Crystallography Newsletter
Volume 10, No. 08, August 2018

In this issue:

Rigaku Oxford Diffraction User Meeting

User Meeting

We are pleased to announce that the 2018 European Users' Meeting will be held in conjunction with the faculty of Chemistry and Pharmacy at the University of Regensburg. Please join us to discover the latest developments from Rigaku Oxford Diffraction and interact with other users to share experiences with their diffractometers.

The user meeting will begin on Thursday September 27th at 1:00 pm and conclude the following day at 1:00 pm. Following the end of the main user meeting there will be a problem solving clinic from 2:30 pm until 5:00 pm. Please fill out this form to attend.

Rigaku Symposium at Yale University

Symposium at Yale

The Yale University Chemical and Biophysical Instrumentation Center, in conjunction with Rigaku Americas Corporation, is pleased to announce the 6th Rigaku Symposium. As with previous symposia, this year's event will feature expert-led workshops and a slate of technical presentations from invited speakers. The lecture and workshop topics that will be covered are chemical crystallography, single crystal analysis, structural biology and small angle X-ray scattering.

The symposium will take place on Friday, October 19, 2018 in the Chemistry Department at Yale University.
Please fill out this form to attend.

Come visit us at:

31st European Crystallographic Meeting, ECM31
Oviedo, Spain, August 22 – 27, 2018

XVII International Small Angle Scattering Conference – SAS2018
Traverse City, Michigan, October 7 – 12, 2018

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

August 2018 Monthly Survey


Last Month's Survey

In my crystallography course, I use a text book that is:

July 2018 survey results

Video of the Month

The world's simplest electromagnetic train. This was made of magnets, copper wire and a dry cell battery.

August 2018 video

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Subscribe to Rigaku eNewsletters

Subscribe to Crystallography Times

Each month, Rigaku distributes two eNewsletters: The Bridge, which focuses on Materials Analysis, and Crystallography Times, which concentrates on X-ray crystallography.


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Crystallography in the News

August 2, 2018. Using neutron crystallography, an international team of researchers managed to pin-point hydrogen-bonding interactions in the C-terminal carbohydrate recognition domain of galectin-3 (galectin-3C). Galectins attach to other proteins via the carbohydrates on their surfaces – a sugar-binding protein. They impact on a range of processes in the cell associated with several diseases, including heart disease and breast cancer.

August 3, 2018. A research team, led by Dr Helen O'Hare from the University of Leicester's Department of Infection, Immunity and Inflammation, has identified functions of a specific protein (Kinase G) that allow groups of bacteria such as Mycobacterium tuberculosis to detect amino acids in their surroundings, allowing the bacteria to regulate their metabolism in response to the available nutrients.

August 7, 2018. Researchers at the Department of Energy's SLAC National Accelerator Laboratory have used room temperature serial femtosecond crystallography to better understand the mechanisms that lead to hearing loss when a class of antibiotics called aminoglycosides (for example, Streptomycin) are introduced to the body.

August 7, 2018. A new classification of symmetry groups in crystal space has been proposed by Russian scientists. The symmetry of forbidden regions was determined by Lobachevsky University researchers for packing solid spheres in the three-dimensional crystal space of different symmetry. According to the results obtained, 230 space symmetry groups are characterized by 33 classes of spatial symmetry of forbidden regions.

August 8, 2018. Klaus Gerwert and his team at Ruhr-Universität Bochum addressed the need for a rapid way to track protein binding by using an infrared (IR) sensor able to track protein conformational changes in just a few minutes. The sensor is based on a crystal that is permeable for IR light and allows tracking of the absorbance spectra.

August 8, 2018. Researchers at Columbia University Irving Medical Center (CUIMC) have found new evidence of how certain transport proteins are working at the molecular level, paving the way for new, improved drugs to treat psychiatric disorders. Neurotransmitter sodium symporters (NSS) regulate signals between nerve cells, and are the molecular target of antidepressants (SSRIs) and of various psychostimulants. Data suggest that the involvement of two binding sites in neurotransmitter transport is not unique to LeuT but shared by other NSS members, and is possibly a universal feature of these many transport proteins.

August 14, 2018. Chemists have overcome a key weakness in the class of materials known as metal-organic frameworks, or MOFs, by introducing extra weaknesses. Copper-based MOFs are often unstable, especially when exposed to moisture – even dampness in the air – explains Russell Morris from the University of St Andrews, UK. By intentionally introducing sacrificial "crumple zones" that water breaks down first, Morris’s team retains the copper-based MOF’s function.

