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Crystals
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Macromolecular Serial Crystallography
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Macromolecular Serial Crystallography

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

Deadline for manuscript submissions: closed (29 February 2020) | Viewed by 17774

Special Issue Editors

Dr. Jose Manuel Martin Garcia

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Guest Editor
Department of Crystallography & Structural Biology, Institute of Physical Chemistry Blas Cabrera (IQF-BC), CSIC Serrano 119, 28006 Madrid, Spain
Interests: macromolecular serial crystallography at synchrotrons radiation sources and X-ray free electron lasers (XFELs); structural biology; protein dynamics; drug discovery; development of protein micro-crystallization and sample delivery methods for serial crystallography
Special Issues, Collections and Topics in MDPI journals
Dr. Shibom Basu

E-Mail Website
Guest Editor
European Molecular Biology Laboratory (EMBL), Grenoble, France
Interests: Serial synchrotron crystallography; beamlines at synchrotrons; X-ray free-electron lasers; experimental phasing by native-SAD; time-resolved crystallography; structure-based drug discovery; automation for data processing and analysis.

Special Issue Information

Dear Colleagues,

Within the structural biology field, X-ray crystallography prevails as the dominant technique to determine the structures of macromolecules, producing more than one hundred thousand structures since its inception. New technologies developed such as X-ray free-electron lasers (XFELs) and their implementation in the field of serial femtosecond crystallography (SFX) has opened up a new era in structural biology. SFX relies on exceptionally bright, micro-focused, and ultra-short X-ray beam pulses used to probe nano/micrometer-sized crystals in a serial fashion at room temperature, resulting in data sets comprised of individual snapshots. As a result, the field is quickly expanding and allowing structural biologists access to previously restricted scientific areas. This emerging field has also cultivated new methods for crystallization, and assessment of nano/microcrystals, sample delivery, and data processing. In addition to its use in XFELs, the serial synchrotron crystallography (SSX) approach is currently experiencing rapid growth and maturing as a routine. Third-generation synchrotron sources, being equipped with beamlines using sophisticated focusing optics, submicron beam diameters, and fast low-noise photon-counting detectors, offer tremendous complementarity to XFELs for structural biology studies.

The main goal of this Special Issue on “Macromolecular Serial Crystallography” will be to gather research manuscripts from experts in the filed (chemists, biologists, physicists, and structural biologists) to create an international platform to provide rich reference information on the latest advances and exciting discoveries in the still emerging technology of serial crystallography in XFELs and synchrotron radiation sources.

Dr. José Manuel Martín-García
Dr. Shibom Basu
Guest Editors

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 femtosecond crystallography
  • X-ray free-electron lasers
  • Synchrotron radiation sources
  • Pink-beam serial crystallography
  • Sample delivery techniques
  • Data processing and analysis for serial crystallography
  • Submicron-crystals

Published Papers (5 papers)

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Editorial

Jump to: Research, Review

2 pages, 158 KiB  
Editorial
Macromolecular Serial Crystallography
by Jose M. Martin-Garcia and Shibom Basu
Crystals 2020, 10(12), 1079; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst10121079 - 26 Nov 2020
Viewed by 1190
Abstract
Within the structural biology field, X-ray crystallography prevails as the dominant technique to determine the structures of macromolecules, producing, as of November 2020, more than 150,000 structures since its inception (https://www [...] Full article
(This article belongs to the Special Issue Macromolecular Serial Crystallography)

Research

Jump to: Editorial, Review

23 pages, 281 KiB  
Communication
Preventing Bio-Bloopers and XFEL Follies: Best Practices from your Friendly Instrument Staff
by Christopher Kupitz and Raymond G. Sierra
Crystals 2020, 10(4), 251; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst10040251 - 27 Mar 2020
Cited by 3 | Viewed by 2688
Abstract
Serial Femtosecond Crystallography (SFX) at X-ray Free electron Lasers (XFELs) is a relatively new field promising to deliver unparalleled spatial and temporal resolution on biological systems and there dynamics. Over the past decade, though, there have been a handful of results that have [...] Read more.
Serial Femtosecond Crystallography (SFX) at X-ray Free electron Lasers (XFELs) is a relatively new field promising to deliver unparalleled spatial and temporal resolution on biological systems and there dynamics. Over the past decade, though, there have been a handful of results that have truly delivered on these promises. Why? SFX has many paradigm shifting techniques not seen in typical structural biology arenas, such as creating a concentrated slurry of microcrystals rather than a handful of loopable prisms worthy of a catalog photo. Then taking that slurry and high speed jetting them towards the vacuum or helium interation region to destroy less than 1% of your sample and waste the other 99. The literature is full of techniques and methods promising to cure what ails your experiment, yet as an instrument scientist will tell you –and a first author might admit after a few drinks at the conference happy hour—is that there are a lot more failures than the success we published, results may vary. We will walk through a best practices on how to prepare your sample and chose a sample delivery technique that will amerliorate your studies rather than undermine your hardwork and hopefully lead to better experimental planning and execution, inching you closer to that scientific goal and that call from Stockholm. This will be written in a more editorialized fashion and is meant to give the reader an idea of what to try or how they should be thinking. Welcome to SFX, now what? Full article
(This article belongs to the Special Issue Macromolecular Serial Crystallography)

