Volume 16, No. 8, August 2024

Hi Crystallographer,

In July, I went to the Protein Society Symposium in Vancouver. This was my first TPS Symposium in perhaps 15 years. I am happy to report macromolecular crystallography is alive and well despite the bias towards cryo-EM that one sees in Science and Nature. I had the pleasure of introducing this year’s Carl-Ivar Brändén Award winner, Tamir Gonen. Hikaru Shimura, past President and CEO of Rigaku, provided the endowment for the Brändén Award. The endowment has grown so much in the 18 years since its inception that it is now able to fund a second award, the Dorothy Crowfoot Hodgkin Award. I also enjoyed getting to see many old friends and acquaintances.

Left to right: The author, Tamir Gonen and Liz Mierling, President of The Protein Society 

I have also just returned from the Denver X-ray Conference, which is another great venue to catch up with old friends.

Speaking of meetings, the European Crystallographic Meeting is coming up in Padova and we have a lot of activities planned, which Fraser describes in detail below. This month we interviewed Max Siegler of Johns Hopkins University. Max will be providing a webinar in late September, so please check the website for up-to-date information. Lee Daniels wrote the tip-of-the-month on to how use the Euler-kappa calculator in CrysAlis^Pro. Lastly, Jeanette is back reviewing books and provides this month's review of On Call by Anthony Fauci.

It seems lots of people are getting COVID these days, so stay positive and test negative.

Joe Ferrara

Rigaku XtaLAB Synergy-R, a Productivity Tool That Means Success!

Throughout the presentation, Fraser White and speaker Dr. Maxime Siegler, Johns Hopkins University, will establish the significant impacts of the acquisition of the Rigaku XtaLAB Synergy-R on the research at JHU and beyond.

Dr. Maxime Siegler has been formerly trained by some well-respected crystallographers, namely Prof. Carol Brock, Prof. Sean Parkin (University of Kentucky) and Prof. Ton Spek (Utrecht University, The Netherlands), with whom he studied chemical X-ray crystallography and the whole process of crystal handling, data collection, structure solution/refinement of all kinds of difficult samples (e.g., air-, solvent- and temperature-sensitive crystals, twinned crystals, wholly disordered crystals, modulated superstructures with high Z', crystals with multiple phase transitions, etc.). Currently, he is the Director of the X-ray Facility at the Johns Hopkins University (Homewood campus), and has been the author/co-author of 348 peer-reviewed papers.

Wednesday, Sep 25, 2024 at 09:00 AM CDT

Time Zone Converter

When did you start in structural science and how long have you been using SCXRD in your research?

My journey into structural science began in 2003 when I joined Professor Carolyn Brock's research lab (Chemistry Department, University of Kentucky) as a Ph.D. student. My research focused on the structures and properties of molecular crystals, particularly investigating a series of complex solid-solid phase transitions. Since then, single-crystal X-ray diffraction (SCXRD) has been an integral part of my scientific career. I first utilized SCXRD as a graduate student, continued to employ it as a postdoctoral fellow under the mentorship of Ton Spek (Chemistry Department, Utrecht University), and currently serve as the director of the service X-ray facility at Johns Hopkins University.

What first attracted you to SCXRD?

My attraction to SCXRD likely stems from its unparalleled ability to provide a direct, three-dimensional visualization of a molecular system at the atomic level. Much like solving a complex puzzle, when the SCXRD data are carefully pieced together, SCXRD yields an unambiguous characterization of crystalline materials, providing invaluable information such as atom connectivity, the nature of chemical bonds, interactions, and crystal packing. Such information is often unattainable using other techniques, making SCXRD truly remarkable.

What is the biggest challenge you are facing in your research just now?

Over the past decade, the scientific community has benefited greatly from significant advancements in XRD instrumentation, particularly in detection devices, X-ray sources, and software. These improvements have undoubtedly facilitated the structure elucidation of smaller and more complex crystalline materials with increased success rates. However, the fundamental challenge of obtaining high-quality crystals remains a significant bottleneck in SCXRD. It is crucial to avoid overreliance on technology and maintain a strong focus on developing optimal pathways for high-quality crystal growth. Providing a robust educational component is essential to equip future generations of scientists with the necessary knowledge in this area.