August 15, 2018. A research collaboration led by Guido Serini, Enrico Giraudo and Luca Tamagnone has used rational design to alter the SEMA3A protein. This stops it binding to NRP-1 while maintaining its positive blood vessel response through the PLXNA4 receptor.

Product Spotlight

HyPix-Arc 150°

Embrace your sample with the latest addition to the HyPix family of detectors from Rigaku Oxford Diffraction, the HyPix-Arc 150°. The HyPix-Arc 150° is a unique curved hybrid photon counting (HPC) detector that offers a whole new perspective on your experiment. By wrapping around the sample, the HyPix-Arc 150° is able to achieve a higher theta coverage than much larger flat detectors. This enables the detector to see all the way up to IUCr recommended resolution limits for any home lab wavelength. This means that all data, from low to high angle, are measured at the same scan speed; that is, with the same precision. It also minimizes the distorting effects of parallax to yield better measurements.

HyPix-Arc 150°
Curved detector
Collecting more data in one image and under the same conditions reduces the need for corrections, enabling faster, higher-quality datasets. This also reduces the dose time needed for a sample, which in turn minimizes the effect of radiation damage, sample decay or other time-dependent fluctuations.

HPC technology
Along with the benefits of a curved detector, all the benefits of the HyPix family's HPC technology are present. With RACE (Rapid Alternating Counter Electronics) technology for fast frame rates, small pixels and direct detection, the latest member of the HyPix family collects supreme quality data faster than ever before.

Why you need a curved detector:

  • Higher theta coverage in a single image
  • Capture more diffracted photons per exposure
  • Lowest reflection profile distortion
  • All reflections measured under the same conditions

Learn more about it here.

Lab in the Spotlight

University of Melbourne team

The University of Melbourne team with Rigaku Applications Specialist. (L to R) Dyanne Cruickshank from Rigaku, Martin Van Koeverden, Dr Robert Gable and Prof Brendan Abrahams from The University of Melbourne.

Crystallographers at the University of Melbourne received a significant boost in capabilities following the installation of the XtaLAB Synergy-S, a state-of-the-art small molecule X-ray diffractometer from Rigaku Oxford Diffraction (Rigaku). The new instrument marries cutting-edge detector, goniometer and X-ray source technologies in one fully integrated system that will generate world-class results for the University of Melbourne researchers. The system was installed by AXT Pty. Ltd., Rigaku's distributor in Australia and New Zealand. The XtaLAB Synergy-S becomes the flagship instrument in the X-ray Diffraction Facility at the University of Melbourne. It adds to the existing small molecule crystallography capabilities, supplementing a Rigaku SuperNova system installed in 2010

The XtaLAB Synergy-S will serve researchers from undergraduate education through postdoctoral research, as well as the academic staff. Dr Robert Gable, Manager of the X-Ray Diffraction Facility, envisions that it will be used by a range of different research teams for a host of different compounds, including organic biomolecules, minerals, coordination polymers, metal complexes used for catalysis or cancer treatment, and polyoxometallates.

The system was purchased following a successful Linkage Infrastructure, Equipment and Facilities (LIEF) grant bid submitted by the University of Melbourne, and other university and research institutes in the area. The University of Melbourne is grateful to the Australian Research Council for their contribution towards the purchase.

Useful Linkuseful link

useful link About TWiT

"Your first podcast of the week is the last word in tech". I mentioned this in my list of favorite podcasts last year but wanted to mention it again. In the past, this podcast/video has included the likes of Jerry Pournelle (science fiction writer and futurist), John C. Dvorak (tech guru), Brianna Wu (game developer and candidate for Massachusetts 8th District) and Matt Cutts (director, US Digital Services). Lots of relevant and timely information about all things tech can be found on the TWiT podcast.

Selected Recent Crystallographic Papers

OChemDb: the free online Open Chemistry Database portal for searching and analysing crystal structure information. Altomare, Angela; Corriero, Nicola; Cuocci, Corrado; Falcicchio, Aurelia; Moliterni, Anna; Rizzi, Rosanna. Journal of Applied Crystallography. Aug2018, Vol. 51 Issue 4, p1229-1236. 7p. DOI: 10.1107/S1600576718008166.

