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Crystals
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Approach of Serial Crystallography
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Approach of Serial Crystallography

A special issue of Crystals (ISSN 2073-4352). This special issue belongs to the section "Macromolecular Crystals".

Deadline for manuscript submissions: closed (30 April 2021) | Viewed by 16103

Special Issue Editor

Prof. Dr. Ki Hyun Nam

E-Mail Website
Guest Editor
Department of Life Science, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
Interests: serial crystallography; serial femtosecond crystallography; room temperature structure; X-ray crystallography; molecular dynamics; macromolecular crystallography
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Serial crystallography (SX) using X-ray-free electron lasers (XFEL) or synchrotron X-rays is an emerging research area that offers the opportunity to determine room temperature structures without causing or reducing radiation damage, respectively. Moreover, pump–probe experiments using optical lasers or liquids application method provide an opportunity to observe time-resolved molecular dynamics, beyond the traditional X-ray crystallography technique. Starting with serial femtosecond crystallography (SFX) using XFEL, SX is now being extensively conducted on synchrotron using serial millisecond crystallography (SMX) or the serial synchrotron crystallography (SSX) technique. The field of SX research has been expanding rapidly in recent years, both in terms of technology and the growing of number of research groups. The research approach or technical know-how by the experts in the SX field will provide useful information not only for colleagues in the field of SX research but also for researchers who want to perform SX.

I invite researchers to contribute to this Special Issue on “Approach of Serial Crystallography”, which is intended to serve as a unique multidisciplinary forum covering broad aspects of current status of SX beamline, research result, review, and research outlook. This issue also collects preliminary and negative research findings in terms of collecting more information and expanding the base of the SX.

Dr. Ki Hyun Nam
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Crystals is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Serial crystallography
  • Approach for serial crystallography
  • Beamline for serial crystallography
  • Sample preparation for serial crystallography
  • Crystallization for serial crystallography
  • Preliminary diffraction study
  • Sample delivery method
  • Strategy of data processing and analysis

Published Papers (5 papers)

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Editorial

Jump to: Research, Review

3 pages, 189 KiB  
Editorial
Approach of Serial Crystallography II
by Ki-Hyun Nam
Crystals 2021, 11(6), 655; https://doi.org/10.3390/cryst11060655 - 09 Jun 2021
Cited by 1 | Viewed by 1619
Abstract
Serial crystallography (SX) is an emerging X-ray crystallographic method for determining macromolecule structures. It can address concerns regarding the limitations of data collected by conventional crystallography techniques, which require cryogenic-temperature environments and allow crystals to accumulate radiation damage. Time-resolved SX studies using the [...] Read more.
Serial crystallography (SX) is an emerging X-ray crystallographic method for determining macromolecule structures. It can address concerns regarding the limitations of data collected by conventional crystallography techniques, which require cryogenic-temperature environments and allow crystals to accumulate radiation damage. Time-resolved SX studies using the pump-probe methodology provide useful information for understanding macromolecular mechanisms and structure fluctuation dynamics. This Special Issue deals with the serial crystallography approach using an X-ray free electron laser (XFEL) and synchrotron X-ray source, and reviews recent SX research involving synchrotron use. These reports provide insights into future serial crystallography research trends and approaches. Full article
(This article belongs to the Special Issue Approach of Serial Crystallography)
6 pages, 178 KiB  
Editorial
Approach of Serial Crystallography
by Ki Hyun Nam
Crystals 2020, 10(10), 854; https://doi.org/10.3390/cryst10100854 - 23 Sep 2020
Cited by 9 | Viewed by 2189
Abstract
Radiation damage and cryogenic sample environment are an experimental limitation observed in the traditional X-ray crystallography technique. However, the serial crystallography (SX) technique not only helps to determine structures at room temperature with minimal radiation damage, but it is also a useful tool [...] Read more.
Radiation damage and cryogenic sample environment are an experimental limitation observed in the traditional X-ray crystallography technique. However, the serial crystallography (SX) technique not only helps to determine structures at room temperature with minimal radiation damage, but it is also a useful tool for profound understanding of macromolecules. Moreover, it is a new tool for time-resolved studies. Over the past 10 years, various sample delivery techniques and data collection strategies have been developed in the SX field. It also has a wide range of applications in instruments ranging from the X-ray free electron laser (XFEL) facility to synchrotrons. The importance of the various approaches in terms of the experimental techniques and a brief review of the research carried out in the field of SX has been highlighted in this editorial. Full article
(This article belongs to the Special Issue Approach of Serial Crystallography)