How does SCXRD fit into your main research interest?

SCXRD has been instrumental in supporting interdisciplinary research across 28 internal and external groups with which I have collaborated. By providing crucial structural insights at the atomic level, we have successfully characterized a diverse array of crystalline materials, encompassing small and large molecules, organics, inorganics, coordination compounds, metal-organic frameworks (MOFs), metal clusters, and proteins. The recent acquisition of the Rigaku Oxford Diffraction XtaLAB Synergy-R diffractometer has markedly enhanced our laboratory's productivity, facilitating high-speed data collection (e.g., complete datasets within minutes for triclinic crystals). This advanced instrumentation has also expanded our capabilities to tackle challenging materials, such as crystals measuring only 10-20 microns, which were previously unattainable using our existing equipment.

Looking into your crystal ball, how do you think SCXRD will change in the next 10 years?

Advancements in artificial intelligence are likely to introduce automation into certain steps of crystal handling, mounting, and data collection processes. Though it is still difficult to predict as human intervention will remain indispensable for tasks demanding judgment, problem-solving, and the interpretation of more complex data. Additionally, I anticipate further advancements in X-ray source, optics, and detector technologies that will enable the analysis of even smaller crystals and more complex crystalline materials. Integrating these developments with other techniques, particularly MicroED (for nanomaterials), will provide a very comprehensive understanding of structural and chemical information of any crystalline materials.

Anything else you’d like to share with our readers?

From my experience, the success of over 90% of SCXRD analyses hinges on selecting a suitable crystal. Hence, the importance of crystal growth cannot be overstated. When initial attempts are unsuccessful (don’t be lazy), be prepared to conduct 10-20 additional experiments under varying conditions as this increased effort is likely to improve the chances of obtaining suitable crystals for SCXRD analysis.

I write this approximately two weeks before the European Crystallographic Meeting (ECM) is due to begin in Padua, Italy on August 26. Long-term weather forecasts look good, with temperatures exceeding 30°C (86°F), so it’s set to be a hot ECM.

This year, the ECM is joining forces with the European Powder Diffraction Conference (EPDIC) to share the venue for the convenience of those interested in powder diffraction and crystallography. EPDIC will begin on August 30, shortly after the conclusion of the ECM. Throughout both events, Rigaku will be at booth #10, where we will be glad to greet you in person and chat with you about our products and any scientific questions you may have. If you are attending either ECM or EPDIC (or both), please do stop by and say hello.

At the ECM, we will share our latest in both X-ray and electron diffraction and we will have oral and poster presentations as well as our lunchtime seminar on Thursday at noon. We will also be attending the ElCryS satellite meeting preceding the ECM, from August 24-26. If you are interested in news from Rigaku, single crystal or powder, a timetable of our activities at the ECM is below so you can easily see where we are presenting. For EPDIC, please refer to the official program.

At this ECM, we are really excited to have something special to share, so I strongly encourage you to attend our lunchtime seminar if you want to be among the first to learn our exciting news.

We look forward to seeing you soon in sunny Italia!

Fraser White

July 13, 2024

Researchers from the US report the structure of an actinium hydroxypyridinone complex contained within a macromolecular scaffold formed by the protein siderocalin, the first crystal structure of an actinium compound.

Tip of the Month – The Euler-kappa calculator

What is it?

A calculator to convert Kappa-goniometer angles to Eulerian (and back).

Why should I use it?

It’s a convenient way to move to positions in an orthogonal coordinate system.

Why should I use it?

Old-school crystallographers may remember the “Eulerian cradle” design for crystal orienting on a diffractometer, which often included a full 360° chi circle, as on the Rigaku AFC-5 or AFC-7, where the chi axis is always perpendicular to the omega axis. It’s slightly easier to calculate how to position a particular reflection onto a particular point in space (important with point detectors where every reflection was measured in the horizontal plane of the beam). And some of us still think in terms of the chi angle; i.e., putting the sample at chi=90° when, for example, aligning a high-pressure cell on the diffractometer.

