Crystallography Newsletter
Volume 10, No. 02, February 2018

In this issue:

ACA Summer Course

Rigaku is a proud sponsor of the ACA Summer Course in Chemical Crystallography being held from June 10 to June 17, 2018, at Notre Dame University. The current incarnation of the course is directed towards Single-Crystal Chemical Crystallography and Powder Diffraction techniques, as applicable to small molecule studies. The course is designed to instruct attendees in the theory and practice of these two aspects of crystallography.

No prior knowledge of crystallography is expected from attendees. However, a good understanding of undergraduate level chemistry, physics and mathematics is desirable. While the course is geared towards graduate level attendees, applications from strong undergraduate students will be considered. Past course attendees have included faculty members and industrial researchers.


The Winter 2018 issue of the
Rigaku Journal is now available

Rigaku Journal

Here is a link to the table of contents, where you can download the entire issue or individual articles:

Rigaku Journal – Winter 2018 Vol. 34 No.01

Join ROD on LinkedIn

Rigaku Oxford Diffraction LinkedIn group shares information and fosters discussion about X-ray crystallography and SAXS topics. Connect with other research groups and receive updates on how they use these techniques in their own laboratories. You can also catch up on the latest newsletter or Rigaku Journal issue. We also hope that you will share information about your own research and laboratory groups.

Rigaku Oxford Diffraction Forum

Rigaku Oxford Diffraction forum screen


Here you can find discussions about software, general crystallography issues and more. It’s also the place to download the latest version of Rigaku Oxford Diffraction’s CrysAlisPro software for single crystal data processing.

We look forward to seeing you on there soon.

Survey of the month

Feb 2018 Monthly Survey


Last month's survey

The US Congress passed the Tax Cuts and Jobs Act and it was signed into law by President Trump. For the US,

Jan 2018 survey results

Videos of the month

I am not sure how many of you will find this interesting but here is a lecture by the coder of Windows Process Explorer and other Sysinternals, Mark Russinovich, on how to fix windows issues. Learning that ctrl-shift-esc brings up the task manager (or Process Explorer) immediately is worth the listen.

1st Feb 2018 video

watch video

Here is a cool video with great visualizations from Visual Science and Skoltech describing how CRISPR-Cas9 works and has evolved into a remarkable tool for gene editing.

2nd Feb 2018 video

watch video

Upcoming events

26th Annual Meeting of the German Crystallographic Society (DGK 2018)
Mar 5 – 8, 2018 in Essen, Germany

NESBA: The Resolution Revolution in cryoEM: Potential for Drug Discovery
Mar 16, 2018 in Waltham, MA, USA

BCA Spring Meeting 2018
Mar 26 – 29, 2018 in Coventry, UK

See full list >

Call for papers

ACA Annual Meeting
(deadline March 30, 2018)

(deadline April 6, 2018)

(deadline April 29, 2018)

(deadline August 14, 2018)

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Crystallography in the news

February 1, 2018. In a new study, USC Viterbi School of Engineering professors Priya Vashishta, Rajiv K. Kalia and Aiichiro Nakano used computer-based models to identify mechanisms or "strategies" used by bacterial spores to evade attack from extreme temperatures, chemicals and radiation.

February 6, 2018. Scientists at the Institute of Cancer Research, London, synthesised a prototype drug (CCT068127) that simultaneously targets two proteins called CDK2 and CDK9. Using X-ray crystallography, in collaboration with researchers at the University of Newcastle on Tyne, the team also visualised CCT068127 in place on a specific part, or domain, of CDK2 – revealing its mechanism of enhanced potency compared to seliciclib.

February 6, 2018. A new Yale study has shown how a membrane receptor vital to human metabolism looks and functions, potentially allowing researchers to better develop drugs to address such diseases as diabetes and obesity. Until now, however, scientists knew little about why or how klotho interacted with FGF21, a specific fibroblast growth factor.

February 12, 2018. A team of researchers led by the Department of Energy's Oak Ridge National Laboratory used neutron macromolecular crystallography to investigate the different states of three glaucoma drugs as they interact with the targeted enzyme, human carbonic anhydrase II (hCA II).