Research

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12 pages, 1556 KiB  
Article
Shock Damage Analysis in Serial Femtosecond Crystallography Data Collected at MHz X-ray Free-Electron Lasers
by Alexander Gorel, Marie Luise Grünbein, Richard Bean, Johan Bielecki, Mario Hilpert, Michele Cascella, Jacques-Philippe Colletier, Hans Fangohr, Lutz Foucar, Elisabeth Hartmann, Mark S. Hunter, Henry Kirkwood, Marco Kloos, Romain Letrun, Thomas Michelat, Robert L. Shoeman, Jolanta Sztuk-Dambietz, Guillaume Tetreau, Herbert Zimmermann, Adrian P. Mancuso, Thomas R.M. Barends, R. Bruce Doak, Claudiu Andrei Stan and Ilme Schlichtingadd Show full author list remove Hide full author list
Crystals 2020, 10(12), 1145; https://doi.org/10.3390/cryst10121145 - 16 Dec 2020
Cited by 5 | Viewed by 3309
Abstract
Serial femtosecond crystallography (SFX) data were recorded at the European X-ray free-electron laser facility (EuXFEL) with protein microcrystals delivered via a microscopic liquid jet. An XFEL beam striking such a jet may launch supersonic shock waves up the jet, compromising the oncoming sample. [...] Read more.
Serial femtosecond crystallography (SFX) data were recorded at the European X-ray free-electron laser facility (EuXFEL) with protein microcrystals delivered via a microscopic liquid jet. An XFEL beam striking such a jet may launch supersonic shock waves up the jet, compromising the oncoming sample. To investigate this efficiently, we employed a novel XFEL pulse pattern to nominally expose the sample to between zero and four shock waves before being probed. Analyzing hit rate, indexing rate, and resolution for diffraction data recorded at MHz pulse rates, we found no evidence of damage. Notably, however, this conclusion could only be drawn after careful identification and assimilation of numerous interrelated experimental factors, which we describe in detail. Failure to do so would have led to an erroneous conclusion. Femtosecond photography of the sample-carrying jet revealed critically different jet behavior from that of all homogeneous liquid jets studied to date in this manner. Full article
(This article belongs to the Special Issue Approach of Serial Crystallography)
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15 pages, 5782 KiB  
Communication
Fixed-Target Serial Synchrotron Crystallography Using Nylon Mesh and Enclosed Film-Based Sample Holder
by Suk-Youl Park, Hyeongju Choi, Cheolsoo Eo, Yunje Cho and Ki Hyun Nam
Crystals 2020, 10(9), 803; https://doi.org/10.3390/cryst10090803 - 10 Sep 2020
Cited by 24 | Viewed by 3285
Abstract
Serial crystallography (SX) technique using synchrotron X-ray allows the visualization of room-temperature crystal structures with low-dose data collection as well as time-resolved molecular dynamics. In an SX experiment, delivery of numerous crystals for X-ray interaction, in a serial manner, is very important. Fixed-target [...] Read more.
Serial crystallography (SX) technique using synchrotron X-ray allows the visualization of room-temperature crystal structures with low-dose data collection as well as time-resolved molecular dynamics. In an SX experiment, delivery of numerous crystals for X-ray interaction, in a serial manner, is very important. Fixed-target scanning approach has the advantage of dramatically minimizing sample consumption as well as any physical damage to crystal sample, compared to other sample delivery methods. Here, we introduce the simple approach of fixed-target serial synchrotron crystallography (FT-SSX) using nylon mesh and enclosed film (NAM)-based sample holder. The NAM-based sample holder consisted of X-ray-transparent nylon-mesh and polyimide film, attached to a magnetic base. This sample holder was mounted to a goniometer head on macromolecular crystallography beamline, and translated along vertical and horizontal directions for raster scanning by the goniometer. Diffraction data were collected in two raster scanning approaches: (i) 100 ms X-ray exposure and 0.011° oscillation at each scan point and (ii) 500 ms X-ray exposure and 0.222° oscillation at each scan point. Using this approach, we determined the room-temperature crystal structures of lysozyme and glucose isomerase at 1.5–2.0 Å resolution. The sample holder produced negligible X-ray background scattering for data processing. Therefore, the new approach provided an opportunity to perform FT-SSX with high accessibility using macromolecular crystallography beamlines at synchrotron without any special equipment. Full article
(This article belongs to the Special Issue Approach of Serial Crystallography)
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Review

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22 pages, 3619 KiB  
Review
Protein Dynamics and Time Resolved Protein Crystallography at Synchrotron Radiation Sources: Past, Present and Future
by Jose M. Martin-Garcia
Crystals 2021, 11(5), 521; https://doi.org/10.3390/cryst11050521 - 08 May 2021
Cited by 21 | Viewed by 4363
Abstract
The ultrabright and ultrashort pulses produced at X-ray free electron lasers (XFELs) has enabled studies of crystallized molecular machines at work under ‘native’ conditions at room temperature by the so-called time-resolved serial femtosecond crystallography (TR-SFX) technique. Since early TR-SFX experiments were conducted at [...] Read more.
The ultrabright and ultrashort pulses produced at X-ray free electron lasers (XFELs) has enabled studies of crystallized molecular machines at work under ‘native’ conditions at room temperature by the so-called time-resolved serial femtosecond crystallography (TR-SFX) technique. Since early TR-SFX experiments were conducted at XFELs, it has been largely reported in the literature that time-resolved X-ray experiments at synchrotrons are no longer feasible or are impractical due to the severe technical limitations of these radiation sources. The transfer of the serial crystallography approach to newest synchrotrons upgraded for higher flux density and with beamlines using sophisticated focusing optics, submicron beam diameters and fast low-noise photon-counting detectors offers a way to overcome these difficulties opening new and exciting possibilities. In fact, there is an increasing amount of publications reporting new findings in structural dynamics of protein macromolecules by using time resolved crystallography from microcrystals at synchrotron sources. This review gathers information to provide an overview of the recent work and the advances made in this filed in the past years, as well as outlines future perspectives at the next generation of synchrotron sources and the upcoming compact pulsed X-ray sources. Full article
(This article belongs to the Special Issue Approach of Serial Crystallography)
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