Remote access to crystallography beamlines at SSRL: novel tools for training, education and collaboration

Remote laboratory training for high school students: grocery store based hands-on project in protein crystallography

The COVID-19 pandemic measures forced students to stay home and confined them to remote learning. This had a large impact on laboratory experiments, which are often impossible to complete from home. This article is a resource for instructors/educators to introduce the topic of structural biology and crystallographic methods. The main focus is to describe a hands-on crystallization laboratory exercise that can be carried out remotely at home with safe household products. X-ray crystallography is a vital technique for determining protein structure and function. This information can be used to understand fundamental biological processes and to help in the design of life-saving medications. Here, a method was developed to teach crystallography using reagents and equipment that can be found in grocery stores. The steps involved in a crystallography experiment are detailed with links and references to additional resources.

Synchrotron radiation based X-ray techniques for analysis of cathodes in Li rechargeable batteries

Li-ion rechargeable batteries are promising systems for large-scale energy storage solutions. Understanding the electrochemical process in the cathodes of these batteries using suitable techniques is one of the crucial steps for developing them as next-generation energy storage devices. Due to the broad energy range, synchrotron X-ray techniques provide a better option for characterizing the cathodes compared to the conventional laboratory-scale characterization instruments. This work gives an overview of various synchrotron radiation techniques for analyzing cathodes of Li-rechargeable batteries by depicting instrumental details of X-ray diffraction, X-ray absorption spectroscopy, X-ray imaging, and X-ray near-edge fine structure-imaging. Analysis and simulation procedures to get appropriate information of structural order, local electronic/atomic structure, chemical phase mapping and pores in cathodes are discussed by taking examples of various cathode materials. Applications of these synchrotron techniques are also explored to investigate oxidation state, metal-oxygen hybridization, quantitative local atomic structure, Ni oxidation phase and pore distribution in Ni-rich layered oxide cathodes.

Making sense of SFX data: standards for data and structure validation for a non-standard experiment that has come of age

SFX diffraction data collection at XFELs is becoming more accessible. To extract the most useful biological information from these non-standard experiments, standards for SFX data analysis and structure validation must be redefined.

A shared vision for macromolecular crystallography over the next five years

Macromolecular crystallography (MX) is the dominant means of determining the three-dimensional structures of biological macromolecules, but the method has reached a critical juncture. New diffraction-limited storage rings and upgrades to the existing sources will provide beamlines with higher flux and brilliance, and even the largest detectors can collect at rates of several hundred hertz. Electron cryomicroscopy is successfully competing for structural biologists' most exciting projects. As a result, formerly scarce beam time is becoming increasingly abundant, and beamlines must innovate to attract users and ensure continued funding. Here, we will show how data collection has changed over the preceding five years and how alternative methods have emerged. We then explore how MX at synchrotrons might develop over the next five years. We predict that, despite the continued dominance of rotation crystallography, applications previously considered niche or experimental, such as serial crystallography, pink-beam crystallography, and crystallography at energies above 25 keV and below 5 keV, will rise in prominence as beamlines specialize to offer users the best value. Most of these emerging methods will require new hardware and software. With these advances, MX will more efficiently provide the high-resolution structures needed for drug development. MX will also be able to address a broader range of questions than before and contribute to a deeper understanding of biological processes in the context of integrative structural biology.

Steps towards XAFS beamline automation and remote access

Although remote access to beamline synchrotron facilities is now a common operation mode at macromolecular crystallography beamlines thanks to substantial efforts in automated processes for sample preparation and handling, experiment planning and analysis, this is still not the case for XAFS beamlines. Here the experience and developments undertaken at LNLS and Diamond in automation are described, in an attempt to tackle the specific challenges posed by the high variability in experimental conditions and configurations that XAFS measurements require.

New developments in crystallography: exploring its technology, methods and scope in the molecular biosciences

Since the Protein Data Bank (PDB) was founded in 1971, there are now over 120,000 depositions, the majority of which are from X-ray crystallography and 90% of those made use of synchrotron beamlines. At the Cambridge Structure Database (CSD), founded in 1965, there are more than 800,000 'small molecule' crystal structure depositions and a very large number of those are relevant in the biosciences as ligands or cofactors. The technology for crystal structure analysis is still developing rapidly both at synchrotrons and in home labs. Determination of the details of the hydrogen atoms in biological macromolecules is well served using neutrons as probe. Large multi-macromolecular complexes cause major challenges to crystallization; electrons as probes offer unique advantages here. Methods developments naturally accompany technology change, mainly incremental but some, such as the tuneability, intensity and collimation of synchrotron radiation, have effected radical changes in capability of biological crystallography. In the past few years, the X-ray laser has taken X-ray crystallography measurement times into the femtosecond range. In terms of applications many new discoveries have been made in the molecular biosciences. The scope of crystallographic techniques is indeed very wide. As examples, new insights into chemical catalysis of enzymes and relating ligand bound structures to thermodynamics have been gained but predictive power is seen as not yet achieved. Metal complexes are also an emerging theme for biomedicine applications. Our studies of coloration of live and cooked lobsters proved to be an unexpected favourite with the public and schoolchildren. More generally, public understanding of the biosciences and crystallography's role within the field have been greatly enhanced by the United Nations International Year of Crystallography coordinated by the International Union of Crystallography. This topical review describes each of these areas along with illustrative results to document the scope of each methodology.