Review

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27 pages, 1413 KiB  
Review
Towards an Optimal Sample Delivery Method for Serial Crystallography at XFEL
by Robert KY Cheng
Crystals 2020, 10(3), 215; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst10030215 - 19 Mar 2020
Cited by 39 | Viewed by 6119
Abstract
The advent of the X-ray free electron laser (XFEL) in the last decade created the discipline of serial crystallography but also the challenge of how crystal samples are delivered to X-ray. Early sample delivery methods demonstrated the proof-of-concept for serial crystallography and XFEL [...] Read more.
The advent of the X-ray free electron laser (XFEL) in the last decade created the discipline of serial crystallography but also the challenge of how crystal samples are delivered to X-ray. Early sample delivery methods demonstrated the proof-of-concept for serial crystallography and XFEL but were beset with challenges of high sample consumption, jet clogging and low data collection efficiency. The potential of XFEL and serial crystallography as the next frontier of structural solution by X-ray for small and weakly diffracting crystals and provision of ultra-fast time-resolved structural data spawned a huge amount of scientific interest and innovation. To utilize the full potential of XFEL and broaden its applicability to a larger variety of biological samples, researchers are challenged to develop better sample delivery methods. Thus, sample delivery is one of the key areas of research and development in the serial crystallography scientific community. Sample delivery currently falls into three main systems: jet-based methods, fixed-target chips, and drop-on-demand. Huge strides have since been made in reducing sample consumption and improving data collection efficiency, thus enabling the use of XFEL for many biological systems to provide high-resolution, radiation damage-free structural data as well as time-resolved dynamics studies. This review summarizes the current main strategies in sample delivery and their respective pros and cons, as well as some future direction. Full article
(This article belongs to the Special Issue Macromolecular Serial Crystallography)
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5 pages, 159 KiB  
Review
Serial Crystallography: Preface
by John C. H. Spence
Crystals 2020, 10(2), 135; https://doi.org/10.3390/cryst10020135 - 23 Feb 2020
Cited by 7 | Viewed by 2560
Abstract
The history of serial crystallography (SC) has its origins in the earliest attempts to merge data from several crystals. This preface provides an overview of some recent work, with a survey of the rapid advances made over the past decade in both sample [...] Read more.
The history of serial crystallography (SC) has its origins in the earliest attempts to merge data from several crystals. This preface provides an overview of some recent work, with a survey of the rapid advances made over the past decade in both sample delivery and data analysis. Full article
(This article belongs to the Special Issue Macromolecular Serial Crystallography)
15 pages, 3583 KiB  
Review
Reaction Initiation in Enzyme Crystals by Diffusion of Substrate
by Marius Schmidt
Crystals 2020, 10(2), 116; https://0-doi-org.brum.beds.ac.uk/10.3390/cryst10020116 - 13 Feb 2020
Cited by 28 | Viewed by 4520
Abstract
Ever since the first structure of an enzyme, lysozyme, was solved, scientists have been eager to explore how these molecules perform their catalytic function. There has been an overwhelmingly large body of publications that report the X-ray structures of enzymes determined after substrate [...] Read more.
Ever since the first structure of an enzyme, lysozyme, was solved, scientists have been eager to explore how these molecules perform their catalytic function. There has been an overwhelmingly large body of publications that report the X-ray structures of enzymes determined after substrate and ligand binding. None of them truly show the structures of an enzyme working freely through a sequence of events that range from the formation of the enzyme–substrate complex to the dissociation of the product. The technical difficulties were too severe. By 1969, Sluyterman and de Graaf had pointed out that there might be a way to start a reaction in an enzyme crystal by diffusion and following its catalytic cycle in its entirety with crystallographic methods. The crystal only has to be thin enough so that the diffusion is not rate limiting. Of course, the key questions are as follows: How thin should the crystal be? Will the existing X-ray sources be able to collect data from a thin enough crystal fast enough? This review shines light on these questions. Full article
(This article belongs to the Special Issue Macromolecular Serial Crystallography)
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