Crystallography in the News

October 1, 2019. Zoë Fisher and Katarina Koruza from the ESS Deuteration and Macromolecular Crystallization (DEMAX) Support lab and Lund University have been using vapor diffusion methods to grow large deuterated protein crystals for neutron techniques as part of SINE2020's Crystal Growth work package.

October 4, 2019. Electron paramagnetic resonance (EPR) spectroscopy on protein single crystals is the ultimate method for determining the electronic structure of paramagnetic intermediates at the active site of an enzyme and relating the magnetic tensor to a molecular structure.

October 7, 2019. The 2019 Nobel Prize in Physiology or Medicine has been awarded to National Institutes of Health grantees Gregg L. Semenza, M.D., Ph.D., of Johns Hopkins University, Baltimore, and William G. Kaelin Jr., M.D., of Dana-Farber Cancer Institute, Boston, who share the prize with Sir Peter J. Ratcliffe, M.D., of the University of Oxford, England, and Francis Crick Institute, London, for their discoveries of how cells sense and adapt to oxygen availability.

October 9, 2019. A new study by chemists at the University of Arkansas shows that X-ray crystallography can provide inaccurate information about a critical set of proteins - those found in cell membranes - which in turn could be leading to poor and inefficient drug design.

October 9, 2019. The 2019 Nobel Prize in Chemistry has been awarded to John B. Goodenough (University of Texas at Austin), M. Stanley Whittingham (State University of New York at Binghamton), and Akira Yoshino (Meijo University) for their work on "the development of lithium ion batteries," according to the Nobel committee. "Lithium ion batteries have revolutionized our lives and are used in everything from mobile phones to laptops and electric vehicles," tweeted the committee. "Through their work, this year's Chemistry Laureates have laid the foundation of a wireless, fossil fuel-free society," it added. The three winners will share a prize of 9 million Swedish kroner ($910,000).

October 14, 2019. A new refrigeration technology based on the twisting and untwisting of fibres has been demonstrated by a team led by Zunfeng Liu at Nankai University in China and Ray Baughman at the University of Texas at Dallas. As the demand for refrigeration expands worldwide, their work could lead to the development of new cooling systems that do not employ gases that are harmful to the environment.

October 16, 2019. If you travel to the outskirts of a town called Pulpí in Spain, you'll find an abandoned silver mine. Descend about 50 metres (164 feet) into it, and you'll enter a strange, shimmering room quite unlike anywhere else on Earth. Scientists might have finally found the origin of this surreal jagged crystal cave.

October 16, 2019. Monash scientists have identified a survival mechanism of bacteria that cause disease in plant and animals, including highly virulent E. coli (Escherichia coli) related diseases. In a study published in PLoS Genetics, researchers show that pathogenic bacteria obtain the essential nutrient iron during infection by pirating it from host proteins.

October 21, 2019. Phagocytosis can be viewed as a primitive immune system used by all cells. When a pathogen is near the cell, the cell membrane will deform to engulf the pathogen and dispose of it. Researchers have found that a two-dimensional sheet formed by the protein GAS7 is critical for this process, identifying through crystallography and microscopy two key hydrophilic loops in the protein.

Product Spotlight

HyPix-6000HE: Hybrid photon counting X-ray detector

Rigaku Oxford Diffraction now offers the HyPix-6000HE Hybrid Photon Counting (HPC) X-ray detector. Like all HPCs, the HyPix-6000HE offers direct X-ray photon counting, single pixel point spread function and extremely low noise. The HyPix-6000HE HPC offers a small pixel size of 100 microns, which allows you to better resolve reflections for long unit cells as well as improving reflection profile analysis. The HyPix-6000HE has a high frame rate of 100 Hz, as well as a unique Zero Dead Time mode providing the ultimate in error-free shutterless data collection.

