Crystallography Newsletter
Volume 10, No. 11, November 2018

In this issue:

Come visit us at:

AsCA 2018/CRYSTAL 32: Conference of the Asian Crystallographic Association (AsCA) and the Society of Crystallographers in Australia and New Zealand (SCANZ)
Auckland, New Zealand, December 2 – 5, 2018

2018 Jana Modulation Workshop
La Jolla, CA, USA, December 10 – 13, 2018

CCP4 Study Weekend: “Integrated, Rational Molecular Replacement”
Nottingham, UK, January 8 – 10, 2019

The CCDC is hiring

The CCDC is currently hiring for several positions throughout the organization. Specifically, they are searching for a User Support Scientist for their US Operation. This person will support the user community in North America by providing both technical and scientific support for a range of issues. They are looking for someone with knowledge of our software and familiarity with structural chemistry or drug discovery research.

For a detailed job description and person specification for the User Support Scientist and all open positions at CCDC, please see: https://www.ccdc.cam.ac.uk/theccdcprofile/careers/

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

Nov 2018 Monthly Survey


Last Month's Survey

The Nobel Prize can be awarded to no more than three people for a given discovery or set of discoveries. Science has reached the point where discoveries are routinely being made by large teams of people working together over many years. Should scientists stop thinking of the Nobel Prize as the Holy Grail and think about other, more inclusive, prizes?

Oct 2018 survey results

Videos of the Month

My next door neighbor already has starting putting up Christmas decorations and the family across the street is already laying out the computerized, synchronized-to-carols visible-from-the-ISS display. Bah, Humbug.

Nov video 01

watch video

In all seriousness, below is a link to a video that describes a novel way to block immunosuppression in cancer with work done in part by the Savvas Savvides Lab (Lab in the Spotlight). See the paper.

Nov video 02

watch video

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Crystallography in the News

November 2, 2018. Two independent research teams have found a way to use electrons to map crystal structures in mere minutes, significantly reducing the wait time. Last month, the teams published their work in Angewandte Chemie. Prof. Donna Huryn, an organic and medicinal chemist at the University of Pittsburgh, said, “I haven't been this excited about a finding in chemistry in a long time … it's going to change the way everybody works.”

November 2, 2018. Researchers from the MPSD's Department of Atomically Resolved Dynamics at the Center for Free-Electron Laser Science, the Centre for Ultrafast Imaging (all in Hamburg), the University of Toronto in Canada and the ETH in Zurich, Switzerland, have developed a new “hit and return” (HARE) method to watch biomolecules at work.

November 6, 2018. Researchers at the University of Oregon have determined the structure of a novel protein secreted by a common gut bacterium in zebrafish that reduces inflammation in the gut and delays death by septic shock. Aeromonas immune modulator (AimA) mutually benefits both the Aeromonas bacteria and their larval zebrafish hosts.

November 6, 2018. Dorothy Hodgkin: Britain's only female Nobel scientist deserves to be on the new £50 note. Hodgkin was the foremost leader and innovator in her field, and the major impact of her work led to her becoming the only female British scientist to win a Nobel Prize. The 1964 award recognised her work in chemistry using X-ray crystallography to find the structure of penicillin (1945) and vitamin B12 (1955).

November 15, 2018. An unusual polymorph of nitrogen, one of the most abundant elements on Earth, has been observed in the laboratory and its structure determined by X-ray crystallography. An international team used a diamond anvil to apply 500 atm to the element nitrogen while heating it to 500°C.

November 20, 2018. An international team of researchers from the universities of Jyväskylä, Turku, Nantes and Illinois has investigated how a mutation in the gene that encodes the Filamin A protein causes heart valvular disease to develop at the molecular level. The researchers determined the protein structure of the mutated fragment by X-ray crystallography.

November 22, 2018. First users have now been welcomed by Diamond Light Source, the UK's national synchrotron light source to its new VMXm beamline. The Versatile Macromolecular Crystallography micro/nanofocus (VMXm) beamline becomes the 32nd operational beamline to open its doors to users, completing the portfolio of seven beamlines dedicated to macromolecular crystallography.

November 22, 2018.Dr Claire Murray, a scientist at Diamond Light Source, discusses the intricate beauty of crystallography and why we shouldn’t be talking about gender equality anymore; it should be a given.

November 23, 2018. Sir Aaron Klug, who received the chemistry Nobel prize in 1982, has died aged 92. Klug won the prize for developing crystallographic electron microscopy—a technique that can produce detailed three-dimensional images of biological structures by combining several 2D images of crystals taken from different angles—as well as for working out the structure of RNA– and DNA–protein complexes such as chromatin.

