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Crystallography Newsletter
Volume 9, No. 3, March 2017
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In this issue:


Rigaku Oxford Diffraction
invites all users of Rigaku equipment
to join us on our X-ray forum

Rigaku Oxford Diffraction forum screen

www.rigakuxrayforum.com

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.


Rigaku Reagents:
Wizard TIME - 96-well block plate

Rigaku Reagents

Membrane proteins require detergent solubilization for purification and crystallization. The Wizard TIME, or Total Integral Membrane Protein Extraction, screen consists of 84 different formulations designed identify detergent reagents that will successfully extract a membrane protein from a membrane preparation. Each detergent formulation consists of a detergent at 2% (w/v) concentration, the stabilizing co-detergent cholesterol hemisuccinate and a buffer. One membrane protein target can be screened per kit. For a limited time, try the TIME kit with your membrane preparation at 25% off.

Wizard TIME promotion: 25% off, expires 06/01/2017. Code: TIME

Contact ReagentOrders@Rigaku.com
For more information, visit the
Rigaku Reagents website.


Survey of the month

Monthly Survey

survey



Last month's survey

What is the worst topic to discuss with colleagues at work?

results


Video of the month

P. P. Ewald: An amazing tale about
the beginning of crystallography

video

This is a "must watch" video for anyone interested in the history of crystallography.

P. P. Ewald, Brooklyn Polytechnic Institute, New York, USA. Filmed at the International Crystallography Conference, 1965, Melbourne, Australia, by the CSIRO Film Unit in collaboration with the Australian Academy of Science. With support from UNESCO, the International Council of Scientific Unions, the Australian Academy of Science, the International Union of Crystallography, the International Union of Pure and Applied Physics, the International Atomic Energy Agency and the University of Melbourne.

video


Upcoming events

MRS Spring Meeting & Exhibit, April 17 – 21, 2017 in Phoenix, Arizona, USA

Korea Lab, April 18 – 21, 2017 in Islan, Korea

See full list >


 

 

 

 

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Crystallography in the news

March 1, 2017. Daniel Lin, a graduate student in the laboratory of André Hoelz, has been awarded the Harold M. Weintraub Graduate Student Award by the Fred Hutchinson Cancer Research Center for "outstanding achievement during graduate studies in the biological sciences (using X-ray crystallography)."

March 6, 2017. Results of a Rice University study of the Orsay virus unique to nematodes, the worms that make up 80 percent of living creatures on Earth, have revealed the molecular structure of a fusion protein that forms unusual fibers and attaches the virus to cells and infects them. The researchers, led by structural biologist Yizhi Jane Tao and geneticist Weiwei Zhong, said the protein is the first pentameric fiber with potential antiviral applications.

March 7, 2017. A proof-of-concept molecular modeling study that analyzes the efficiency of amine solutions in capturing carbon dioxide is the first step toward the design of cheaper, more efficient amine chemicals for capturing carbon dioxide – and reducing harmful CO2 emissions – in industrial installations.

March 9, 2017. A significant new chemical attribute of plutonium has been found by researchers: the identification and structural verification of the +2 oxidation state in a molecular system.

March 9, 2017. A team of researchers, led by scientists at the University of Chicago and the Argonne National Laboratory, used SAXS to identify a new class of colloidal systems involving inorganic solvents – a discovery that could offer new applications for nanotechnology and better functional materials.

March 15, 2017. The crystalline protein envelope of an insect virus has been examined by high-intensity X-ray pulses. The study by Henry Chapman of the Center for Free-Electron Laser Science is described in the Proceedings of the National Academy of Sciences and represents the smallest protein crystals examined so far by X-ray crystallography.

March 16, 2017. Nine students in the Department of Chemistry and Biochemistry at the State University of New York at Fredonia, representing sophomore, junior and senior classes, are making an impact in the scientific community – one crystal structure at a time.

March 16, 2017. Thanks to an innovative nozzle, scientists can now analyse more types of proteins while using fewer of the hard-to-get protein crystals. The nozzle can reduce protein consumption eightfold in serial X-ray crystallography experiments.

March 17, 2017. Scientists at Tokyo Institute of Technology have used high-resolution crystallography to uncover the mechanism behind protein-assisted synthesis of gold nanoparticles, providing a platform for designing nanomaterials tailored for biomedical application.

