Crystallography in the News

March 1, 2018. Rebecca Hochstein, who earned her doctorate in MSU's Department of Microbiology and Immunology in 2015, is lead author of a study that explains how a lemon-shaped virus that lives in Yellowstone hot springs assembles itself and how the virus ejects the DNA it carries into host cells.

March 6, 2018. New research published in Nature Methods will dramatically improve how scientists "see inside" molecular structures in solution, allowing for much more precise ways to image data in various fields, from astronomy to drug discovery. The new method has solved the phase problem for a particular molecular determination technique called solution scattering. The phase problem is where critical information about the phase of a molecule is lost during the experimental process of making a physical measurement.

March 12, 2018. Scientists have previously found that carbon-carbon bonds, which typically measure about 1.54 ?? in length, can be elongated through the use of bulky substituents to endow molecules with special properties. Now, researchers led by Takanori Suzuki and Yusuke Ishigaki at Hokkaido University have synthesized a molecule with the longest reported C???C bond, measuring 1.806 Å in length.

March 12, 2018. Bryan Roth, M.D, Ph. D., and colleagues recently published a paper in the journal Cell entitled Crystal Structure of an LSD-Bound Human Serotonin Receptor. The paper contains some very elegant science, in particular, the details of how LSD binds to specific serotonin receptors. The details of this binding were visualized at the atomic level using X-ray crystallography.

March 13, 2018. Research originating from the laboratory of Assistant Professor of Chemistry Max Majireck at Hamilton College describes the discovery of a novel and potentially valuable class of compound known as an N-(1-alkoxyvinyl) pyridinium salt. During the past 80 years, only a few scattered reports have been published on similar types of compounds, but since most were found to be unstable.

March 15, 2018. The Protein Society, the premier international society dedicated to supporting protein research, announced the winners of the 2018 Protein Society Awards, which will be conferred at their 32nd Annual Symposium (July 9 – 12, 2018, Boston, Massachusetts).

March 15, 2018. The Carl Branden Award, sponsored by Rigaku Corporation, honors an outstanding protein scientist who has also made exceptional contributions in the areas of education and/or service to the field. The 2018 recipients of this award are Professors Jane and Dave Richardson (Duke University).

March 15, 2018. Using X-ray crystallography, a team at Australia's CSIRO discovered a unique structure in the platypus milk protein which, when solved, formed a three dimensional fold, similar to a ringlet. The researchers named this never-before-seen protein the Shirley Temple, in tribute to the former child-actor's distinctive curly hair.

March 16, 2018. A research team at the Indian Institute of Technology Roorkee has discovered the antiviral prospective of piperazine molecule and determined the mechanism to combat the deadly chikungunya, an infectious viral disease, which is transmitted to humans by mosquitoes infected with the virus. Using the macromolecular X-ray crystallography facility at Institute Instrumentation Center (IIC) at IIT Roorkee, the molecular interactions of piperazine with capsid protein were exposed at the atomic level in this study.

March 21, 2018. In the April 2018 issue of SLAS Discovery, a review article by Prof. Stefan Broer, Ph.D. of the Australian National University highlights opportunities and challenges in using amino acid transporters as drug targets.

Product Spotlight

CrysAlis^Pro v39: User-inspired software

CrysAlis^Pro lies at the heart of the Rigaku Oxford Diffraction user experience, as it is used both for controlling instruments and processing data. From the very inception of CrysAlis^Pro, one of the core goals of the software development team was to ensure that high-quality data can be produced by anyone. Through several iterations of CrysAlis^Pro, development has been inspired by user feedback and incorporates the considerable experience of our engineers and scientists.

Whether working at the diffractometer or processing your previously collected data offline, CrysAlis^Pro workflows can be either manual or fully automated to fit your preferred way of working.