February 13, 2018. Chemistry Ph.D. candidate Elahe Moazzen has won a 2018 Ludo Frevel Crystallography Scholarship and will receive $2,500 to assist in the continuation of her crystallographic research. She is one of 10 students awarded this year, selected on a competitive basis by the International Centre for Diffraction Data (ICDD) scholarship committee.

February 16, 2018. The 2018 Wolf Prize in Chemistry has been awarded to Professor Makoto Fujita, professor in the Department of Applied Chemistry at the University of Tokyo's Graduate School of Engineering, for his research on metal-guided synthesis and "for conceiving metal-directed assembly principles leading to large highly porous complexes." The prize is shared with Professor Omar Yaghi of the University of California, Berkeley, for his research "pioneering reticular chemistry via metal-organic frameworks and covalent organic framework."

February 18, 2018. Using multiple techniques such as structural modeling, X-ray scattering, X-ray crystallography and electron microscopy, Shruthi Viswanath, a postdoctoral scholar at the University of California, San Francisco, with a team of researchers, found that the Spc110 protein provides a greater function in the spindle pole bodies of simple organisms like yeasts than originally believed.

February 23, 2018. Researchers at the Indian Institute of Technology, Roorkee have discovered the antibacterial properties of a natural compound chlorogenic acid, an aromatic compound found in many plant species including coffee. The team gained the structural insights into the mechanism of antibacterial properties of the natural compound using X-ray crystallography.

Product spotlight

XtaLAB Synergy-i

The XtaLAB Synergy-i is a cutting-edge diffractometer for all your crystallography needs. This upgradeable system allows you to further enhance your capabilities when the need arises.

The XtaLAB Synergy-i single crystal X-ray diffractometer includes a high-flux, low maintenance microfocus sealed tube source, a high-precision 4-circle kappa goniometer and one of Rigaku's own Hybrid Photon Counting (HPC) X-ray detectors, the HyPix Bantam. Containing the latest microfocus source technology the XtaLAB Synergy-i can be upgraded to dual source (Cu/Mo) to address a wider range of research interests. For ease of use and high performance, the system is controlled by the fully-integrated, user-inspired CrysAlisPro software package which is capable of collecting and processing data efficiently and accurately, so you achieve the best data possible.

The XtaLAB Synergy-i is a full-featured single crystal X-ray diffractometer that requires little maintenance, maximizing your uptime and throughput.

XtaLAB Synergy-i


  • The scintillator-free hybrid photon counting (HPC) detector has been designed by Rigaku to ensure cutting-edge performance with true digital photon counting technology for unparalleled sensitivity.
  • The microfocus PhotonJet- i sources (Cu/Mo), available in dual or single source configurations, have low power consumption, yet provide high flux in order to study a variety of sample types.
  • The 4-circle Kappa goniometer ensures that the most efficient data coverage is achieved even for the lowest symmetry P1 samples whether Cu or Mo radiation is used.


  • Up to 50 W microfocus X-ray tube with multilayer optics
  • New cabinet design with controlled sample and cabinet lighting
  • The system conforms to the most stringent of X-ray safety guidelines
  • CrysAlisPro: Powerful, user-friendly software, comes standard with AutoChem3.0 for fully-automated structure solution and refinement
  • Simple dual-source upgrade
  • Can be used to perform high pressure measurements
  • Compatible with most low temperature devices incl. the Cryostream 700, 800, 800+ and Cobra.

For more about XtaLAB Synergy-i >

Featured Application Note

Improving data quality for a highly absorbing mineral, Hereroite, with the PhotonJet™ Ag source

By Dr. Mark Welch, Natural History Museum, UK
Dr. Dyanne Cruickshank, Rigaku Oxford Diffraction, UK

For home-lab instruments considerable benefits can be found for these types of samples by employing silver radiation, which has a shorter wavelength (0.56 Å).

Lab in the spotlight

Nathan D. Schley Nathan D. Schley, Ph.D.
Department of Chemistry
Vanderbilt University

The aim of the Schley research group is the application of organometallic chemistry to unmask latent reactivity in organic substrates. Oxidation of simple hydrocarbons provides functional groups which serve as handles for further transformations, but methods for selective oxidation of C-H bonds are limited. The Schley group's goal is to meet the challenge of enabling new oxidative, catalytic transformations of C-H bonds by making use of unconventional activation strategies.

