Crystallography Newsletter
Volume 8, No. 02, February 2016

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


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: EZ Screen Builder

EZ Screen Builder


The EZ Screen Builder is a fast and simple way to follow up on any crystallization hit!

Use this tool to custom design your optimization screen around any commercial screen condition. The EZ Screen Builder allows you to select and modify solution conditions to meet your needs. After designing your optimization screen, you can choose either to download pipetting instructions or to order the block directly from www.RigakuReagents.com for same day shipment to your lab.

Survey of the month

Monthly Survey


Video of the month

The New Chemistry of
Metal-Organic Frameworks (MOF's)


Omar Yaghi,
Chemistry Professor, UC Berkeley
Director, Molecular Foundry, Berkeley Lab


Upcoming events

PITTCON, March 6 – 10, 2016 in Atlanta, GA, USA

Radiation Damage Workshop, March 9 – 11, 2016 in Lund, Sweden

ACS – Spring, March 13 – 17, 2016 in San Diego, CA, USA

Annual Meeting of the German Crystallographic Society (DGK), March 14 – 17, 2016 in Stuttgart, Germany

See full list >

Last month's survey

In many parts of the world at the moment the weather is quite cold and dreary. In between experiments are you daydreaming about




















book cover

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Crystallography in the news

Feburary 1, 2016. Sodium is constantly transported across our cells membrane in exchange for protons. This regulates sodium levels, cell volume and internal pH. Researchers, led by Dr. David Drew at the Department of Biochemistry and Biophysics at Stockholm University, have now been able to show the details of how the protein NapA carries out this sodium/proton transporter process.

Febuary 1, 2016. Johns Hopkins biologist Scott Bailey receives $250,000 President's Frontier Award. Bailey has made breakthroughs visualizing the atomic structure of a large multiprotein complex with a key role in bacterial immunity. This sets the stage for the development of new drugs to prevent antibiotic resistance and may someday lead to precision treatments for genetic disorders.

February 8, 2016. Researchers at Karolinska Institutet in Sweden have taken a step closer to understanding the mechanism that leads to the fusion of egg and sperm at fertilisation. They have determined the 3D structure of Juno, a mammalian egg protein essential for triggering gamete fusion. Their findings are not only interesting from an evolutionary perspective, but also reveal the shape of a possible target for future non-hormonal contraceptives.

Feburary 10, 2016. An international team of scientists led by the University of Liverpool has produced a "structural movie" revealing the step-by-step creation of S-Adenosylmethionine (SAMe), a major methyl donor that is produced by the highly conserved Methionine Adenosyltransferase (MAT) family of enzymes. Methylation is an underpinning process of life and provides control for biological processes such as DNA synthesis, cell growth and apoptosis.

February 14, 2016. Researchers from the Fred Hutchinson Cancer Research Center report the development and validation of computational methods for de novo design of tandem repeat protein architectures driven purely by geometric criteria defining the inter-repeat geometry, without reference to the sequences and structures of existing repeat protein families. They have applied these methods to design a series of closed a-solenoid repeat structures (a-toroids) in which the inter-repeat packing geometry is constrained so as to juxtapose the amino (N) and carboxy (C) termini; several of these designed structures have been validated by X-ray crystallography.

February 15, 2016. Researchers from Arizona State University (ASU), Deutsches Elektronen-Synchrotron (DESY) and Stanford Linear Accelerator Laboratory (SLAC) describe a simple way to determine the X-ray crystal structure of proteins and other molecules, many of which are inaccessible by existing methods. The work demonstrated that it is possible to use the continuous diffraction of imperfect crystals to obtain better molecular images than with Bragg peaks alone.

Feburary 19, 2016. Trinity College Dublin researchers, led by Professor of Membrane Structural and Functional Biology Martin Caffrey, have produced the first molecular blueprint of Globomycin – a naturally occurring antimicrobial agent which experts say could prove to be an effective infection killer into the future. Globomycin's potential ability to bind to and stop a particular enzyme behind the production of a protein that can lead to antibiotic resistance was marked out some time ago.