Key Features

Easy sample screening and the "What is this?" feature lets you quickly and automatically identify samples, often in under a minute. All you need to do is center the sample and provide a list of elements. CrysAlis^Pro with AutoChem does the rest. Knowing what your sample structure is before you collect your full dataset lets you plan better strategies and saves valuable diffractometer time.

Diagnosis and handling of problems is even easier with the Ewald 3D module, new in v39. This ultra-fast tool allows you to interactively visualize your diffraction pattern in three dimensions within seconds to minutes depending on the size of your dataset. Common issues like twinning, slipping crystals, modulation etc. are now even easier to spot allowing you to quickly identify issues, address them and move on.

Improved powder handling tools allow for ring detection, fitting and alignment to ensure calibration of the system is optimal at any position and if necessary can be adjusted offline.

Support for older Rigaku instrumentation is growing all the time. Upgrade your system for a better user experience by contacting your local sales representative today.

Registered users can download CrysAlis^Pro v39 from our user forum.

Lab in the Spotlight

Gloria Borgstahl, Ph.D.
Department of Biochemistry and Molecular Biology
Department of Pharmaceutical Sciences
Eppley Institute, University of Nebraska Medical Center

Prof. Borgstahl is interested in developing novel X-ray crystallography methods and in studying the macromolecules essential to the protection of biological macromolecules and the maintenance and replication of DNA.

Lately, her group has developed protocols for the processing of incommensurately modulated diffraction data from protein crystals. "We have studied these modulations through computer modeling and have started to create software to refine these structures in (3+1)D superspace."

Her laboratory has had a long-standing interest in the proteins involved in DNA metabolism using X-ray crystallography and molecular modeling. In particular, they study human replication protein A (RPA) and RAD52. RPA is a single-stranded DNA binding protein that is a key player in DNA metabolism and together with RAD52 anneals repetitive DNA sequences at double-strand breaks. This annealing reaction is a drug target in homologous recombination deficient hereditary cancers.

Her laboratory also has an interest in superoxide dismutase (SOD) enzymes that are critical in preventing damage to all biological macromolecules. They are investigating the catalytic mechanism by which superoxide dismutases affect oxygen radicals. They are employing neutron diffraction to solve crystal structures of SOD in order to see hydrogen positions and avoid reduction of the active site metal by X-rays. In order to obtain crystals of suitable size and purity for neutron diffraction, we hope to grow crystals in microgravity on the international space station.

Useful Link

The Experiment Experiment

Here is a 2016 Planet Money episode with a 2018 update on two of the problems we face as scientists: not reporting negative results and changing protocols until we get the result that fits the hypothesis.

Multifarious injection chamber for molecular structure study (MICOSS) system: development and application for serial femtosecond crystallography at Pohang Accelerator Laboratory X-ray Free-Electron Laser. Park, Jaehyun; Kim, Seonghan; Kim, Sangsoo; Nam, Ki Hyun. Journal of Synchrotron Radiation. Mar2018, Vol. 25 Issue 2, p323-328. 5p. DOI: 10.1107/S160057751800022X.

Coded diffraction system in X-ray crystallography using a boolean phase coded aperture approximation. Pinilla, Samuel; Poveda, Juan; Arguello, Henry. Optics Communications. Mar2018, Vol. 410, p707-716. 10p. DOI: 10.1016/j.optcom.2017.11.035.

Efficient resolution of venlafaxine and mechanism study via X-ray crystallography. Zhi-Jin Liu; Han Liu; Xuan-Wen Chen; Min Lin; Yu Hu; Xun Tuo; Zhong-Yi Yuan; Xiao-Xia Sun. Chirality. Mar2018, Vol. 30 Issue 3, p268-274. 7p. DOI: 10.1002/chir.22790.

Molecular structure in the solid state by X-ray crystallography and SSNMR and in solution by NMR of two 1,4-diazepines. Nieto, Carla I.; Sanz, Dionisia; Claramunt, Rosa M.; Torralba, M. Carmen; Torres, M. Rosario; Alkorta, Ibon; Elguero, José. Journal of Molecular Structure. Mar2018, Vol. 1155, p205-214. 10p. DOI: 10.1016/j.molstruc.2017.10.112.