Application of the small-angle X-ray scattering technique for structural analysis studies: A review. Li, Jingpeng; Jiao, Aiquan; Chen, Shuo; Wu, Zhengzong; Xu, Enbo; Jin, Zhengyu. Journal of Molecular Structure. Aug2018, Vol. 1165, p391-400. 10p. DOI: 10.1016/j.molstruc.2017.12.031.

Coded aperture design for solving the phase retrieval problem in X-ray crystallography. Pinilla, Samuel; García, Hans; Díaz, Luis; Poveda, Juan; Arguello, Henry. Journal of Computational & Applied Mathematics. Aug2018, Vol. 338, p111-128. 18p. DOI: 10.1016/j.cam.2018.02.002.

Exploring the interactions between model proteins and Pd(ii) or Pt(ii) compounds bearing charged N,N-pyridylbenzimidazole bidentate ligands by X-ray crystallography. Ferraro, Giarita; Mansour, Ahmed M.; Merlino, Antonello. Dalton Transactions: An International Journal of Inorganic Chemistry. 8/14/2018, Vol. 47 Issue 30, p10130-10138. 9p. DOI: 10.1039/c8dt01663a.

Structure of (SiEt3)2(B12F12). Another example of R3Si—F—E bridge bonding (E=B, Al, Si). Malischewski, M.; Bukovsky, Eric V.; Strauss, Steven H.; Seppelt, Konrad. Journal of Fluorine Chemistry. Aug2018, Vol. 212, p107-111. 5p. DOI: 10.1016/j.jfluchem.2018.04.010.

The rise of neutron cryo-crystallography. Kwon, Hanna; Langan, Patricia S.; Coates, Leighton; Raven, Emma L.; Moody, Peter C. E. Acta Crystallographica: Section D, Structural Biology. Aug2018, Vol. 74 Issue 8, p792-799. 7p. DOI: 10.1107/S205979831800640X.

Crystal-on-crystal chips for in situ serial diffraction at room temperature. Ren, Zhong; Ayhan, Medine; Bandara, Sepalika; Bowatte, Kalinga; Kumarapperuma, Indika; Gunawardana, Semini; Shin, Heewhan; Wang, Cong; Zeng, Xiaoli; Yang, Xiaojing. Lab on a Chip - Miniaturisation for Chemistry & Biology. 8/7/2018, Vol. 18 Issue 15, p2246-2256. 11p. DOI: 10.1039/c8lc00489g.

Channel current analysis estimates the pore-formation and the penetration of transmembrane peptides. Sekiya, Yusuke; Shimizu, Keisuke; Kawano, Ryuji; Sakashita, Shungo; Usui, Kenji. Analyst. 8/7/2018, Vol. 143 Issue 15, p3540-3543. 4p. DOI: 10.1039/c8an00243f.

Structural Basis for Auto-Inhibition of the NDR1 Kinase Domain by an Atypically Long Activation Segment. Xiong, Shawn; Lorenzen, Kristina; Couzens, Amber L.; Templeton, Catherine M.; Rajendran, Dushyandi; Mao, Daniel Y.L.; Juang, Yu-Chi; Chiovitti, David; Kurinov, Igor; Guettler, Sebastian; Gingras, Anne-Claude; Sicheri, Frank. Structure. Aug2018, Vol. 26 Issue 8, p1101-1115.e6. 1p. DOI: 10.1016/j.str.2018.05.014.

Biological small-angle neutron scattering: recent results and development. Mahieu, Emilie; Gabel, Frank. Acta Crystallographica: Section D, Structural Biology. Aug2018, Vol. 74 Issue 8, p715-726. 11p. DOI: 10.1107/S2059798318005016.

Pushing the Limits of Molecular Crystal Structure Determination From Powder Diffraction Data in High-Throughput Chemical Environments. Kabova, Elena A.; Blundell, Charles D.; Shankland, Kenneth. Journal of Pharmaceutical Sciences. Aug2018, Vol. 107 Issue 8, p2042-2047. 6p. DOI: 10.1016/j.xphs.2018.04.010.