Product spotlight: PX Scanner

The PX Scanner is a fully integrated system for in situ screening and data collection of crystals in SBS crystallization plates and microfluidic chips. This turnkey system combines sample visualization and in situ X-ray screening to deliver a compact tool to evaluate sample quality without the need to remove crystals from their protected growth environment. The system includes a microfocus sealed tube Cu X-ray generator, crystal imaging system, automated tray stage with 6 degrees of tilt, CCD detector and intuitive CrystalEyes software. With the PX Scanner, one can quickly identify whether a crystal contains salt or protein and evaluate diffraction quality for samples without removal from the crystallization plate.

The PX Scanner has been found to be useful not only for evaluating crystals of macromolecular compounds but also as a way of evaluating crystalline sponge crystals before they are used to soak up small quantities of valuable target molecules.

PX Scanner
In situ X-ray crystallography system with imager

For more about the PX Scanner.

Lab in the spotlight

Prof. Makoto Fujita Professor Makoto Fujita
Department of Applied Chemistry
The University of Tokyo

Single crystal X-ray analysis is a powerful tool for determining the structures of molecules and is widely used both in academic and industrial research. However, this analytical method has an intrinsic limitation that target samples have to be crystallized beforehand. As a result, most oily compounds or extremely small-quantity samples have not been analyzed by single crystal X-ray study solely because there was no way to crystallize them.

Prof. Makoto Fujita Research Group

Prof. Makoto Fujita's research group at the University of Tokyo's Graduate School of Engineering solved this problem using a material called a "crystalline sponge". Crystalline sponges are porous coordination network crystals capable of aligning incoming guest molecules inside their pores along an ordered framework of organic ligands and metal ions. Once the incoming guest molecules are regularly ordered, the resulting crystalline sponges meet the requirement for X-ray analysis, thus the structure of the guest molecule can be determined by X-ray crystallography without crystallizing the sample itself. The Fujita group demonstrated that molecular structures of non-crystalline samples were unambiguously determined by simply soaking a crystal of crystalline sponge in a solution containing from 80 ng up to 5 µg of the target sample.

Makoto Fujita Research

Useful tools: The Gavrog Project

Gavrog stands for Generation, Analysis and Visualization of Reticular Ornaments using Gavrog. It is about pretty pictures, solid state chemistry and rather involved mathematics. Think Escher, crystals, Alhambra, soap bubbles. If you find the pictures on this page interesting, or appealing, you might like to check it out.

Selected recent crystallographic papers

Macromolecular diffractive imaging using imperfect crystals. Kartik Ayyer,Oleksandr M. Yefanov, Dominik Oberthür, Shatabdi Roy-Chowdhury, Lorenzo Galli, Valerio Mariani, Shibom Basu, Jesse Coe, Chelsie E. Conrad, Raimund Fromme, Alexander Schaffer, Katerina Dörner, Daniel James, Christopher Kupitz, Markus Metz, Garrett Nelson, Paulraj Lourdu Xavier, Kenneth R. Beyerlein, Marius Schmidt, Iosifina Sarrou, John C. H. Spence, Uwe Weierstall, Thomas A. White, Jay-How Yang, Yun Zhao et al. Nature. 530, 202-206 (11 February 2016). DOI: 10.1038/nature16949.

Crystal structures reveal the molecular basis of ion translocation in sodium/proton antiporters. Mathieu Coincon, Povilas Uzdavinys, Emmanuel Nji, David L. Dotson, Iven Winkelmann, Saba Abdul-Hussein, Alexander D. Cameron, Oliver Beckstein, David Drew. Nature Structure and Molecular Biology (1 February 2016). DOI: 10.1038/nsmb.3164.

Methods in integrated structural biology. Owens, Ray. Methods. Feb2016, Vol. 95, p1-2. 2p. DOI: 10.1016/j.ymeth.2015.12.014.

A structured interdomain linker directs self-polymerization of human uromodulin. Bokhove, Marcel; Kaoru Nishimura; Brunati, Martina; Ling Han; de Sanctis, Daniele; Rampoldi, Luca; Jovine, Luca. Proceedings of the National Academy of Sciences of the United States of America. 2/9/2016, Vol. 113 Issue 6, p1552-1557. 6p. DOI: 10.1073/pnas.1519803113.