Combined analysis of 1,3-benzodioxoles by crystalline sponge X-ray crystallography and laser desorption ionization mass spectrometry. Hayashi, Yukako; Ohara, Kazuaki; Taki, Rika; Saeki, Tomomi; Yamaguchi, Kentaro. Analyst. 3/21/2018, Vol. 143 Issue 6, p1475-1481. 7p. DOI: 10.1039/c7an01906h.

The thermochemistry and crystallography of the metal tris-acetylacetonates. Lalancette, Roger A.; Arslan, Evrim; Bernal, Ivan; Willhelm, Daniel; Grebowicz, Janusz; Pluta, Miroslaw. Journal of Thermal Analysis & Calorimetry. Mar2018, Vol. 131 Issue 3, p2809-2819. 11p. DOI: 10.1007/s10973-017-6799-x.

A multidisciplinary study of 3-(ß-d-glucopyranosyl)-5-substituted-1,2,4-triazole derivatives as glycogen phosphorylase inhibitors: Computation, synthesis, crystallography and kinetics reveal new potent inhibitors. Kun, Sándor; et al. European Journal of Medicinal Chemistry. Mar2018, Vol. 147, p266-278. 13p. DOI: 10.1016/j.ejmech.2018.01.095.

"To Be or Not to Be" Protonated: Atomic Details of Human Carbonic Anhydrase-Clinical Drug Complexes by Neutron Crystallography and Simulation. Kovalevsky, Andrey; Aggarwal, Mayank; Velazquez, Hector; Cuneo, Matthew J.; Blakeley, Matthew P.; Weiss, Kevin L.; Smith, Jeremy C.; Fisher, S. Zoë; McKenna, Robert. Structure. Mar2018, Vol. 26 Issue 3, p383-390.e3. 1p. DOI: 10.1016/j.str.2018.01.006.

Na₃Tb(PO₄)₂: Synthesis, crystal structure and greenish emitting properties. Zhao, Dan; Ma, Zhao; Liu, Bao-Zhong; Zhang, Rui-Juan; Wu, Zhi-Qiang; Wang, Jian; Duan, Pei-Gao. Journal of Physics & Chemistry of Solids. Mar2018, Vol. 114, p201-206. 6p. DOI: 10.1016/j.jpcs.2017.10.044.

Structural, solvatochromism and magnetic properties of two halogen bridged dinuclear copper (II) complexes: A density functional study. Koohzad, Sara; Golchoubian, Hamid; Jagličić, Zvonko. Inorganica Chimica Acta. Mar2018, Vol. 473, p60-69. 10p. DOI: 10.1016/j.ica.2017.12.026.

Synthesis, characterization and biological studies of a novel Cu(II) Schiff base complex. Thirunavukkarasu, Thangavel; Sparkes, Hazel A.; Natarajan, Karuppannan; Gnanasoundari, V.G. Inorganica Chimica Acta. Mar2018, Vol. 473, p255-262. 8p. DOI: 10.1016/j.ica.2018.01.006.

SAXS and homology modelling based structure characterization of pectin methylesterase a family 8 carbohydrate esterase from Clostridium thermocellum ATCC 27405. Rajulapati, Vikky; Sharma, Kedar; Dhillon, Arun; Goyal, Arun. Archives of Biochemistry & Biophysics. Mar2018, Vol. 641, p39-49. 11p. DOI: 10.1016/j.abb.2018.01.015.

Small-angle scattering of polychromatic X-rays: effects of bandwidth, spectral shape and high harmonics. Chen, Sen; Luo, Sheng-Nian. Journal of Synchrotron Radiation. Mar2018, Vol. 25 Issue 2, p496-504. 8p. DOI: 10.1107/S1600577517018355.