New synchrotron powder diffraction facility for long-duration experiments

A new synchrotron X-ray powder diffraction instrument has been built and commissioned for long-duration experiments on beamline I11 at Diamond Light Source. The concept is unique, with design features to house multiple experiments running in parallel, in particular with specific stages for sample environments to study slow kinetic systems or processes. The instrument benefits from a high-brightness X-ray beam and a large area detector. Diffraction data from the commissioning work have shown that the objectives and criteria are met. Supported by two case studies, the results from months of measurements have demonstrated the viability of this large-scale instrument, which is the world's first dedicated facility for long-term studies (weeks to years) using synchrotron radiation.

Synchrotron-based macromolecular crystallography module for an undergraduate biochemistry laboratory course

This paper describes the introduction of synchrotron-based macromolecular crystallography (MX) into an undergraduate laboratory class. An introductory 2 week experimental module on MX, consisting of four laboratory sessions and two classroom lectures, was incorporated into a senior-level biochemistry class focused on a survey of biochemical techniques, including the experimental characterization of proteins. Students purified recombinant protein samples, set up crystallization plates and flash-cooled crystals for shipping to a synchrotron. Students then collected X-ray diffraction data sets from their crystals via the remote interface of the Molecular Biology Consortium beamline (4.2.2) at the Advanced Light Source in Berkeley, CA, USA. Processed diffraction data sets were transferred back to the laboratory and used in conjunction with partial protein models provided to the students for refinement and model building. The laboratory component was supplemented by up to 2 h of lectures by faculty with expertise in MX. This module can be easily adapted for implementation into other similar undergraduate classes, assuming the availability of local crystallographic expertise and access to remote data collection at a synchrotron source.

Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source

The SIBYLS beamline (12.3.1) of the Advanced Light Source at Lawrence Berkeley National Laboratory, supported by the US Department of Energy and the National Institutes of Health, is optimized for both small-angle X-ray scattering (SAXS) and macromolecular crystallography (MX), making it unique among the world's mostly SAXS or MX dedicated beamlines. Since SIBYLS was commissioned, assessments of the limitations and advantages of a combined SAXS and MX beamline have suggested new strategies for integration and optimal data collection methods and have led to additional hardware and software enhancements. Features described include a dual mode monochromator [containing both Si(111) crystals and Mo/B(4)C multilayer elements], rapid beamline optics conversion between SAXS and MX modes, active beam stabilization, sample-loading robotics, and mail-in and remote data collection. These features allow users to gain valuable insights from both dynamic solution scattering and high-resolution atomic diffraction experiments performed at a single synchrotron beamline. Key practical issues considered for data collection and analysis include radiation damage, structural ensembles, alternative conformers and flexibility. SIBYLS develops and applies efficient combined MX and SAXS methods that deliver high-impact results by providing robust cost-effective routes to connect structures to biology and by performing experiments that aid beamline designs for next generation light sources.

Remote Internet access to advanced analytical facilities: a new approach with Web-based services

Over the past decade, the increasing availability of the World Wide Web has held out the possibility that the efficiency of scientific measurements could be enhanced in cases where experiments were being conducted at distant facilities. Examples of early successes have included X-ray diffraction (XRD) experimental measurements of protein crystal structures at synchrotrons and access to scanning electron microscopy (SEM) and NMR facilities by users from institutions that do not possess such advanced capabilities. Experimental control, visual contact, and receipt of results has used some form of X forwarding and/or VNC (virtual network computing) software that transfers the screen image of a server at the experimental site to that of the users' home site. A more recent development is a web services platform called Science Studio that provides teams of scientists with secure links to experiments at one or more advanced research facilities. The software provides a widely distributed team with a set of controls and screens to operate, observe, and record essential parts of the experiment. As well, Science Studio provides high speed network access to computing resources to process the large data sets that are often involved in complex experiments. The simple web browser and the rapid transfer of experimental data to a processing site allow efficient use of the facility and assist decision making during the acquisition of the experimental results. The software provides users with a comprehensive overview and record of all parts of the experimental process. A prototype network is described involving X-ray beamlines at two different synchrotrons and an SEM facility. An online parallel processing facility has been developed that analyzes the data in near-real time using stream processing. Science Studio and can be expanded to include many other analytical applications, providing teams of users with rapid access to processed results along with the means for detailed discussion of their significance.

Automatic loop centring with a high-precision goniometer head at the SLS macromolecular crystallography beamlines

Automatic loop centring has been developed as part of the automation process in crystallographic data collection at the Swiss Light Source. The procedure described here consists of an optional set-up part, in which the background images are taken, and the actual centring part. The algorithm uses boundary and centre-of-mass detection at two different microscope image magnifications. Micromounts can be handled as well. Centring of the loops can be achieved in 15-26s, depending on their initial position, and as fast as manual centring. The alignment of the sample is carried out by means of a new flexural-hinge-based compact goniometer head. The device features an electromagnet for robotic wet mounting of samples. The circle of confusion was measured to be smaller than 1 µm (r.m.s.); its bidirectional backlash is below 2 µm.