The Difference of Structural State and Deformation Behavior between Teenage and Mature Human Dentin. Panfilov, Peter; Zaytsev, Dmitry; Antonova, Olga V.; Alpatova, Victoria; Kiselnikova, Larissa P. International Journal of Biomaterials. 2/16/2016, p1-7. 7p. DOI: 10.1155/2016/6073051.

Structural Features of Ion Transport and Allosteric Regulation in Sodium-Calcium Exchanger (NCX) Proteins. Giladi, Moshe; Tal, Inbal; Khananshvili, Daniel. Frontiers in Physiology. 2/9/16, p1-13. 13p. DOI: 10.3389/fphys.2016.00030.

Understanding the fabric of protein crystals: computational classification of biological interfaces and crystal contacts. Capitani, Guido; Duarte, Jose M.; Baskaran, Kumaran; Bliven, Spencer; Somody, Joseph C. Bioinformatics. 2/15/2016, Vol. 32 Issue 4, p481-489. 9p. DOI: 10.1093/bioinformatics/btv622.

Structural studies on tobacco streak virus coat protein: Insights into the pleomorphic nature of ilarviruses. Gulati, Ashutosh; Alapati, Kavitha; Murthy, Abhinandan; Savithri, H.S; Murthy, M.R.N. Journal of Structural Biology. Feb2016, Vol. 193 Issue 2, p95-105. 11p. DOI: 10.1016/j.jsb.2015.12.007.

Structural basis for human PRDM9 action at recombination hot spots. Patel, Anamika; Horton, John R.; Wilson, Geoffrey G.; Xing Zhang; Xiaodong Cheng. Genes & Development. 2/1/2016, Vol. 30 Issue 3, p257-265. 9p. DOI: 10.1101/gad.274928.115.

New alicyclic thiosemicarbazone chelated zinc(II3 antitumor complexes: Interactions with DNA/protein, nuclease activity and inhibition of topoisomerase-I. Vikneswaran, R.; Eltayeb, Naser Eltaher; Ramesh, S.; Yahya, R. Polyhedron. Feb2016, Vol. 105, p89-95. 7p. DOI: 10.1016/j.poly.2015.12.012.

A tale of the epidermal growth factor receptor: The quest for structural resolution on cells. Tynan, Christopher J.; Lo Schiavo, Valentina; Zanetti-Domingues, Laura; Needham, Sarah R.; Roberts, Selene K.; Hirsch, Michael; Rolfe, Daniel J.; Korovesis, Dimitrios; Clarke, David T.; Martin-Fernandez, Marisa L. Methods. Feb2016, Vol. 95, p86-93. 8p. DOI: 10.1016/j.ymeth.2015.10.009.

Hybrid Structural Analysis of the Arp2/3 Regulator Arpin Identifies Its Acidic Tail as a Primary Binding Epitope. Fetics, Susan; Thureau, Aurélien; Campanacci, Valérie; Aumont-Nicaise, Magali; Dang, Irène; Gautreau, Alexis; Pérez, Javier; Cherfils, Jacqueline. Structure. Feb2016, Vol. 24 Issue 2, p252-260. 9p. DOI: 10.1016/j.str.2015.12.001.

The structure of Resuscitation promoting factor B from M. tuberculosis reveals unexpected ubiquitin-like domains. Ruggiero, Alessia; Squeglia, Flavia; Romano, Maria; Vitagliano, Luigi; De Simone, Alfonso; Berisio, Rita. BBA – General Subjects. Feb2016, Vol. 1860 Issue 2, p445-451. 7p. DOI: 10.1016/j.bbagen.2015.11.001.

Characterization of the C-Terminal Nuclease Domain of Herpes Simplex Virus pUL15 as a Target of Nucleotidyltransferase Inhibitors. Takashi Masaoka; Haiyan Zhao; Hirsch, Danielle R.; D'Erasmo, Michael P.; Meck, Christine; Varnado, Brittany; Gupta, Ankit; Meyers, Marvin J.; Baines, Joel; Beutler, John A.; Murelli, Ryan P.; Liang Tang; Le Grice, Stuart F. J. Biochemistry. 2/9/2016, Vol. 55 Issue 5, p809-819. 11p. DOI: 10.1021/acs.biochem.5b01254.