Product Spotlight

Optimization from Rigaku Reagents
When you return from the holidays, you discover that you have a crystallization hit. Now what do you do? Optimizing around that hit can help you achieve even more favorable crystallization conditions. Our customized optimization reagents help you save time, conserve materials, and improve both accuracy and precision in preparing solutions and reagents.

Formulas for optimization
Did you get a hit using a Wizard or Cryo screen? If so, optimize with the formulations found in each screen.

Wizard Classic 1 Wizard Classic 2 Wizard Classic 3 Wizard Classic 4
Wizard Cyro 1 Wizard Cryo 2

EZ-Screen Builder
When you get a hit on a commercial screen, why spend time calculating the optimization? Use the Rigaku Reagents EZ-Screen Builder, to custom design your optimization screen online, and receive a 96 deep-well block via FedEx.

Wizard pH Buffer – 96 well block plate
The Wizard pH Buffer screen is an optimization screen that can be applied to your crystallization hit optimization to simultaneously explore the effects of pH and buffer composition on crystal growth. The Wizard pH Buffer screen is a set of 96 unique buffer solutions encompassing 12 unique buffer systems at 8 pH points, incrementally varied by 0.4 pH units.

96-well block plate formulations are 1.0 ml each in a 96 deep-well matrix block plate. All formulations are prepared with ASTM type-1 water and high-purity chemicals, 0.2 µm filtered in sterile packaging.

 Wizard pH Buffer

Lab in the Spotlight

Savvas Savvides
Savvas Savvides

The Savvas Savvides Lab at Vlaams Instituut voor Biotechnologie (VIB) employs an integrative structural biology approach in conjunction with molecular interaction studies and cellular interrogation of the systems under study to elucidate the structural and mechanistic principles underlying the assembly, activation and pathophysiology of macromolecular complexes pivotal to inflammation, immunity, and cancer. The cornerstone of the lab's research philosophy depends on a rigorous hypothesis-driven interrogation of the protein complexes under study, and is closely tied with collaborations with leading academic research groups in Belgium and abroad as well as industrial partners.

The lab currently focuses on 3 main research areas:

  • Pro-inflammatory signaling complexes and antagonist design
  • Extracellular assembly and activation principles of oncogenic receptor tyrosine kinases
  • In vivo protein crystals in immunity, inflammation, and cancer

For more details about a recent success of one of the Savvas lab's collaborations see the second video of the month, left.

Useful Link

useful link Running VAX/VMS Under Linux Using SIMH

There has been a thread on CCP4 about reading a VAX-created MTZ file from 1992. The thread has broken a record for length. While there were lots of interesting answers, this one from Ed Berry at Upstate Medical University caught my attention. Here are step-by-step instructions for setting up an OpenVMS (VAX OS) system using the SIMH emulator in a Linux box. Now I just have to find a DAT drive to read the tapes I asked about a couple of months ago.

Selected Recent Crystallographic Papers

Median-Truncated Nonconvex Approach for Phase Retrieval With Outliers. Zhang, Huishuai; Chi, Yuejie; Liang, Yingbin. IEEE Transactions on Nuclear Science. Nov2018, Vol. 64 Issue 11, p7287-7310. 24p. DOI: 10.1109/TIT.2018.2847695.

X-ray Raman scattering: a new in situ probe of molecular structure during nucleation and crystallization from liquid solutions. Al-Madhagi, Laila H.; Chang, Sin-Yuen; Balasubramanian, Mahalingam; Kroner, Anna B.; Shotton, Elizabeth J.; Willneff, Elizabeth A.; Mishra, Bhoopesh; Schroeder, Sven L. M. CrystEngComm. 11/21/2018, Vol. 20 Issue 43, p6871-6884. 14p. DOI: 10.1039/c8ce00929e.

Two polymorphs and a sulfate of buprofezin: Crystal structure and Hirshfeld surface analysis. Zhu, Zhiying; Zhou, Yuming; Yao, Qingzhao; Sun, Baiwang; Wang, Mingliang; Zhong, Xi; Wang, Beibei; Xue, Yi; Chen, Xinchun. Polyhedron. Nov2018, Vol. 155, p85-93. 9p. DOI: 10.1016/j.poly.2018.08.034.

Crystal structure of glycosyltrehalose synthase from Sulfolobus shibatae DSM5389. Okazaki, Nobuo; Blaber, Michael; Kuroki, Ryota; Tamada, Taro. Acta Crystallographica: Section F, Structural Biology Communications. Nov2018, Vol. 74 Issue 11, p741-746. 6p. DOI: 10.1107/S2053230X1801453X.