Isolation and initial structural characterization of a 27 kDa protein from Zingiber officinale. Rasheed, Saima; Malik, Shoaib Ahmad; Falke, Sven; Arslan, Ali; Fazel, Ramin; Schl??ter, Hartmut; Betzel, Christian; Choudhary, M. Iqbal. Journal of Molecular Structure. Mar2018, Vol. 1156, p330-335. 6p. DOI: 10.1016/j.molstruc.2017.11.116.

Integrative structure and functional anatomy of a nuclear pore complex. Kim, Seung Joong; et al. Nature. 2018/03/14 online. DOI: 10.1038/nature26003.

Longest C???C Single Bond among Neutral Hydrocarbons with a Bond Length beyond 1.8 Å. Yusuke Ishigaki; et al. Chem. online 8 March 2018. DOI: 10.1016/j.chempr.2018.01.011.

The spread of true and false news online. Vosoughi, Soroush; et al. Science. Vol. 359, Issue 6380, pp. 1146-1151 (march 2018). DOI: 10.1126/science.aap9559.

Unconventional superconductivity in magic-angle graphene superlattices. Cao, Yuan; et al. Nature. online 05 March 2018. DOI: 10.1038/nature26160.

Book Reviews

High-Resolution Electron Microscopy, Fourth Edition, John C. H. Spence, Oxford University Press, Oxford, 2017, 432 pp., ISBN: 978-0-19-879583-4.

The author of this textbook is the Richard Snell Professor of Physics at Arizona State University, a fellow of both the Royal Society and the ACA. The first edition was originally published in 1980. The fourth edition was published in 2013 as a hard cover and in 2017 as a paperback. There are some references dated between 2013 and 2017, inclusive, that suggest the book is bit more current than the copyright page indicates.

Spence goes into each area of electron microscopy in great mathematical detail with the exception of the first chapter, which covers some basics and history. The next three chapters (2-4) cover electron optics, wave optics, and coherence and Fourier optics. The following two chapters (5-6) cover the types of experiments one can perform with electron microscopy: transmission electron microscopy of thin crystals and imaging molecules, including the hot topic of CryoEM.

The next six chapters (7-12) cover the practical aspects of the instrumentation: image processing, super-resolution and diffractive imaging, scanning transmission electron microscopy, source and detectors, electron-optical parameters, stability and experimental methods. The last chapter examines ancillary techniques.

Overall, Spence offers over four decades of expertise and refinement in one source. If you are looking for a book that will provide a detailed reference for electron microscopy, this is the one for you.

A Little Dictionary of Crystallography, 2nd Edition, Andre Authier and Gervais Chapuis, Editors, 2017, International Union of Crystallography, 300 pages.

To call this book a dictionary is a bit of a misnomer. About the only entry that fits this definition is the entry for crystallography itself. Over 300 terms are defined and expounded upon in the book. In addition to a definition of a specific term that might cover a page or more, you may find French, German, Italian, Spanish, Russian and even Japanese (?????????) translations, examples, historical notes, references and cross-references within ALDOC. Given all this, I might call this a handbook. ALDOC covers a wide range of terms, with the majority related to the fundamentals of the science of crystallography. In addition, there are entries from the fields of chemical and macromolecular crystallography, as well as entries relevant to X-ray spectroscopic methods (EXAFS, IXS, XAFS, etc.). There are more than 20 entries on the subject of twinning, providing clear explanations of all the nomenclature. Is every crystallography term included? No, but you will find most here and in sufficient detail to settle any argument, or conversely start an argument.

This book is not available on Amazon because it is a nonstandard size. However, it is currently available on a print-on-demand basis from Lulu. It is printed in a size smaller than a conventional IUCr text but larger than a paperback. It is also quite inexpensive and well worth the cost.

Reviews by Joseph Ferrara
Deputy Director, X-ray Research Laboratory, Rigaku