Crystallography in the news

November 2, 2016. Niki Caro has been set to direct Exposure. The film tells the story of scientist Rosalind Franklin and her critical role in the discovery of DNA's structure. The script is by Hayley Schore & Roshan Sethi.

November 4, 2016. What was the "mother" molecule that led to the formation of life? And how did it replicate itself? One prominent school of thought proposes that RNA is the answer to the first question. Researchers in this camp demonstrate RNA has more flexibility in how it recognizes itself than previously believed. The finding might change how we picture the first chemical steps towards replication and life.

November 8, 2016. The Integrated Resource for Reproducibility in Macromolecular Crystallography (IRRMC) is part of the Big Data to Knowledge programme of the National Institutes of Health and has been developed to archive raw data from diffraction experiments and, equally importantly, to provide related metadata. The database contains 3070 macromolecular diffraction experiments (5983 datasets) and their corresponding partially curated metadata, accounting for around 3% of all depositions in the Protein Data Bank.

November 13, 2016. Molecular Physiology and Biological Physics Prof. Wladek Minor and members of his lab recently discovered how zinc is transported by mammalian albumin in the human body. Albumin, a protein that transports important materials throughout the human body, was found to be imperative in the movement of zinc, which is needed for immune function and the healing of wounds.

November 13, 2016. An international team of scientists from the United States and China recently made headlines by publishing a paper detailing the crystal structure of the human cannabinoid receptor type 1 (CB1). This is a major discovery, as the CB1 is responsible for THC's euphoric "high" as well as some of its therapeutic applications.

November 15, 2016. X-rays can damage crystals, so precise structure determinations of fragile proteins is often stymied by the very technique one hopes to use. Serial femtosecond crystallography can circumvent this problem where a rapid fire snapshot is obtained before the protein is obliterated. A study of the effects of using this technique in a study of photosystem II helps map the damage as it occurs.

November 21, 2016. A new study by scientists from the Florida campus of The Scripps Research Institute (TSRI) offers a novel structure-based drug design strategy aimed at altering the basic landscape of this type of breast cancer treatment. The findings show that the current approach is not the only, or even the best, way to block the estrogen receptor.

November 21, 2016. New drugs, better batteries and new materials are just a few of the discoveries expected to emerge from an €86 million investment in the Bernal Institute at the University of Limerick. The institute will house more than 260 researchers, including six world experts who already hold Bernal research chairs and who lead teams making discoveries in crystal engineering, fluid mechanics and microscopy among other disciplines.

November 21, 2016. The Small-Molecule X-Ray Crystallography Facility, based in the University of Kentucky Department of Chemistry, has been awarded a prestigious and highly competitive grant from the Major Research Instrumentation (MRI) program of the National Science Foundation (NSF). The award of $383,133 (70 percent NSF, 30 percent UK matching funds) will fund the acquisition of a state-of-the-art microfocus X-ray diffractometer.

November 21, 2016. The DuBois lab at St. Jude Children's Research Hospital is laying the foundation for new antiviral therapies and vaccines for human astroviruses. In a new study, Rebecca DuBois used X-ray crystallography to show how a specific protein structure on the surface of the virus is blocked by a neutralizing antibody, thus preventing the virus from infecting human cells.

Rigaku Oxford Diffraction North American
Users' Meeting Report — by Eric Reinheimer

From October 31^st to November 1^st, the North American office of Rigaku Oxford Diffraction hosted its first users' meeting at its offices in The Woodlands, TX. Over 30 attendees and employees of Rigaku Oxford Diffraction came together to discuss crystallography and advances in hardware and software introduced by ROD in the past year.

After opening remarks by Dr. Joseph Ferrara, Chief Science Officer of ROD, lectures were delivered by Dr. Mathias Meyer, ROD Software Manger and Dr. Eric Reinheimer, Small Molecule Applications Scientist, on developments related to the CrysAlis^Pro software package and small molecule crystallographic applications currently ongoing within the North American ROD Applications Lab respectively.