Lab in the Spotlight

UCB Laboratory

The UCB Laboratory on Bainbridge Island is responsible for the majority of the crystallography work by the Seattle Structural Genomics Center for Infectious Disease (SSGCID). SSGCID is one of two Centers funded by NIAID in response to RFP-NIAID-DMID-NIHAI2016061, RFP-NIH-NIAID-DMID-07-19 and RFP-NIAID-DMID-NIHAI2011124 and is a consortium of four Pacific Northwest institutions (Seattle Children's Research Institute, University of Washington, UCB and Washington State University). SSGCID's primary mission is to determine the 3D atomic structures of proteins and other molecules with an important biological role in human pathogens themselves, or molecules involved in host-pathogen interactions, by applying state-of-the art high-throughput (HTP) technologies and methodologies. Pathogens include those on the NIAID Category A-C agents as well as emerging and re-emerging infectious disease organisms, each year for a period of five years. This program supports research projects that utilize experimental approaches to better characterize the molecular mechanisms of protein targets and gain further insight into the functional roles of these targets. SSGCID at UCB is managed by co-PIs Tom Edwards and Peter Horanyi, site manager Don Lorimer. Jan Abendroth manages the x-ray data collection, structure solution and upkeep of the in-house system.

A quick survey of the PDB shows that in 12 years of SSGCID activity, the group has deposited 1209 structures. Of those 1209 structures, 314 were solved using data collected on the Rigaku home laboratory equipment at UCB. The equipment currently includes an FR-E+ Superbright outfitted with a pair of Osmic optics, AFC11 goniometers, Saturn 944+ CCD detectors and ACTOR sample changers. Below is a picture of the system. One very interesting note about the SSGCID's deposits is that over 50 were solved using iodine quick soaks. Even though the system is eleven (11) years old it is still used on a daily basis for the SSGCID's ongoing projects as well as UCB's internal projects.

Useful Links

You may already have seen this posted on CNET, Apple News or Popular Mechanics; nevertheless, I am posting here this because it is so cool: Miners find diamond trapped inside another diamond.

Evolving SAXS versatility: solution X-ray scattering for macromolecular architecture, functional landscapes, and integrative structural biology. Brosey, Chris A; Tainer, John A. Current Opinion in Structural Biology. Oct2019, Vol. 58, p197-213. 17p. DOI: 10.1016/j.sbi.2019.04.004.

From then till now: changing data collection methods in single crystal X-ray crystallography since 1912. Powell, Harold R. Crystallography Reviews. Oct2019, Vol. 25 Issue 4, p264-294. 31p. DOI: 10.1080/0889311X.2019.1615483.

An industry perspective of crystallography: its communities and its educational courses and labs. Šišak Jung, Dubravka. Crystallography Reviews. Oct2019, Vol. 25 Issue 4, p295-315. 21p. DOI: 10.1080/0889311X.2019.1631295.

Sequence and structure determination of a metalloproteinase: integration of mass spectrometry, phylogenetic and crystallography. Borges, Rafael Junqueira; Marchi Salvador, Guilherme Henrique; Dos Santos, Lucilene Delazari; Uson, Isabel; De Mattos Fontes, Marcos Roberto. Toxicon. Oct2019:Supplement 1, Vol. 168, pS12-S12. 1p. DOI: 10.1016/j.toxicon.2019.06.066.

3D printed droplet generation devices for serial femtosecond crystallography enabled by surface coating. Echelmeier, Austin; Kim, Daihyun; Cruz Villarreal, Jorvani; Coe, Jesse; Quintana, Sebastian; Brehm, Gerrit; Egatz-Gomez, Ana; Nazari, Reza; Sierra, Raymond G.; Koglin, Jason E.; Batyuk, Alexander; Hunter, Mark S.; Boutet, Sébastien; Zatsepin, Nadia; Kirian, Richard A.; Grant, Thomas D.; Fromme, Petra; Ros, Alexandra. Journal of Applied Crystallography. Oct2019, Vol. 52 Issue 5, p997-1008. 12p. DOI: 10.1107/S1600576719010343.

