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Crystals
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Serial X-ray Crystallography
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Serial X-ray Crystallography

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

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 19034

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 liquid application methods provide an opportunity to observe time-resolved molecular dynamics, beyond the traditional X-ray crystallography technique. The field of serial femtosecond crystallography (SFX) and serial synchrotron crystallography (SSX) research has been expanding rapidly in recent years, both in terms of technology and the growing 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 “Serial X-ray Crystallography”, which is intended to serve as a unique multidisciplinary forum covering broad aspects of the current status of SX beamline, research results, reviews, and research outlooks. 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 2100 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
  • Serial femtosecond crystallography
  • Serial synchrotron crystallography
  • Ambient Crystallography
  • X-ray free electron laser
  • Time-resolved crystallography
  • Approach of serial crystallography

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Published Papers (5 papers)

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Editorial

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3 pages, 191 KiB  
Editorial
Serial X-ray Crystallography II
by Ki Hyun Nam
Crystals 2023, 13(2), 222; https://doi.org/10.3390/cryst13020222 - 25 Jan 2023
Viewed by 1278
Abstract
Traditional macromolecular crystallography (MX) and recently spotlighted cryogenic electron microscopy (Cryo-EM) techniques have contributed greatly to the development of macromolecule structures and the related fields [...] Full article
(This article belongs to the Special Issue Serial X-ray Crystallography)
6 pages, 1129 KiB  
Editorial
Serial X-ray Crystallography
by Ki Hyun Nam
Crystals 2022, 12(1), 99; https://doi.org/10.3390/cryst12010099 - 13 Jan 2022
Cited by 7 | Viewed by 2895
Abstract
Serial crystallography (SX) is an emerging technique to determine macromolecules at room temperature. SX with a pump–probe experiment provides the time-resolved dynamics of target molecules. SX has developed rapidly over the past decade as a technique that not only provides room-temperature structures with [...] Read more.
Serial crystallography (SX) is an emerging technique to determine macromolecules at room temperature. SX with a pump–probe experiment provides the time-resolved dynamics of target molecules. SX has developed rapidly over the past decade as a technique that not only provides room-temperature structures with biomolecules, but also has the ability to time-resolve their molecular dynamics. The serial femtosecond crystallography (SFX) technique using an X-ray free electron laser (XFEL) has now been extended to serial synchrotron crystallography (SSX) using synchrotron X-rays. The development of a variety of sample delivery techniques and data processing programs is currently accelerating SX research, thereby increasing the research scope. In this editorial, I briefly review some of the experimental techniques that have contributed to advances in the field of SX research and recent major research achievements. This Special Issue will contribute to the field of SX research. Full article
(This article belongs to the Special Issue Serial X-ray Crystallography)
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Research

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11 pages, 1849 KiB  
Article
Pink-Beam Serial Synchrotron Crystallography at Pohang Light Source II
by Yongsam Kim and Ki Hyun Nam
Crystals 2022, 12(11), 1637; https://doi.org/10.3390/cryst12111637 - 14 Nov 2022
Cited by 11 | Viewed by 1850
Abstract
Serial crystallography (SX) enables the determination of room-temperature structures with minimal radiation damage. The photon flux of the pink beam of 1.2% bandwidth (BW) is one order higher than that of the monochromatic beam from a silicon crystal monochromator, and the energy resolution [...] Read more.
Serial crystallography (SX) enables the determination of room-temperature structures with minimal radiation damage. The photon flux of the pink beam of 1.2% bandwidth (BW) is one order higher than that of the monochromatic beam from a silicon crystal monochromator, and the energy resolution of 1.2% BW is enough to solve the structure; therefore, it is useful to use the pink beam for time-resolved serial synchrotron crystallography (SSX). Here, we demonstrate a pink-beam serial synchrotron crystallographic study at the 1C beamline at the Pohang Light Source II. Lysozyme crystals embedded in a beef tallow injection matrix were delivered through a syringe into the X-ray interaction point. Pink-beam SSX was performed with different X-ray exposure positions to the injection stream (center and edge) and X-ray exposure times (50 and 100 ms). All lysozyme crystal structures were successfully determined at a high resolution of 1.7 Å. Background analysis showed that X-ray diffraction data exposed to the edge of the injection stream could improve the signal-to-noise ratio. All the diffraction data and room-temperature lysozyme structures were comprehensively compared. The data collection strategy and analysis will be helpful in further pink-beam SSX experiments and their applications. Full article
(This article belongs to the Special Issue Serial X-ray Crystallography)
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12 pages, 2316 KiB  
Article
Processing of Multicrystal Diffraction Patterns in Macromolecular Crystallography Using Serial Crystallography Programs
by Ki Hyun Nam
Crystals 2022, 12(1), 103; https://doi.org/10.3390/cryst12010103 - 13 Jan 2022
Cited by 7 | Viewed by 3105
Abstract
Cryocrystallography is a widely used method for determining the crystal structure of macromolecules. This technique uses a cryoenvironment, which significantly reduces the radiation damage to the crystals and has the advantage of requiring only one crystal for structural determination. In standard cryocrystallography, a [...] Read more.
Cryocrystallography is a widely used method for determining the crystal structure of macromolecules. This technique uses a cryoenvironment, which significantly reduces the radiation damage to the crystals and has the advantage of requiring only one crystal for structural determination. In standard cryocrystallography, a single crystal is used for collecting diffraction data, which include single-crystal diffraction patterns. However, the X-ray data recorded often may contain diffraction patterns from several crystals. The indexing of multicrystal diffraction patterns in cryocrystallography requires more precise data processing techniques and is therefore time consuming. Here, an approach for processing multicrystal diffraction data using a serial crystallography program is introduced that allows for the integration of multicrystal diffraction patterns from a single image. Multicrystal diffraction data were collected from lysozyme crystals and processed using the serial crystallography program CrystFEL. From 360 images containing multicrystal diffraction patterns, 1138 and 691 crystal lattices could be obtained using the XGANDALF and MOSFLM indexing algorithms, respectively. Using this indexed multi-lattice information, the crystal structure of the lysozyme could be determined successfully at a resolution of 1.9 Å. Therefore, the proposed approach, which is based on serial crystallography, is suitable for processing multicrystal diffraction data in cryocrystallography. Full article
(This article belongs to the Special Issue Serial X-ray Crystallography)
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Other

Jump to: Editorial, Research

10 pages, 2013 KiB  
Perspective
A Short Review on Cryoprotectants for 3D Protein Structure Analysis
by Kiyoung Jang, Hyun Gi Kim, Sandi Hnit San Hlaing, MinSoung Kang, Hui-Woog Choe and Yong Ju Kim
Crystals 2022, 12(2), 138; https://doi.org/10.3390/cryst12020138 - 19 Jan 2022
Cited by 7 | Viewed by 9034
Abstract
The three-dimensional structure of protein is determined by analyzing diffraction data collected using X-ray beams. However, X-ray beam can damage protein crystals during data collection, lowering the quality of the crystal data. A way to prevent such damage is by treating protein crystals [...] Read more.
The three-dimensional structure of protein is determined by analyzing diffraction data collected using X-ray beams. However, X-ray beam can damage protein crystals during data collection, lowering the quality of the crystal data. A way to prevent such damage is by treating protein crystals with cryoprotectants. The cryoprotectant stabilizes the protein crystal and prevents lowering the quality of the diffraction data. Many kinds of cryoprotectants are commercially available, and various treatment methods have also been reported. However, incorrect selection or treatment of such cryoprotectants may lead to deterioration of crystal diffraction data when using X-ray beams. Full article
(This article belongs to the Special Issue Serial X-ray Crystallography)
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