Changing the site energy of per-614 in the Peridinin-chlorophyll a-protein does not alter its capability of chlorophyll triplet quenching. Agostini, Alessandro; Niklas, Jens; Schulte, Tim; Di Valentin, Marilena; Bortolus, Marco; Hofmann, Eckhard; Lubitz, Wolfgang; Carbonera, Donatella. BBA - Bioenergetics. Aug2018, Vol. 1859 Issue 8, p612-618. 7p. DOI: 10.1016/j.bbabio.2018.05.008.

Evaluation of models determined by neutron diffraction and proposed improvements to their validation and deposition. Liebschner, Dorothee; Afonine, Pavel V.; Moriarty, Nigel W.; Langan, Paul; Adams, Paul D. Acta Crystallographica: Section D, Structural Biology. Aug2018, Vol. 74 Issue 8, p800-813. 13p. DOI: 10.1107/S2059798318004588.

On the Calculation of SAXS Profiles of Folded and Intrinsically Disordered Proteins from Computer Simulations. Skepö, Marie; Henriques, João; Lindorff-Larsen, Kresten; Arleth, Lise. Journal of Molecular Biology. Aug2018, Vol. 430 Issue 16, p2521-2539. 19p. DOI: 10.1016/j.jmb.2018.03.002.

Predicting data quality in biological X-ray solution scattering. Wang, Chenzheng; Lin, Yuexia; Bougie, Devin; Gillilan, Richard E. Acta Crystallographica: Section D, Structural Biology. Aug2018, Vol. 74 Issue 8, p727-738. 11p. DOI: 10.1107/S2059798318005004.

Conformational States of ABC Transporter MsbA in a Lipid Environment Investigated by Small-Angle Scattering Using Stealth Carrier Nanodiscs. Josts, Inokentijs; Nitsche, Julius; Maric, Selma; Mertens, Haydyn D.; Moulin, Martine; Haertlein, Michael; Prevost, Sylvain; Svergun, Dmitri I.; Busch, Sebastian; Forsyth, V. Trevor; Tidow, Henning. Structure. Aug2018, Vol. 26 Issue 8, p1072-1079.e4. 1p. DOI: 10.1016/j.str.2018.05.007.

Cationic Au(I) complexes with aryl-benzothiazoles and their antibacterial activity. Stenger-Smith, Jenny; Chakraborty, Indranil; Mascharak, Pradip K. Journal of Inorganic Biochemistry. Aug2018, Vol. 185, p80-85. 6p. DOI: 10.1016/j.jinorgbio.2018.05.003.

An unexpected formation of a Ru(III) benzylidene complex during activation of a LatMet-type ring-opening polymerisation catalyst. Gawin, Anna; Malecki, Pawel; Dranka, Maciej; Zachara, Janusz; Skompska, Magdalena; Kajetanowicz, Anna; Grela, Karol. Journal of Catalysis. Aug2018, Vol. 364, p345-353. 9p. DOI: 10.1016/j.jcat.2018.05.014.

Synthesis, characterization, and DFT studies of novel spiroacenaphthylene-1,3-oxazines. Yavari, Issa; Khajeh-Khezri, Aliyeh; Aliveisi, Rahman; Halvagar, Mohammad Reza. Journal of Physical Organic Chemistry. Aug2018, Vol. 31 Issue 8, p1-1. 12p. DOI: 10.1002/poc.3871.

A new diphosphine-carbonyl complex of ruthenium: an efficient precursor for C–C and C–N bond coupling catalysis. Mukherjee, Aparajita; Hrovat, David A.; Richmond, Michael G.; Bhattacharya, Samaresh. Dalton Transactions: An International Journal of Inorganic Chemistry. 8/14/2018, Vol. 47 Issue 30, p10264-10272. 9p. DOI: 10.1039/c8dt01085d.

Utilizing Coarse-Grained Modeling and Monte Carlo Simulations to Evaluate the Conformational Ensemble of Intrinsically Disordered Proteins and Regions. Cragnell, Carolina; Rieloff, Ellen; Skepö, Marie. Journal of Molecular Biology. Aug2018, Vol. 430 Issue 16, p2478-2492. 15p. DOI: 10.1016/j.jmb.2018.03.006.

Continuous protein crystallisation platform and process: Case of lysozyme. Yang, Huaiyu; Peczulis, Peter; Inguva, Pavan; Li, Xiaoyu; Heng, Jerry Y.Y. Chemical Engineering Research & Design: Transactions of the Institution of Chemical Engineers Part A. Aug2018, Vol. 136, p529-535. 7p. DOI: 10.1016/j.cherd.2018.05.031.