A prototype system for dynamically polarized neutron protein crystallography. Pierce, J.; Crow, L.; Cuneo, M.; Edwards, M.; Herwig, K.W.; Jennings, A.; Jones, A.; Li, L.; Meilleur, F.; Myles, D.A.A.; Robertson, L.; Standaert, R.; Wonder, A.; Zhao, J.K. Nuclear Instruments & Methods in Physics Research Section A. Oct2019, Vol. 940, p430-434. 5p. DOI: 10.1016/j.nima.2019.06.023.

Well-based crystallization of lipidic cubic phase microcrystals for serial X-ray crystallography experiments. Andersson, Rebecka; Safari, Cecilia; Båth, Petra; Bosman, Robert; Shilova, Anastasya; Dahl, Peter; Ghosh, Swagatha; Dunge, Andreas; Kjeldsen-Jensen, Rasmus; Nan, Jie; Shoeman, Robert L.; Kloos, Marco; Doak, R. Bruce; Mueller, Uwe; Neutze, Richard; Brändén, Gisela. Acta Crystallographica: Section D, Structural Biology. Oct2019, Vol. 75 Issue 10, p937-946. 10p. DOI: 10.1107/S2059798319012695.

Deriving and refining atomic models in crystallography and cryo-EM: the latest Phenix tools to facilitate structure analysis. Klaholz, Bruno P. Acta Crystallographica: Section D, Structural Biology. Oct2019, Vol. 75 Issue 10, p878-881. 4p. DOI: 10.1107/S2059798319013391.

Impact of the ΔPhe configuration on the Boc-Gly-ΔPhe-NHMe conformation: experiment and theory. Buczek, Aneta; Siodlak, Dawid; Bujak, Maciej; Makowski, Maciej; Kupka, Teobald; Broda, Malgorzata A. Structural Chemistry. Oct2019, Vol. 30 Issue 5, p1685-1697. 13p. DOI: 10.1007/s11224-019-01387-w.

A new octa-Mn-substituted poly(polyoxotungstate). Li, Hai-Lou; Lian, Chen; Yin, Da-Peng; Yang, Guo-Yu. Dalton Transactions: An International Journal of Inorganic Chemistry. 10/14/2019, Vol. 48 Issue 38, p14306-14311. 6p. DOI: 10.1039/c9dt02805f.

New class of non-symmetrical homo-dibenzimidazolium salts and their dinuclear Silver(I) di-NHC complexes. Haziz, Umie F.M.; Haque, Rosenani A.; Amirul, A.A.; Aidda, O.Noor; Razali, Mohd R. Journal of Organometallic Chemistry. Oct2019, Vol. 899, pN.PAG-N.PAG. 1p. DOI: 10.1016/j.jorganchem.2019.120914.

Three dimensional manganese(II) coordination polymers constructed from 2,2-dimethylglutarate and bis(pyridyl) type ligands. Köse Yaman, Pelin; Erer, Hakan; Yesilel, Okan Zafer. Polyhedron. Oct2019, Vol. 171, p317-322. 6p. DOI: 10.1016/j.poly.2019.07.008.

Euphonoids A-G, cytotoxic diterpenoids from Euphorbia fischeriana. Yan, Xue-Long; Zhang, Jun-Sheng; Huang, Jia-Luo; Zhang, Yao; Chen, Jia-Qi; Tang, Gui-Hua; Yin, Sheng. Phytochemistry. Oct2019, Vol. 166, pN.PAG-N.PAG. 1p. DOI: 10.1016/j.phytochem.2019.112064.

Understanding the structure and role of DNA-PK in NHEJ: How X-ray diffraction and cryo-EM contribute in complementary ways. Wu, Qian; Liang, Shikang; Ochi, Takashi; Chirgadze, Dimitri Y.; Huiskonen, Juha T.; Blundell, Tom L. Progress in Biophysics & Molecular Biology. Oct2019, Vol. 147, p26-32. 7p. DOI: 10.1016/j.pbiomolbio.2019.03.007.