Libration of phenyl groups detected by VT-SSNMR: Comparison with X-ray crystallography. Nieto, Carla I.; Cabildo, Pilar; García, M. Ángeles; Claramunt, Rosa M.; Elguero, José; Alkorta, Ibon. Magnetic Resonance in Chemistry. Nov2018, Vol. 56 Issue 11, p1083-1088. 6p. DOI: 10.1002/mrc.4754.

Crystal structure of saposin D in an open conformation. Gebai, Ahmad; Gorelik, Alexei; Nagar, Bhushan. Journal of Structural Biology. Nov2018, Vol. 204 Issue 2, p145-150. 6p. DOI: 10.1016/j.jsb.2018.07.011.

Functionalization of 1,3-diphosphacyclobutadiene cobalt complexes via Si–P bond insertion. Rödl, Christian; Malberg, Jennifer Bissmeyer neé; Wolf, Robert. Zeitschrift für Naturforschung B: A Journal of Chemical Sciences. Nov2018, Vol. 73 Issue 11, p895-909. 15p. DOI: 10.1515/znb-2018-0121.

Phthalorubines: Fused-Ring Compounds Synthesized from Phthalonitrile. Zheng, Wei; Zhao, Yuan; Zhuang, Wen-Hao; Wu, Jing-Jing; Wang, Fang-Zhou; Li, Cheng-Hui; Zuo, Jing-Lin. Angewandte Chemie International Edition. 11/19/2018, Vol. 57 Issue 47, p15384-15389. 6p. DOI: 10.1002/anie.201807281.

Quo vadis, Acta Crystallographica F? van Raaij, Mark J. Acta Crystallographica: Section F, Structural Biology Communications. Nov2018, Vol. 74 Issue 11, p688-689. 2p. DOI: 10.1107/S2053230X18015340.

A uranium(IV) imido amido triazenido complex formed via addition of a C-H bond across a U-N multiple bond. Boreen, Michael A.; Arnold, John. Polyhedron. Nov2018, Vol. 155, p149-152. 4p. DOI: 10.1016/j.poly.2018.08.046.

Kernel Homology in Gold Nanoclusters. Zhuang, Shengli; Liao, Lingwen; Yuan, Jinyun; Wang, Chengming; Zhao, Yan; Xia, Nan; Gan, Zibao; Gu, Wanmiao; Li, Jin; Deng, Haiteng; Yang, Jinlong; Wu, Zhikun. Angewandte Chemie International Edition. 11/19/2018, Vol. 57 Issue 47, p15450-15454. 5p. DOI: 10.1002/anie.201808997.

Structural basis for potent inhibition of d-amino acid oxidase by thiophene carboxylic acids. Kato, Yusuke; Maita, Nobuo; Kurosawa, Sumire; Yorita, Kazuko; Fukui, Kiyoshi; Hin, Niyada; Thomas, Ajit G.; Rojas, Camilo; Slusher, Barbara S.; Tsukamoto, Takashi. European Journal of Medicinal Chemistry. Nov2018, Vol. 159, p23-34. 12p. DOI: 10.1016/j.ejmech.2018.09.040.

Synthesis, molecular structure, vibrational and theoretical studies of a new non-centrosymmetric organic sulphate with promising NLO properties. Ben M'leh, Cherifa; Brandán, Silvia Antonia; Issaoui, Noureddine; Roisnel, Thierry; Marouani, Houda. Journal of Molecular Structure. Nov2018, Vol. 1171, p771-785. 15p. DOI: 10.1016/j.molstruc.2018.06.041.

Crystal structure of the central and the C-terminal RNase domains of colicin D implicated its translocation pathway through inner membrane of target cell. Chang, Jung-Wei; Sato, Yusuke; Ogawa, Tetsuhiro; Arakawa, Takatoshi; Fukai, Shuya; Fushinobu, Shinya; Masaki, Haruhiko. Journal of Biochemistry. Nov2018, Vol. 164 Issue 5, p329-339. 11p. DOI: 10.1093/jb/mvy056.

Neural-network-based order parameters for classification of binary hard-sphere crystal structures. Boattini, Emanuele; Ram, Michel; Smallenburg, Frank; Filion, Laura. Molecular Physics. Nov2018, Vol. 116 Issue 21/22, p3066-3075. 10p. DOI: 10.1080/00268976.2018.1483537.

Conformational Analysis of Carboxymethylamylose by Potentiometric Titration and SAXS. Takada, Masako; Wada, Kaori; Muroga, Yoshio; Ikake, Hiroki; Shimizu, Shigeru. Starch / Staerke. Nov2018, Vol. 70 Issue 11/12, pN.PAG-N.PAG. 1p. DOI: 10.1002/star.201800016.