After breaking for lunch, a lecture was presented by Dr. Horst Puschmann, head software developer for Olexsys.org, on structure solution and refinement using Olex2 and AutoChem. To bring the first day of the meeting to a close, Dr. Ray Butcher, Professor of Inorganic Chemistry at Howard University, delivered the keynote address, titled "Examples of Twinning and Pseudosymmetry," during which he highlighted several examples of twinning and instances of pseudosymmetry he has encountered during his illustrious career.

The second day of the meeting gave some of the attendees the opportunity to highlight how the inclusion of small molecule crystallography and, specifically, the ROD line of products has enhanced their individual research programs. The first speaker, Dr. Dimtriy Soldatov from the University of Guelph, presented his seminar titled "How the First SuperNova in Canada Nucleated a New X-Ray Facility in Guelph," during which he spoke about how the purchase of the SuperNova perpetuated not only advances in his research and those of his institutional colleagues, but of several collaborators as well. Next, Dr. Daron Janzen from St. Catherine University presented a seminar titled "Benchtop Diffractometers: Implementation of an X-ray Crystallography Consortium of Undergraduate Institutions Based at St. Catherine University," during which Dr. Janzen highlighted work performed using the XtaLAB mini benchtop diffractometer by his research students, as well as those of other faculty members and their students in a consortium of primarily undergraduate institutions. The third speaker, Dr. Rene Boere from the University of Lethbridge, presented his seminar titled "The first six months: user experiences on moving to a SuperNova/CrysAlisPro environment," during which he described his and his department's experiences in resolving some difficult data collections after switching to a SuperNova/CrysAlis^Pro platform. The final user talk titled "Incorporating single crystal X-ray diffraction into the undergraduate curriculum; first steps," was delivered by Dr. Cassandra Eagle from East Tennessee State University, during which she outlined the initial steps for the successful integration of single crystal X-ray diffraction concepts into the undergraduate curriculum. Prior to the lunch break, talks were delivered by Drs. Alexandra Griffin and Angela Criswell, Global Product Managers from ROD for small molecule and macromolecular crystallography respectively, on the new products available from Rigaku Oxford Diffraction for both crystallographic disciplines.

After lunch, all users moved to the Applications Lab, where Drs. Mathias Meyer, Horst Puschmann and Eric Reinheimer led smaller groups in data processing with CrsyAlis^Pro, structure solution and refinement using Olex2/AutoChem and data collection strategies using CrsyAlis^Pro. In these smaller groups, attendees were afforded more intimate interactions with scientists as well as each other, and had the opportunity to see the synergistic efforts that Rigaku Oxford Diffraction has put forth in perpetuating advances in single crystal X-ray diffraction.

Product spotlight: XtaLAB Synergy-R

The World's Fastest Diffractometer
A unique combination of cutting edge technologies allows the XtaLAB Synergy-R to claim the title of "World's Fastest Diffractometer". The synergistic effect of a bright, rotating anode X-ray source, a fast goniometer, an extremely low-noise, photon-counting detector, fast and efficient strategy algorithm, and highly parallelized control/processing software leads to an instrument that can perform a single crystal experiment so rapidly, that for normal crystals, XtaLAB Synergy-R can be considered a walkup structure solution machine. For difficult samples, it can greatly reduce data collection time and it has the flexibility to easily help you optimize your experiment. For more >

Rigaku's XtaLAB Synergy-R for structural analysis of small molecule samples

Lab in the spotlight

Dr. Chilla Malla Reddy
Associate Professor
Department of Chemical Science
Indian Institute of Science Education and Research Kolkata

Dr. C Malla Reddy did his Ph.D. in Supramolecular Chemistry & Crystal engineering from the University of Hyderabad in 2006. Thereafter he continued his research as a post-doctoral fellow at Karlsruhe Institute of Technology, Germany, 2007-2008. He moved to Indian Institute of Science Education and Research (IISER) Kolkata as an assistant professor in the department of chemical sciences. In 2014 he was promoted to associate professor. For the year 2014-2015, he was awarded the prestigious Swarna Jayanti fellowship by the Department of Science and Technology, Government of India.