Discrete π-Stacks from Self-Assembled Perylenediimide Analogues. Su, Feng; Chen, Guangmei; Korevaar, Peter A.; Pan, Fangfang; Liu, Huijiao; Guo, Zongxia; Schenning, Albertus P. H. J.; Zhang, Hui-Jun; Lin, Jianbin; Jiang, Yun-Bao. Angewandte Chemie International Edition. Oct2019, Vol. 58 Issue 43, p15273-15277. 5p. DOI: 10.1002/anie.201907838.

A history and an industry perspective of crystallography. Bombicz, Petra. Crystallography Reviews. Oct2019, Vol. 25 Issue 4, p263-263. 1p. DOI: 10.1080/0889311X.2019.1641098.

Biological small angle scattering: by Eaton E. Lattman, Thomas D. Grant and Edward H. Snell (IUCr Monographs on Crystallography 29, Oxford Science Publications), Oxford University Press, 2018, 268 pp., £65, ISBN 978-0-19-967087-1. By: Bóta, Attila. Crystallography Reviews. Oct2019, Vol. 25 Issue 4, p316-318. 3p. DOI: 10.1080/0889311X.2019.1592168.

Book Review

The Physics of Everyday Things: The Extraordinary Science Behind an Ordinary Day
By James Kakalios
ISBN 978-0-7704-3775-6

James Kakalios' newest book is a delightful endeavor into the physics of everyday life. Kakalios does not take the time to explain the basic concepts of physics, but rather the basic (or not-so-basic) physics  of mundane mechanisms. These range from alarm clocks and toasters to car engines and airplanes—all things that we largely take for granted in our everyday lives. At times, Kalakios leans towards oversimplification of certain concepts, but as he himself admits in the chapter where he explains how an MRI machine works, "if you know all this—why are you reading this book?"

The Physics of Everyday Things is not geared towards physicists or engineers, but rather physics enthusiasts. The ideal audience for this book might be a younger student of physics—perhaps a high school student or college freshman—or someone who hasn't studied physics since their earlier days. In order to enjoy the book and thoroughly appreciate it, the reader must have some knowledge of physics fundamentals. But someone who lives and breathes physics for a living might find it a little too trite to be entertaining.

How To: Absurd Scientific Advice for Common Real-World Problems
By Randall Munroe
ISBN 978-0525537090

This is the latest work from the mind of Randall Munroe, best known for his hysterical online comic strip xkcd. If you are a fan of Munroe's comics, you will certainly enjoy this book. It combines his iconic comic style with very scientific pseudo self-help advice.

Mostly, Munroe takes real-world problems and scenarios and performs a reverse reductio ad absurdum, presenting the reader with the most absurd yet scientifically sound solutions to some terribly banal inquiries. Would they work in actuality? Possibly not, but they work in theory—and make for wildly entertaining hypothetical scenarios bolstered by delightfully sarcastic comic illustrations.

Some of the highlights include "How to Throw a Pool Party," "How to Move," "How to Play Tag," and "How to Build a Lava Moat." If you are thinking "one of these is not like the others," you are correct. "How to Build a Lava Moat" is an example of one of the chapters that answered a question I don't imagine most readers would have ever thought to ask, although the resulting response is highly entertaining. "How to Throw a Pool Party" was quite hilarious as well, as it operated under the initial assumption that one does not necessarily have a pool and needs to build one before hosting a party in it.

However, the best chapter was "How to Make an Emergency Landing." For this section, Munroe conducted a question-and-answer series with test pilot and astronaut Chris Hadfield. The contrast between Munroe's increasingly absurd queries, which include "How to Land on a Farm," "How to Land on an Aircraft Carrier," "How to Land on a Hostile Aircraft Carrier," and "How to Land a Space Shuttle in Downtown LA," and Hadfield's serious and scientifically sound expert responses, makes for a wildly entertaining departure from the typical format Munroe follows in his other chapters.

All in all, the book is a wonderfully comedic approach to everyday self-help grounded in very real but very absurd scientific solutions.

Reviews by Jeanette S. Ferrara, MA