March 17, 2017. A new version of Rosetta can predict the 3-D structure of proteins at a fraction of the cost of traditional methods. It revealed the configuration of more than 600 proteins of distinct types that have been difficult to characterize using standard techniques.

March 23, 2017. A research study demonstrating the possibility to attain extremely high quality crystals developed from gold nanoparticles has been published in the Journal of the American Chemical Society by a research team headed by Professor Flavio Maran of the University of Padova (Italy) and Academy Professor Kari Rissanen of the University of Jyväskylä (Finland).


Product spotlight

XtaLAB Synergy-R: High-flux rotating anode X-ray diffractometer

The XtaLAB Synergy-R is one of the most powerful small molecule diffractometers available. It includes a high-flux, low-maintenance microfocus rotating anode, the PhotonJet-R, with a high-precision kappa goniometer and Rigaku's own Hybrid Photon Counting detector (HPC), the HyPix-6000HE. The PhotonJet-R X-ray source consists of a MicroMax-007 HF rotating anode and a newly designed optic. It is available with either Cu or Mo anodes.

For labs with high-throughput requirements, increasing the flux will reduce data collection time and thus increase the number of samples that can be studied in your laboratory. For extremely small samples, additional flux will extend the minimum size limits for crystals that you can study.

XtaLAB Synergy-R

For more about XtaLAB Synergy-R


Lab in the spotlight

Professor Alexandra M. Z. Slawin Professor Alexandra M. Z. Slawin
Director of the Molecular Structure Laboratory
University of St. Andrews

Prof. Slawin is Professor of Chemical Crystallography and Director of the Molecular Structure Laboratory at St. Andrews, and the University's first female Chemistry Professor.

"In a typical year we collect more than 1500 datasets supporting over 200 researchers from St. Andrews, Scotland and abroad. The majority of these datasets yield answers which enable the chemical problems in e.g. catalysis, drug discovery, ligand design, energy materials to be advanced. Generally, we publish our work in chemical journals with the structures alongside the chemistry in e.g. Angew. Chemie, J. Amer. Chem. Soc., Dalton Trans., Inorganic Chem., Organometallics. Since 2010 our lab has deposited on average >300 structures associated with peer reviewed publications a year into the CCDC."

Prof. Slawin has published 60 papers in Angew. Chemie, 49 in Organometallics, 45 in JACS, 44 in Chem. Comm., and 30 in Inorganic Chem.

Molecular Structure Laboratory group at St. Andrews Univ


Useful link: Development of X-ray Pixel Array Detectors (PDF)

Confused about the differences between a phosphor-coupled detector and a pixel array detector?

useful link

This article by Sol M. Gruner provides an easy-to-understand comparison between phosphor-based indirect-detection detectors and direct-detection detectors.


Selected recent crystallographic papers

125 Years Zeitschrift für Anorganische und Allgemeine Chemie. Fässler, Thomas F.; Klapötke, Thomas M.; Limberg, Christian. Zeitschrift für Anorganische und Allgemeine Chemie. 3/16/2017, Vol. 643 Issue 6, p406-409. 4p. DOI: 10.1002/zaac.201710004.

Improved single-step enrichment methods of cross-linked products for protein structure analysis and protein interaction mapping. Schmidt, Rico; Sinz, Andrea. Analytical & Bioanalytical Chemistry. Mar2017, Vol. 409 Issue 9, p2393-2400. 8p. DOI: 10.1007/s00216-017-0185-1.

SAXS Structural Studies of Dps from Deinococcus radiodurans Highlights the Conformation of the Mobile N-Terminal Extensions. Santos, Sandra P.; Cuypers, Maxime G.; Round, Adam; Finet, Stephanie; Narayanan, Theyencheri; Mitchell, Edward P.; Romão, Célia V. Journal of Molecular Biology. Mar2017, Vol. 429 Issue 5, p667-687. 21p. DOI: 10.1016/j.jmb.2017.01.008.

Epitope-dependent mechanisms of CD27 neutralization revealed by X-ray crystallography. Obmolova, Galina; Teplyakov, Alexey; Malia, Thomas J.; Wunderler, Nicole; Kwok, Deborah; Barone, Linda; Sweet, Raymond; Ort, Tatiana; Scully, Michael; Gilliland, Gary L. Molecular Immunology. Mar2017, Vol. 83, p92-99. 8p. DOI: 10.1016/j.molimm.2017.01.005.

