg spots and reduce sample consumption while maintaining data quality. By utilizing sensitive data-quality indicators, such as anomalous signals and de novo phasing results from microcrystals, the benefits of using pink X-ray pulses to obtain accurate structure-factor amplitudes were quantified.
Article
Chemistry, Physical
Cecilia M. Casadei, Ahmad Hosseinizadeh, Spencer Bliven, Tobias Weinert, Jorg Standfuss, Russell Fung, Gebhard F. X. Schertler, Robin Santra
Summary: Low-pass spectral analysis (LPSA) is an effective algorithm for retrieving dynamics in model data affected by incompleteness and weighting errors. In this study, LPSA is applied to experimental time-resolved crystallography data and the parametric sensitivity is analyzed. The presence of high-frequency contamination in dynamical modes is investigated using synthetic data with various uncertainties and errors. A method is proposed to handle missing observations and improved dynamics retrieval is achieved.
STRUCTURAL DYNAMICS-US
(2023)
Article
Chemistry, Multidisciplinary
Martins Balodis, Manuel Cordova, Albert Hofstetter, Graeme M. Day, Lyndon Emsley
Summary: The determination of the three-dimensional atomic-level structure of powdered solids is an important goal in current chemistry. This study successfully determined the crystal structures of ampicillin, piroxicam, cocaine, and two polymorphs of the drug molecule AZD8329 using machine-learned isotropic chemical shifts generated on-the-fly to guide a Monte Carlo-based structure determination process.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Review
Biotechnology & Applied Microbiology
Ji-Yoon Guk, Min-Jeong Jang, Jin-Wook Choi, Yeon Mi Lee, Seungill Kim
Summary: Genome phasing is a recently developed assembly method that separates heterozygous eukaryotic genomic regions and builds haplotype-resolved assemblies. Using haplotype-resolved genome assemblies in plants can reveal significant differences among haplotypes regarding chromosomal rearrangements and expression of specific alleles, contributing to the understanding of biological characteristics of plant species. However, there are limitations in current genome-phasing methods that need to be addressed for further improvements.
PLANT BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Siran Li, Sarah Park, Catherine Ye, Cassidy Danyko, Matthew Wroten, Peter Andrews, Michael Wigler, Dan Levy
Summary: In this study, a novel method for haplotype-phased sequence assembly using short-read sequencers is described. With the introduction of mutation patterns and correction strategies, it achieves accurate assembly and phasing of long genomic regions with low error rates.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Instruments & Instrumentation
Seiki Baba, Hiroaki Matsuura, Takashi Kawamura, Naoki Sakai, Yuki Nakamura, Yoshiaki Kawano, Nobuhiro Mizuno, Takashi Kumasaka, Masaki Yamamoto, Kunio Hirata
Summary: This study demonstrates the importance of selecting a radiation dose lower than 10 MGy for de novo structure determination using SWSX. Data collection at a dose of 5 MGy is shown to be optimal for balancing signal availability while minimizing damage.
JOURNAL OF SYNCHROTRON RADIATION
(2021)
Article
Multidisciplinary Sciences
Zev N. Kronenberg, Arang Rhie, Sergey Koren, Gregory T. Concepcion, Paul Peluso, Katherine M. Munson, David Porubsky, Kristen Kuhn, Kathryn A. Mueller, Wai Yee Low, Stefan Hiendleder, Olivier Fedrigo, Ivan Liachko, Richard J. Hall, Adam M. Phillippy, Evan E. Eichler, John L. Williams, Timothy P. L. Smith, Erich D. Jarvis, Shawn T. Sullivan, Sarah B. Kingan
Summary: FALCON-Phase is a phasing tool that uses ultra-long-range Hi-C chromatin interaction data to extend phase blocks of partially-phased diploid assemblies to chromosome or scaffold scale. This method is accurate without parental data and performs better in samples with higher heterozygosity, achieving up to 97% accuracy for some species.
NATURE COMMUNICATIONS
(2021)
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
Nanoscience & Nanotechnology
Alejandro Prieto-Castaneda, Siseth Martinez-Caballero, Antonia R. Agarrabeitia, Inmaculada Garcia-Moreno, Santiago de la Moya, Maria J. Ortiz, Juan A. Hermoso
Summary: The study introduces a ytterbium(III) complex as a phasing agent for de novo protein structure determination at approximately 1 A, offering high phasing power and high-quality electron density maps while maintaining crystallographic resolution. This agent presents a new possibility for X-ray crystallography of complex biomacromolecules.
ACS APPLIED BIO MATERIALS
(2021)
Article
Biochemical Research Methods
Nicolas Foos, Mahmoud Rizk, Max H. Nanao
Summary: The use of single isomorphous replacement (SIR) has decreased due to difficulties in sample preparation and identification of isomorphous native and derivative data sets. This study presents a method that can address these issues and simplify the SIR experiment. By soaking a single heavy atom into a microcrystalline slurry and performing automated serial data collection, a set of data collections with varying heavy-atom occupancies is obtained. Differential merging statistics are utilized to segregate the data sets into 'native' and 'derivative' groups, enabling successful determination of phases experimentally by SIR.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
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)