Many of us use the command line in CrysAlis^Pro to drive the angles to a specific location; i.e., the command ‘gt a -10 0 50 12’ moves to omega=-10°, detector_theta=0°, kappa=50° and phi=12°. Less common but useful is to move to Eulerian angles: ‘gt e 0 0 90 0’ to move to chi=0° (with others at Eulerian zero). This is approximately the same as ‘gt a -57 0 134 -57’ but a lot easier to visualize!

You can access a (currently undocumented) menu in CrysAlis^Pro by typing ‘gt e’ with no other parameters. The following appears:

This allows the transformation from one coordinate system to the other. A press of the blue Euler→Kappa button switches the calculation to the other direction. If performed in online mode, the [GT a] button populates the command-line with the resulting ‘gt a …’ command.

Enjoy another way to test your 3-dimensional visualization!

Review: On Call: A Doctor’s Journey in Public Service

By Anthony Fauci, M.D.

ISBN  9780593657478 

Anthony Fauci was a public servant in the medical profession for five decades before the COVID-19 pandemic, during which he was thrust into the limelight as the voice of scientific reason in the midst of a global crisis. Fauci became a routine punching bag for Fox News pundits, run-of-the-mill, everyday conservatives, and, perhaps most notably, the then-president of the United States of America, along with everyone else who was frustrated with how the United States government was handling the pandemic response, blaming him for everything from masking mandates to remote work policies to the general state of the economy. Realistically speaking, none of that was his fault.

Considering Fauci’s “claim to fame” in the public sphere was his apparent role in shaping public policy during the COVID-19 pandemic—even though Fauci worked for the National Institute of Allergy and Infectious Diseases, NIAID, not the Centers for Disease Control and Prevention, CDC —his memoir focuses comparatively little on the pandemic. It starts with his early childhood and youth in Bensonhurst, Brooklyn, his high school and college years, his time at Cornell Medical School, and his eventual move into public medical service. Once Fauci becomes a public servant, that’s when things get interesting.

Fauci spends a good chunk of the book detailing his experiences working both nationally and internationally to combat the HIV/AIDS epidemic in the 1980s and 1990s. This was an endeavor pursued across multiple administrations. But he was also in “the room” when bird flu, swine flu, and Ebola were making headlines in the last few decades, and his experiences and perspectives on those issues and how they were handled under different political administrations paints a very telling picture in comparison to the handling of the coronavirus pandemic.

It is clear from On Call that Fauci views himself first and foremost as a medical doctor and secondly as a public servant. His role at NIAID is one that has lasted through multiple administrations, across decades of both Republican and Democratic presidents. He speaks highly of working with and for George H.W. Bush, his son George W. Bush, and Barack Obama —all very different presidents with very different agendas while in office. It is impossible to tell Fauci’s political alignment from the book, which gives it a uniquely political neutral tone that’s delightfully refreshing in the current era of pundit-driven polarity.

Despite the professional and personal abuse Fauci received both from the American public and the American president during the COVID-19 pandemic, he remains optimistic. Fauci describes his differences in opinion (and sometimes, in fact) from some of his administrative superiors, but does so in a way that maintains professionalism and respect —a courtesy that was not reciprocated during the later years of his tenure at NIAID. It should concern us as a country that a civilian doctor and public servant received so many death threats during COVID-19 (as did his immediate family) that he had to be assigned a security team.

On Call is an interesting read with a perspective on the last five decades of health policy in the United States that one would be pressed to find elsewhere. Fauci sprinkles personal tidbits—–like his proficiency at making the baked pasta dish timpano and his love of his daughter’s dog—–delicately delicately and efficiently, breaking up the narrative and reminding the reader that before anything else—–doctor, public servant, father, husband, etc., Fauci is a human being.

Review by Jeanette S. Ferrara, MFA

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