Antibody adsorption in protein-A affinity chromatography – in situ measurement of nanoscale structure by small-angle X-ray scattering. Plewka, Jacek; Silva, Gonçalo L.; Tscheließnig, Rupert; Rennhofer, Harald; Dias-Cabral, Cristina; Jungbauer, Alois; Lichtenegger, Helga C. Journal of Separation Science. Nov2018, Vol. 41 Issue 22, p4122-4132. 11p. DOI: 10.1002/jssc.201800776.

Resonant Soft X-Ray Scattering Provides Protein Structure with Chemical Specificity. Ye, Dan; Le, Thinh P.; Kuei, Brooke; Zhu, Chenhui; Zwart, Peter H.; Wang, Cheng; Gomez, Enrique D.; Gomez, Esther W. Structure. Nov2018, Vol. 26 Issue 11, p1513-1513. 1p. DOI: 10.1016/j.str.2018.07.018.

Book Review

book cover The Perfectionists: How Precision Engineers Created the Modern World
By Simon Winchester

Simon Winchester's The Perfectionists: How Precision Engineers Created the Modern World is a marvelous work of popular science, tracing the history of high-precision engineering from 1776 to present day. Precision engineering is a subdiscipline of effectively all other engineering disciplines. As the name suggests, precision is tantamount. High tolerances, repeatable results, and stability over time are the tenets of the practice.

The book's prologue starts with a delightful anecdote about a young Winchester and his father—a precision engineer to whom the book is dedicated. When Winchester was a boy, his father brought home some gauge blocks (also known as Jo blocks) from work. These metal blocks, used for measuring things to incredibly high tolerances, are so precisely ground flat that pressing them together makes them virtually impossible to break apart. The only way to separate them is not by pulling, but rather by sliding. The man who invented them was Carl Edvard Johansson, who makes an appearance later in the book.

Winchester then gives his readers a brief but thorough refresher course on the difference between precision and accuracy. Though often used interchangeably, the two terms mean something vastly different. Winchester presents the classic example of hitting a bullseye. If all of the shots are clustered together but are not near the center of the target, they are precise but not accurate. If all of the shots are near the center of the target but not necessarily close to each other, they are accurate but not precise. If all of the shots are clustered directly on the bullseye and even on top of each other, they are both precise and accurate. It is an incredibly important distinction in any field, but especially in engineering.

The prologue's combination of a brief, illustrative anecdote and detailed engineering explanation echoes through the rest of the book. Winchester begins each chapter with a contextualizing tale, either from history or from his personal repertoire. Even if the connection might seem tenuous at the beginning, Winchester deftly pivots back to a milestone of precision engineering in each case. He then offers a concise but significant explanation of exactly how precise that milestone's engineering is.

He dedicates each chapter of The Perfectionists to a subject with an increasingly higher tolerance, which not so coincidentally follows a fairly consistent timeline. Tolerance, per Winchester, is “the permissible variation in size from a specified standard allowed for a machined part.” He starts with steam engines (tolerance: 10-1), then turns to ship-building (10-3), guns (10-5), screws (10-7), cars (10-10), planes (10-12), lenses for telescopes and cameras (10-13), GPS (10-17), and finally, computer chips (10-35).

In a great moment, Winchester turned to Eli Whitney. Whitney is perhaps best known to schoolchildren across America as the inventor of the cotton gin, but as Winchester so eloquently puts it, he was a “charlatan” of precision engineering. In early 19th century America, reliable weaponry was something of a challenge. Handmade by gunsmiths, rifles were prone to misfires. Something as simple as an uneven surface on the inside of a barrel could mean the difference between shooting someone or being shot at first on the battlefield. Gun repairs could take weeks, as each part had to be fixed by hand. Thomas Jefferson, while a US ambassador to France, became aware of the country’s practice of gun-making. The French made interchangeable parts for their weaponry. If something on a rifle failed to perform or broke, it could be easily swapped out for a newer part.

Jefferson pushed for the US to contract someone to make American weaponry following the French system. And Whitney—who knew nothing about the musket-making business—used his connections as an alumnus of Yale to win the government commission. He even went so far as to present his “work” in front of President John Adams and Jefferson, then vice-president, and for lack of a better word, totally bamboozled them.

Winchester's Whitney revelation is one of many such juicy historical tidbits peppered throughout The Perfectionists. His prose flows effortlessly, and although it sometimes dips too quickly or too deeply into engineering jargon, the ever-self-aware Winchester includes a “Glossary of Possibly Unfamiliar Terms.” It spans eight pages from “accuracy”to “wabi-sabi.”

All in all, a wonderful read for a fall weekend.

Review by Jeanette S. Ferrara, MA


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