The Schley group's current research focuses on the activation of ethers. Although ubiquitous in organic chemistry, the relative inertness of ethers relative to other functional groups has largely relegated simple alkyl ethers to roles as reaction solvents. As a result, there are significant opportunities for new methods for ether functionalization. The Schley group is developing organometallic platforms for ether α-C-H cleavage to the corresponding metallo-alkoxyalkyl or alkoxycarbene species including as part of new catalytic reactions of ethers. Alongside this work, they are investigating mild methods for ether cleavage and deoxygenation, including in substrates like carbohydrates with significant applications in human health.

Useful link

useful link How To Grow Your Own Crystals

Here is the link to a Science Friday interview with Jason Benedict, ACA member, Professor at SUNY-Buffalo, and National Coordinator of the US Crystal Growing Competition.

Selected recent crystallographic papers

Structural diversity of the nucleosome. Masako Koyama; Hitoshi Kurumizaka. Journal of Biochemistry. Feb2018, Vol. 163 Issue 2, p85-95. 11p. DOI: 10.1093/jb/mvx081.

Reconstructing three-dimensional protein crystal intensities from sparse unoriented two-axis X-ray diffraction patterns. Corrigendum. Lan, Ti-Yen; Wierman, Jennifer L.; Tate, Mark W.; Philipp, Hugh T.; Elser, Veit; Gruner, Sol M. Journal of Applied Crystallography. Feb2018, Vol. 51 Issue 1, p230-230. 0p. DOI: 10.1107/S1600576718000171.

Polymeric Copper(II) Paddlewheel Carboxylate: Structural Description, Electrochemistry, and DNA-binding Studies. Iqbal, Muhammad; Ali, Sqib; Tahir, Muhammad Nawaz. Zeitschrift f??r Anorganische und Allgemeine Chemie. 2/15/2018, Vol. 644 Issue 3, p172-179. 8p. DOI: 10.1002/zaac.201700375.

Disruption of human stratum corneum lipid structure by sodium dodecyl sulphate. Yanase, K.; Hatta, I. International Journal of Cosmetic Science. Feb2018, Vol. 40 Issue 1, p44-49. 6p. DOI: 10.1111/ics.12430.

Alpha repeat proteins (αRep) as expression and crystallization helpers. Chevrel, Anne; Mesneau, Agnes; Sanchez, Dyana; Celma, Louisa; Quevillon-Cheruel, Sophie; Cavagnino, Andrea; Nessler, Sylvie; Li de la Sierra-Gallay, Ines; van Tilbeurgh, Herman; Minard, Philippe; Valerio-Lepiniec, Marie; Urvoas, Agathe. Journal of Structural Biology. Feb2018, Vol. 201 Issue 2, p88-99. 12p. DOI: 10.1016/j.jsb.2017.08.002.

Identification of protein W, the elusive sixth subunit of the Rhodopseudomonas palustris reaction center-light harvesting 1 core complex. Jackson, Philip J.; Hitchcock, Andrew; Swainsbury, David J.K.; Qian, Pu; Martin, Elizabeth C.; Farmer, David A.; Dickman, Mark J.; Canniffe, Daniel P.; Hunter, C. Neil. BBA - Bioenergetics. Feb2018, Vol. 1859 Issue 2, p119-128. 10p. DOI: 10.1016/j.bbabio.2017.11.001.

Synthesis, spectra and X-ray crystallography of dipyridin-2-ylmethanone oxime and its CuX2(oxime)2 complexes: Thermal, Hirshfeld surface and DFT analysis. Warad, Ismail; Abdoh, Muneer; Al Ali, Anas; Shivalingegowda, Naveen; Kumara, Karthik; Zarrouk, Abdelkader; Lokanath, Neartur Krishnappagowda. Journal of Molecular Structure. Feb2018, Vol. 1154, p619-625. 7p. DOI: 10.1016/j.molstruc.2017.10.087.