Crystals that are elastic
See video_s1_xvid under Supporting information

Crystals that bend
See video_s2_xvid under Supporting information
See "Video of bending of crystals of 1a"

Research Interests
The focus of Reddy's research group is to design the properties of organic materials by establishing a reliable structure-property correlation. Their current major projects include (i) the understanding of structure-mechanical property relationship in flexible organic crystals (ii) design of new solid forms of active pharmaceutical ingredients (APIs) with improved mechanical behaviour and tabletability, (iii) establishing design principles for efficient mechanochromic luminescent solid state fluorophores. The general characterization techniques they use include nanoindentation, hot-stage microscopy, Raman spectroscopy, powder and single crystal X-ray diffraction, TGA, DSC, SEM, TEM etc.

Interesting link:

Protopedia Tutorial: How do we get the oxygen we breathe

When we breathe, or respire, oxygen from the air is taken up by blood in our lungs and soon delivered to each of the cells in our body through our circulatory system. Among other uses, our cells use oxygen as the final electron acceptor in a process called aerobic respiration — a process that converts the energy in food and nutrients into a form of energy that the cell can readily use (molecules of ATP, adenosine triphosphate). The cells of large organisms like humans use aerobic respiration because other forms of energy production are less efficient, and oxygen is plentiful. But, although oxygen is transported in our blood to reach each of the cells in our body, oxygen does not dissolve well in blood. So how is oxygen transported in the blood?

Radiation damage within nucleoprotein complexes studied by macromolecular X-ray crystallography. Bury, Charles S.; Carmichael, Ian; McGeehan, John E.; Garman, Elspeth F. Radiation Physics & Chemistry. Nov2016, Vol. 128, p118-125. 8p. DOI: 10.1016/j.radphyschem.2016.05.023.

Structurally well-characterized new multinuclear Cu(II) and Zn(II) clusters: X-ray crystallography, theoretical studies, and applications in catalysis. Ansari, Istikhar A.; Sama, Farasha; Raizada, Mukul; Shahid, M.; Ahmad, Musheer; Siddiqi, Zafar A. New Journal of Chemistry. Nov2016, Vol. 40 Issue 11, p9840-9852. 13p. DOI: 10.1039/c6nj02150f.

Waters in room temperature and cryo protein crystal structures. Carugo, Oliviero. Zeitschrift für Kristallographie. Crystalline Materials. Nov2016, Vol. 231 Issue 11, p681-689. 9p. DOI: 10.1515/zkri-2016-1986.

A public database of macromolecular diffraction experiments. Grabowski, Marek; Langner, Karol M.; Cymborowski, Marcin; Porebski, Przemyslaw J.; Sroka, Piotr; Zheng, Heping; Cooper, David R.; Zimmerman, Matthew D.; Elsliger, Marc-André; Burley, Stephen K.; Minor, Wladek. Acta Crystallographica Section D: Structural Biology. Nov2016, Vol. 72 Issue 11, p1181-1193. 12p. DOI: 10.1107/S2059798316014716.

Radiation Damage in Macromolecular Crystallography. Garman, Elspeth F.; Weik, Martin. Synchrotron Radiation News. Nov/Dec2016, Vol. 28 Issue 6, p15-19. 5p. DOI: 10.1080/08940886.2015.1101322.

Isostructural polymorphs: qualitative insights from energy frameworks. Jha, Kunal Kumar; Dutta, Sanjay; Kumar, Vijay; Munshi, Parthapratim. CrystEngComm. 11/21/2016, Vol. 18 Issue 43, p8497-8505. 9p. DOI: 10.1039/c6ce01501h.

A Versatile System for High-Throughput In Situ X-ray Screening and Data Collection of Soluble and Membrane-Protein Crystals. Broecker, Jana; Klingel, Viviane; Wei-Lin Ou; Balo, Aidin R.; Kissick, David J.; Ogata, Craig M.; Anling Kuo; Ernst, Oliver P. Crystal Growth & Design. Nov2016, Vol. 16 Issue 11, p6318-6326. 9p. DOI: 10.1021/acs.cgd.6b00950.

Macromolecular Crystallography. Ralston, Corie; Moffat, Keith. Synchrotron Radiation News. Nov/Dec2016, Vol. 28 Issue 6, p2-3. 2p. DOI: 10.1080/08940886.2015.1101319.