Single-crystal X-ray diffraction and NMR crystallography of a 1:1 cocrystal of dithianon and pyrimethanil. Pöppler, Ann-Christin; Corlett, Emily K.; Pearce, Harriet; Seymour, Mark P.; Reid, Matthew; Montgomery, Mark G.; Brown, Steven P. Acta Crystallographica: Section C, Structural Chemistry. Mar2017, Vol. 73 Issue 3, p149-156. 7p. DOI: 10.1107/S2053229617000870.

Synthesis and X-ray Crystallography of Two Lead(II) Decahydro-closo-Decaborate Hydrates. Zimmermann, Lucas W.; Kleeberg, Fabian M.; Schleid, Thomas. Zeitschrift für Anorganische und Allgemeine Chemie. Mar2017, Vol. 643 Issue 5, p365-372. 8p. DOI: 10.1002/zaac.201600257.

Coarse-Grained Molecular Modeling of the Solution Structure Ensemble of Dengue Virus Nonstructural Protein 5 with Small-Angle X-ray Scattering Intensity. Guanhua Zhu; Wuan Geok Saw; Nalaparaju, Anjaiah; Grüber, Gerhard; Lanyuan Lu. Journal of Physical Chemistry B. 3/16/2017, Vol. 121 Issue 10, p2252-2264. 13p. DOI: 10.1021/acs.jpcb.7b00051.

Small-scale screening method for low-viscosity antibody solutions using small-angle X-ray scattering. Fukuda, Masakazu; Watanabe, Atsushi; Hayasaka, Akira; Muraoka, Masaru; Hori, Yuji; Yamazaki, Tadao; Imaeda, Yoshimi; Koga, Akiko. European Journal of Pharmaceutics & Biopharmaceutics. Mar2017, Vol. 112, p132-137. 6p. DOI: 10.1016/j.ejpb.2016.11.027.

Performance of various models in structural characterization of n-butanol: Molecular dynamics and X-ray scattering studies. Cerar, Jure; Lajovic, Andrej; Jamnik, Andrej; Tomšic, Matija. Journal of Molecular Liquids. Mar2017, Vol. 229, p346-357. 12p. DOI: 10.1016/j.molliq.2016.12.057.

Complexes of cis-dioxomolybdenum(VI) with a chiral tetradentate tripodal-like ligand system: Syntheses, structures and catalytic activities. Ghosh, Sabari; Kurapati, Sathish Kumar; Pal, Samudranil. Polyhedron. Mar2017, Vol. 125, p26-33. 8p. DOI: 10.1016/j.poly.2016.08.025.

Axially chiral racemic half-sandwich nickel(ii) complexes by ring-closing metathesis. Buchowicz, Wlodzimierz; Banach, Lukasz; Kaminski, Radoslaw; Buchalski, Piotr. Dalton Transactions: An International Journal of Inorganic Chemistry. 3/28/2017, Vol. 46 Issue 12, p3805-3808. 4p. DOI: 10.1039/c6dt04811k.

Terpenoids with potent antimycobacterial activity against Mycobacterium tuberculosis from Trigonostemon reidioides roots. Kaemchantuek, Praphakorn; Chokchaisiri, Ratchanaporn; Prabpai, Samran; Kongsaeree, Palangpon; Chunglok, Warangkana; Utaipan, Tanyarath; Chamulitrat, Walee; Suksamrarn, Apichart. Tetrahedron. Mar2017, Vol. 73 Issue 12, p1594-1601. 8p. DOI: 10.1016/j.tet.2017.02.006.

Structural characterization of metal(II) thiocyanato complexes derived from bis(2-(H-pyrazol-1-yl)ethyl)amine. Mautner, Franz A.; Fischer, Roland C.; Rashmawi, Lubna G.; Louka, Febee R.; Massoud, Salah S. Polyhedron. Mar2017, Vol. 124, p237-242. 6p. DOI: 10.1016/j.poly.2017.01.001.

Structural and Thermodynamic Properties of Nanoparticle-Protein Complexes: A Combined SAXS and SANS Study. Spinozzi, Francesco; Ceccone, Giacomo; Moretti, Paolo; Campanella, Gabriele; Ferrero, Claudio; Combet, Sophie; Ojea-Jimenez, Isaac; Ghigna, Paolo. Langmuir. Mar2017, Vol. 33 Issue 9, p2248-2256. 9p. DOI: 10.1021/acs.langmuir.6b04072.