The [Fe{(SePPh2)2N}2] Complex Revisited: X-ray Crystallography, Magnetometry, High-Frequency EPR, and Mössbauer Studies Reveal Its Tetrahedral FeIISe4 Coordination Sphere. Ferentinos, Eleftherios; Chatziefthimiou, Spyros; Boudalis, Athanassios K.; Pissas, Michael; Mathies, Guinevere; Gast, Peter; Groenen, Edgar J. J.; Sanakis, Yiannis; Kyritsis, Panayotis. European Journal of Inorganic Chemistry. 2/14/2018, Vol. 2018 Issue 6, p713-721. 9p. DOI: 10.1002/ejic.201701459.

Determination of inter-ionic and intra-ionic interactions in a monofluorinated imidazolium ionic liquid by a combination of X-ray crystallography and NOE NMR spectroscopy. Lingscheid, Yves; Paul, Mathias; Bröhl, Andreas; Neudörfl, Jörg-Martin; Giernoth, Ralf. Magnetic Resonance in Chemistry. Feb2018, Vol. 56 Issue 2, p80-85. 6p. DOI: 10.1002/mrc.4608.

A single β-octyl glucoside molecule induces HIV-1 Nef dimer formation in the absence of partner protein binding. Wu, Mousheng; Alvarado, John J.; Augelli-Szafran, Corinne E.; Ptak, Roger G.; Smithgall, Thomas E. PLoS ONE. 2/7/2018, Vol. 13 Issue 2, p1-14. 14p. DOI: 10.1371/journal.pone.0192512.

Mouse IgG2c Fc loop residues promote greater receptor-binding affinity than mouse IgG2b or human IgG1. Falconer, Daniel J.; Barb, Adam W. PLoS ONE. 2/6/2018, Vol. 13 Issue 2, p1-17. 17p. DOI: 10.1371/journal.pone.0192123.

Jatrophane diterpenoids from Euphorbia sororia as potent modulators against P-glycoprotein-based multidrug resistance. Hu, Rui; Gao, Jie; Rozimamat, Rushangul; Aisa, Haji Akber. European Journal of Medicinal Chemistry. Feb2018, Vol. 146, p157-170. 14p. DOI: 10.1016/j.ejmech.2018.01.027

Synthesis, crystal structure, luminescent properties and antibacterial activities of zinc complexes with bipyridyl and salicylate ligands. Chooset, Sirinart; Kantacha, Anob; Chainok, Kittipong; Wongnawa, Sumpun. Inorganica Chimica Acta. Feb2018, Vol. 471, p493-501. 9p. DOI: 10.1016/j.ica.2017.11.053.

Host–guest capability of a three-dimensional heterometallic macrocycle. Fan, Qi-Jia; Lin, Yue-Jian; Hahn, F. Ekkehardt; Jin, Guo-Xin. Dalton Transactions: An International Journal of Inorganic Chemistry. 2/21/2018, Vol. 47 Issue 7, p2240-2246. 7p. DOI: 10.1039/c7dt04453d.

Reconstitution of SNARE proteins into solid-supported lipid bilayer stacks and X-ray structure analysis. Xu, Yihui; Kuhlmann, Jan; Brennich, Martha; Komorowski, Karlo; Jahn, Reinhard; Steinem, Claudia; Salditt, Tim. BBA - Biomembranes. Feb2018, Vol. 1860 Issue 2, p566-578. 13p. DOI: 10.1016/j.bbamem.2017.10.023.

An optimized SEC-SAXS system enabling high X-ray dose for rapid SAXS assessment with correlated UV measurements for biomolecular structure analysis. Ryan, Timothy M.; Trewhella, Jill; Murphy, James M.; Keown, Jeremy R.; Casey, Lachlan; Pearce, F. Grant; Goldstone, David C.; Chen, Kelan; Luo, Zhenyao; Kobe, Bostjan; McDevitt, Christopher A.; Watkin, Serena A.; Hawley, Adrian M.; Mudie, Stephen T.; Samardzic Boban, Vesna; Kirby, Nigel. Journal of Applied Crystallography. Feb2018, Vol. 51 Issue 1, p97-111. 14p. DOI: 10.1107/S1600576717017101.

Interpretation of solution scattering data from lipid nanodiscs. Graziano, Vito; Miller, Lisa; Yang, Lin. Journal of Applied Crystallography. Feb2018, Vol. 51 Issue 1, p157-166. 9p. DOI: 10.1107/S1600576717018441.