Structural and functional basis of phospholipid oxygenase activity of bacterial lipoxygenase from Pseudomonas aeruginosa. Banthiya, Swathi; Kalms, Jacqueline; Galemou Yoga, Etienne; Ivanov, Igor; Carpena, Xavi; Hamberg, Mats; Kuhn, Hartmut; Scheerer, Patrick. BBA - Molecular & Cell Biology of Lipids. Nov2016, Vol. 1861 Issue 11, p1681-1692. 12p. DOI: 10.1016/j.bbalip.2016.08.002.

Time-Resolved In Situ X-ray Diffraction Reveals Metal-Dependent Metal-Organic Framework Formation. Wu, Yue; Henke, Sebastian; Kieslich, Gregor; Schwedler, Inke; Yang, Miaosen; Fraser, Duncan A. X.; O'Hare, Dermot. Angewandte Chemie International Edition. 11/2/2016, Vol. 55 Issue 45, p14081-14084. 4p. DOI: 10.1002/anie.201608463.

Syntheses, supramolecular structures, and thermal behavior of heteronuclear gold(III)–mercury(II) dithiocarbamatochloride complexes [Au{S₂CN(CH₃)}][HgCl₄] and ([Au{S₂CN(C₂H₅)₂}₂]₂[Hg₂Cl₆]•OC(CH₃)₂)_n by ¹³C MAS NMR, X-ray diffraction, and simultaneous thermal analysis data. Loseva, O.; Rodina, T.; Smolentsev, A.; Ivanov, A. Russian Journal of Coordination Chemistry. Nov2016, Vol. 42 Issue 11, p719-729. 11p. DOI: 10.1134/S1070328416110063.

Synthesis and structural characterization of iron complexes bearing N-aryl-phenanthren-o-iminoquinone ligands. Xu, Bin; Ma, Anjie; Jia, Teng; Hao, Zhiqiang; Gao, Wei; Mu, Ying. Dalton Transactions: An International Journal of Inorganic Chemistry. 11/28/2016, Vol. 45 Issue 44, p17966-17973. 8p. DOI: 10.1039/c6dt03572h.

Structural insight into proteolytic activation and regulation of the complement system. Schatz-Jakobsen, Janus A.; Pedersen, Dennis V.; Andersen, Gregers R. Immunological Reviews. Nov2016, Vol. 274 Issue 1, p59-73. 15p. DOI: 10.1111/imr.12465.

pHLIP Peptide Interaction with a Membrane Monitored by SAXS. Narayanan, Theyencheri; Weerakkody, Dhammika; Karabadzhak, Alexander G.; Anderson, Michael; Andreev, Oleg A.; Reshetnyak, Yana K. Journal of Physical Chemistry B. Nov2016, Vol. 120 Issue 44, p11484-11491. 8p. DOI: 10.1021/acs.jpcb.6b06643.

Monte Carlo simulation algorithm for B-DNA. Howell, Steven C.; Qiu, Xiangyun; Curtis, Joseph E. Journal of Computational Chemistry. 11/5/2016, Vol. 37 Issue 29, p2553-2563. 12p. DOI: 10.1002/jcc.24474.

The Structure of Treponema pallidum Tp0624 Reveals a Modular Assembly of Divergently Functionalized and Previously Uncharacterized Domains. Parker, Michelle L.; Houston, Simon; Wetherell, Charmaine; Cameron, Caroline E.; Boulanger, Martin J. PLoS ONE. 11/10/2016, Vol. 11 Issue 11, p1-17. 17p. DOI: 10.1371/journal.pone.0166274.

Crystal structures of two nitroreductases from hypervirulent Clostridium difficile and functionally related interactions with the antibiotic metronidazole. Wang, Bing; Powell, Samantha M.; Hessami, Neda; Najar, Fares Z.; Thomas, Leonard M.; Karr, Elizabeth A.; West, Ann H.; Richter-Addo, George B. Nitric Oxide. Nov2016, Vol. 60, p32-39. 8p. DOI: 10.1016/j.niox.2016.09.003.