Architectural Features of Human Mitochondrial Cysteine Desulfurase Complexes from Crosslinking Mass Spectrometry and Small-Angle X-Ray Scattering. Cai, Kai; Frederick, Ronnie O.; Dashti, Hesam; Markley, John L. Structure. Aug2018, Vol. 26 Issue 8, p1127-1136.e4. 1p. DOI: 10.1016/j.str.2018.05.017.

Chemical Reactions at Isolated Single-Sites Inside Metal-Organic Frameworks. Wang, Yuemin; Wöll, Christof. Catalysis Letters. Aug2018, Vol. 148 Issue 8, p2201-2222. 22p. DOI: 10.1007/s10562-018-2432-2.

Frontispiece: Quantum Crystallography: Current Developments and Future Perspectives. Genoni, Alessandro; Bucinský, Lukas; Claiser, Nicolas; Contreras-García, Julia; Dittrich, Birger; Dominiak, Paulina M.; Espinosa, Enrique; Gatti, Carlo; Giannozzi, Paolo; Gillet, Jean-Michel; Jayatilaka, Dylan; Macchi, Piero; Madsen, Anders Ø.; Massa, Lou; Matta, Chérif F.; Merz, Jr., Kenneth M.; Nakashima, Philip N. H.; Ott, Holger; Ryde, Ulf; Schwarz, Karlheinz. Chemistry - A European Journal. Aug2018, Vol. 24 Issue 43, p1-1. 1p. DOI: 10.1002/chem.201884361.

Book Review

book cover Energy: A Human History by Richard Rhodes, Simon & Schuster, 2018, 480 pages, ISBN: 978-1-5011-0535-7.

Richard Rhodes’s Energy is a must-read. Although the title is tad misleading--it is by no means a comprehensive history of the relationship between energy and humanity--Energy is a delightful take on the modern history of that relationship.

After a brief foreword that addresses climate change and its complicated connections to humanity's relationship with energy (and reveals that chemists have known automobile pollution causes Los Angeles’ smog problem for 70 years), Rhodes dives right in.

He starts with a particularly interesting anecdote about William Shakespeare and his theater partners, the Burbage brothers. In winter 1598, the men deconstructed the Globe theater and moved it, piece by piece, across the Thames. What does this have to do with energy?

Shakespeare and the Burbage brothers had to disassemble their original theater and rebuild it because, in Elizabethan England, wood was a scarce resource--not because of a lack of trees per se but because so many aspects of the society depended on it. Buildings were all made from wood. The country’s massive armada warships were made from wood. Wood burned in all the fires that kept England warm in the winter. That is, until the British turned to coal.

The rest as they say, is history. Humanity's love affair with coal is one that has continued to this day--and coal’s higher efficiency as a burning fuel led to further innovation--like steam engines in boats and trains.

No history of energy is complete without a discussion of electricity (for a more comprehensive history of electricity, try Craig R. Roach’s Simply Electrifying).

Rhodes gives a fair bit of "screen time" to Thomas Edison, who was a proponent of direct current (DC)--and very little to Nikola Tesla (a single mention on page 200). Tesla developed an alternating current induction motor for Westinghouse Electric Company that contributed to Westinghouse winning the so-called "War of the Electric Currents" against the Edison Electric Light Company.

“That story has been told in great detail elsewhere,” Rhodes explains, "somewhat exaggerating the role of the inventive Serbian engineer Nikola Tesla, whose only important contribution to the 'war' was the alternating-current electric motor." Tesla may have only made a single important contribution to that 'war'--but it was certainly a winning one.

But wood, coal, and electricity are hardly the only energy sources Rhodes explores. Bird droppings, whale oil, alcohol, petroleum, and nuclear energy all have their story told.

Rhodes’ narrative style--presenting seemingly non-sequitur anecdotes to demonstrate a critical facet of modern humanity’s relationship with energy, and then filling in the subsequent gaps with detailed but well-crafted history lessons--makes reading Energy not feel like reading a history book.

Unlike many books that have a color photo insert in the middle, with high resolution images printed on higher quality paper, Energy’s illustrations are scattered throughout the text. Given how many of the concepts require visualization, or are significantly aided by it, having those illustrations in close proximity to the text that refers to them is refreshing and makes for a more pleasant reading experience.

Review by Jeanette S. Ferrara, MA


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