Book review

book cover The Best American Science and Nature Writing 2017, Edited by Hope Jahren, Houghton Harcourt Mifflin Publishing Co., New York, 2017, 352 pages ISBN: 978-1328715517

The Best American Science and Nature Writing contains an expertly curated set of exemplary pieces from 2016, culled by biologist/science writer Hope Jahren. Jahren is well known for her memoir Lab Girl, which offered brutally honest insight into the pursuit of science as a woman in the past few decades.

The Best contains 24 pieces of science and nature writing from American publications. Jahren sorted the pieces into three categories: Emergent Fields, Changing Land and Resources, and The "Real Life" of Scientists. That essentially boils down to "new stuff," "climate change", and "profiles" (not every story fits into those narrower categories, but the pieces that stood out the most certainly did).

Writing a good, compelling long-form science story is hard, especially when you are describing an emergent field—something that is at the forefront of human understanding. As a writer, you are faced with explaining a concept to your audience that even the scientists who specialize in the subject don't yet fully understand. That said, the four pieces in "Emergent Fields,??? by Sarah Everts, Maria Konnikova, Kim Tingley, and Nicola Twilley, do a fairly good job of just that. But like any piece on emergent science—though certainly important—they leave the reader wanting more, which is decidedly unsatisfactory. But given the nature of the work, it seems inevitable. Konnikova's "Altered Tastes,??? originally published in The New Republic, was particularly intriguing. She explicates a brief history of food science in the context of the study of neurogastronomy—essentially the relationship between your stomach and your brain (and the rest of your body).

Part II, Changing Land and Resources, had ten pieces. Given the current political climate (and the current climate climate), many of these pieces resonated more than those in the previous section. We live in a world where its "most powerful man??? is a vehement climate change denier, and that is quite frankly, deeply upsetting. Two of the works from this section resonated in particular—Adrian Glick Kudler's "Something Uneasy in the Los Angeles Air??? and Nathaniel Rich's "The Invisible Catastrophe,??? originally published in Curbed and The New York Times Magazine, respectively. Kudler's piece, on the Santa Ana winds—their history, their devastation, and the fascination they inspire—seemed particularly relevant given the devastating fires that wracked the greater Los Angeles area this past winter. The Santa Ana winds have always blown—but the role of climate change in increasing the extent of their devastation is a harder causality to pinpoint. Rich's piece (also on the greater Los Angeles area) tells a story about an old, drained J. Paul Getty oil field in Aliso Canyon that was bought by Pacific Lighting in the 1970s. Pacific Lighting used the land to store excess supplies of natural gas—methane. Fast forward to 2016—residents of a housing development on the land above this methane storage ground were reporting strange phenomena—painful headaches, dying pet parrots, even cancer. This story seems like d??j?? vu—and should, at least for anyone who saw the Academy-Award winning, based on a true story Erin Brokovich, almost 20 years ago—or more recently, the documentary Gasland or its sequel Gasland II. It is definitely discouraging to say the least.

Part III, The "Real Lives??? of Scientists, had more memorable pieces than the other two, but that might just be the nature of the writing. Profiles have an inherently human element, and that element makes it easier to form a compelling narrative. Included in this section are Azeen Ghorayshi's "He Fell in Love with His Grad Student—Then Fired Her for It,??? from Buzzfeed and Kathryn Joyce's "Out Here, No One Can Hear You Scream??? from Huffington Post Highline/The Nation Institute Investigative Fund. Both are horrifying tales of sexual harassment towards female researchers perpetrated by their male coworkers. Given the recent outbreak of scandals in every industry, particularly entertainment, these pieces resonate—these stories need to be told, and they deserve attention.

The standout piece from the book is the longest: David Epstein's "The DIY Scientist, the Olympian, and the Mutated Gene,??? from ProPublica. Epstein, the author of The Sports Gene, a book that details the possible relationship between genetic predisposition and athleticism, tells a story about the aftermath of his book. Long story short, a woman who suffered from a rare form of muscular dystrophy reached out to Epstein, wanting to be put in contact with an Olympic athlete who she suspected suffered from a similar condition. You'll have to read Epstein's piece if you want to find out what ensued.

Jahren includes a list of dozens of other noteworthy pieces from 2016—which are worth hunting down and reading, if you haven't already.

Review by Jeanette S. Ferrara, MA


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