Collaborative crystal structure prediction. Hwang, Sangheum; Yoo, Jiho; Lee, Chanhee; Lee, Sang Hyun. Expert Systems with Applications. Nov2016, Vol. 63, p222-230. 9p. DOI: 10.1016/j.eswa.2016.07.001.

Crystal Structure of a Complex of the Intracellular Domain of Interferon λ Receptor 1 (IFNLR1) and the FERM/SH2 Domains of Human JAK1. Zhang, Di; Wlodawer, Alexander; Lubkowski, Jacek. Journal of Molecular Biology. Nov2016, Vol. 428 Issue 23, p4651-4668. 18p. DOI: 10.1016/j.jmb.2016.10.005.

Structure-Based Design of a Covalent Inhibitor of the SET Domain-Containing Protein 8 (SETD8) Lysine Methyltransferase. Butler, Kyle V.; Anqi Ma; Wenyu Yu; Fengling Li; Tempel, Wolfram; Babault, Nicolas; Pittella-Silva, Fabio; Jason Shao; Junyi Wang; Minkui Luo; Vedadi, Masoud; Brown, Peter J.; Arrowsmith, Cheryl H.; Jian Jin. Journal of Medicinal Chemistry. Nov2016, Vol. 59 Issue 21, p9881-9889. 9p. DOI: 10.1021/acs.jmedchem.6b01244.

Structure of Escherichia coli Flavodiiron Nitric Oxide Reductase. Romão, Célia V.; Vicente, João B.; Borges, Patrícia T.; Victor, Bruno L.; Lamosa, Pedro; Silva, Elísio; Pereira, Luís; Bandeiras, Tiago M.; Soares, Cláudio M.; Carrondo, Maria A.; Turner, David; Teixeira, Miguel; Frazão, Carlos. Journal of Molecular Biology. Nov2016, Vol. 428 Issue 23, p4686-4707. 22p. DOI: 10.1016/j.jmb.2016.10.008.

Book review

Fashion, Faith and Fantasy in the New Physics of the Universe, Roger Penrose, Princeton University Press, Princeton, 2016, 520 pages, ISBN: 978-0-691-11979-3.

This book is the result of a series of lectures Roger Penrose gave at Princeton in the early 2000s. I heard about it on Science Friday so I bought a copy. Be forewarned: this is not light reading. This is not a text book, but the concepts might have been better related had this been presented as a textbook.

The first three chapters cover the fields of String Theory (Fashion), Quantum Field Theory (Faith) and the Big Bang Theory with Inflation (Fantasy). The titles of the chapters are meant to let the reader know how Penrose feels about the particular subject.

The chapters on String Theory and the Big Bang Theory receive treatments that suggest there are fundamental flaws with both theories: many more than four dimensions for the former and inflation after the Big Bang for the latter. He makes a good point that both theories are virtually impossible to prove and physics should focus on that which can be proven. The chapter on Quantum Field Theory concludes with the paradigm that the current theory works well enough "for all practical purposes."

I interpret the first three chapters as a diatribe against the aforementioned theories that allows Penrose to segue into the final chapter. Here he makes the case for his own pet theory, Twistor Theory (A New Physics for the Universe). The chapter ends with a discussion on conformal cyclic cosmology. CCC suggests that we are simply in a never ending cycle of big bang (minimum entropy) to black hole death (maximum entropy) and ultimately a sea of massless particles resulting in another big bang, over a time period on the order of 10¹⁰⁰ years for each cycle.

There is a quote at the end that seems relevant today. One could remove "scientific" from the paragraph and describe a broader problem with information glut:

Let me end by making a few final comments about the role of fashion in its frequent grip on scientific ideas. I very much admire and benefit from the way that modern technology, mainly by way of the internet, allows immediate access to so much of the broadening body of scientific knowledge. Yet I fear that this very breadth may itself led to a tightening of the grip of fashion. There is so much out there which is now so accessible that it is extremely difficult to know which things among that multitude contain new ideas to which attention should be paid. How does one make judgments as to what may be important and what owes its prominence merely to its popularity?

There is a detailed mathematical appendix that covers some of the concepts in the main text, including iterated exponents, fields and topology.

You will need your thinking cap for this book, and be prepared to expand your horizons.

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