Progesterone solubilization within reverse hexagonal mesophase. Hagage-Dobensky, Delphine; Aserin, Abraham; Garti, Nissim. Colloids & Surfaces A: Phys. Eng. Asp. Mar2017, Vol. 516, p254-261. 8p. DOI: 10.1016/j.colsurfa.2016.12.015.

Structural and molecular determinants affecting the interaction of retinol with human CRBP1. Menozzi, Ilaria; Vallese, Francesca; Polverini, Eugenia; Folli, Claudia; Berni, Rodolfo; Zanotti, Giuseppe. Journal of Structural Biology. Mar2017, Vol. 197 Issue 3, p330-339. 10p. DOI: 10.1016/j.jsb.2016.12.012.

Spectroscopic, single crystal X-ray, Hirshfeld, in vitro and in silico biological evaluation of a new series of potent thiazole nucleus integrated with pyrazoline scaffolds. Salian, Vinutha V.; Narayana, Badiadka; Sarojini, Balladka K.; Kumar, Madan S.; Nagananda, Govinahalli S.; Byrappa, Kullaiah; Kudva, Avinash K. Spectrochimica Acta Part A: Molecular & Biomolecular Spectroscopy. Mar2017, Vol. 174, p254-271. 18p. DOI: 10.1016/j.saa.2016.11.046.

100 Years Since Albert W. Hull's Contributions to Powder Diffraction. Hubbard, Camden. Powder Diffraction. Mar2017, Vol. 32 Issue 1, p1-1. 1p. DOI: 10.1017/S0885715616000798.


Book review

Skills for a Scientific Life by John R. Helliwell, CRC Press, Boca Raton, 2017, 215 pp., ISBN-13: 978-1498768757

When I agreed to review this book, I had no idea that Helliwell had referenced me as a reviewer in his chapter on how to review a book. Nevertheless, I kept this review unbiased, just like the previous review I wrote for a book by the same author.

Helliwell has been a scientist renowned for his contributions to the crystallography community and to society in general for over three decades. In recognition of his contributions to the crystallographic community, Helliwell was named winner of the American Crystallographic Association's 2014 Patterson Award and the European Crystallographic Association???s 2015 Max Perutz Prize, just to name two of his many honors.

In this book, the author sets out describe how to be a good scientist and a good citizen. While the book is directed towards academic scientists and scientists-to-be, industrial scientists will benefit from reading it. For example, the chapter on promoting gender equality is relevant to all aspects of human endeavor, given the steps backward we have been reading about lately. This book is half memoir and half how-to-manual. In other words, Helliwell provides guidance on being a well-balanced scientist through numerous examples from his own scientific career.

The book is broken into eight sections consisting of a total of 34 chapters. Each chapter is a short essay covering a particular topic, so the book is an easy read. The sections broadly cover how to know if you are really cut out to be a scientist, how to be a better researcher, how to be a good citizen scientist, how to be a good teacher, how to reach larger audiences, how to be a leader in the community, and guidance on dealing with the outside world.

There is one error, in which Eisenhower is wrongfully given credit for starting the Manhattan Project. This will be rectified in subsequent printings. I do have one complaint???the typeface is rather small. This is typically done to make the reader pay attention, but it is not necessary and makes it difficult for older readers like myself.


Another book I recommend is Thank You for Being Late by Thomas Freidman. The New York Times op-ed columnist's latest work could not have come at a better time. Friedman does a great job of analyzing how the latest technology is changing the world and how to have a healthy respect for that change. Perhaps the most important lesson is that life is a learning process and that in order to thrive we have to keep learning.

The final book of the Dark Forest trilogy, Death's End, by Cixin Liu and translated by Ken Liu, has come out. This is first-class science fiction and when I have some time I will go back and reread The Three-Body Problem and The Dark Forest to catch any of the nuances I may have missed the first time around.

March is TRYPOD month. Apparently, only 1 in 5 Americans listen to podcasts, so podcast publishers are trying to raise awareness to the general public by asking people who listen to podcasts to let others know about them. Here is my contribution. I listen to a wide variety. KCRW's Left, Right and Center and KAMU's 1A are balanced (really) political podcasts. WHYY's FreshAir is always a great listen, with interviews and reviews for modern living. To balance things out, I listen to PRI's ScienceFriday podcast, the Nature Podcast and This Week in Technology from TWIT.tv. Finally, humor is the best medicine and I really look forward to NPR's Wait, Wait Don't Tell Me every Saturday.

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

Rigaku


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