Extension of the sasCIF format and its applications for data processing and deposition. Kachala, Michael; Westbrook, John; Svergun, Dmitri. Journal of Applied Crystallography. Feb2016, Vol. 49 Issue 1, p302-310. 8p. DOI: 10.1107/S1600576715024942.

The maturation mechanism of γ-glutamyl transpeptidases: Insights from the crystal structure of a precursor mimic of the enzyme from Bacillus licheniformis and from site-directed mutagenesis studies. Pica, Andrea; Chi, Meng-Chun; Chen, Yi-Yu; d'Ischia, Marco; Lin, Long-Liu; Merlino, Antonello. BBA – Proteins & Proteomics. Feb2016, Vol. 1864 Issue 2, p195-203. 9p. DOI: 10.1016/j.bbapap.2015.10.006.

Spherical polar Fourier assembly of protein complexes with arbitrary point group symmetry. Ritchie, David W.; Grudinin, Sergei. Journal of Applied Crystallography. Feb2016, Vol. 49 Issue 1, p158-167. 9p. DOI: 10.1107/S1600576715022931.

Reduction of lattice disorder in protein crystals by high-pressure cryocooling. Huang, Qingqiu; Gruner, Sol M.; Kim, Chae Un; Mao, Yuxin; Wu, Xiaochun; Szebenyi, Doletha M. E. Journal of Applied Crystallography. Feb2016, Vol. 49 Issue 1, p149-157. 8p. DOI: 10.1107/S1600576715023195.

Safeguarding Structural Data Repositories against Bad Apples. Minor, Wladek; Dauter, Zbigniew; Helliwell, John R.; Jaskolski, Mariusz; Wlodawer, Alexander. Structure. Feb2016, Vol. 24 Issue 2, p216-220. 5p. DOI: 10.1016/j.str.2015.12.010.

Three-dimensional cobalt(II) and cadmium(II) MOFs containing 1,4-naphthalenedicarboxylate: Catalytic activity of Cd-MOF. Choi, In-Hwan; Kim, Youngmee; Lee, Do Nam; Huh, Seong. Polyhedron. Feb2016, Vol. 105, p96-103. 8p. DOI: 10.1016/j.poly.2015.12.022.

DARA: a web server for rapid search of structural neighbours using solution small angle X-ray scattering data. Kikhney, Alexey G.; Panjkovich, Alejandro; Sokolova, Anna V.; Svergun, Dmitri I. Bioinformatics. 2/15/2016, Vol. 32 Issue 4, p616-618. 3p. DOI: 10.1093/bioinformatics/btv611.

Structural characterization of the N-terminal part of the MERS-CoV nucleocapsid by X-ray diffraction and small-angle X-ray scattering. Papageorgiou, Nicolas; Lichière, Julie; Baklouti, Amal; Ferron, François; Sévajol, Marion; Canard, Bruno; Coutard, Bruno. Acta Crystallographica Section D: Structural Biology. Feb2016, Vol. 72 Issue 2, p192-202. 10p. DOI: 10.1107/S2059798315024328.

Ordering of protein and water molecules at their interfaces with chitin nano-crystals. Valverde Serrano, Clara; Leemreize, Hanna; Bar-On, Benny; Barth, Friedrich G.; Fratzl, Peter; Zolotoyabko, Emil; Politi, Yael. Journal of Structural Biology. Feb2016, Vol. 193 Issue 2, p124-131. 8p. DOI: 10.1016/j.jsb.2015.12.004.

Monitoring Photochemical Reactions in Single Crystals by X-ray Diffraction: Practical Aspects. Konieczny, Krzysztof; Bakowicz, Julia; Turowska-Tyrk, Ilona. Journal of Chemical Crystallography. Feb2016, Vol. 46 Issue 2, p77-83. 7p. DOI: 10.1007/s10870-016-0630-6.

Book review:

Perspectives in Crystallography
By John Helliwell, CRC Press, Boca Raton, FL, 2016, 171 pages, ISBN: 978-1-4987-3210-9.

Helliwell's Perspectives is a collection of articles and lectures by the author celebrating the 100th anniversary of the first crystal structures (1912) and the UNESCO International Year of Crystallography. The book covers a broad range of topics in crystallography from the author's perspective, hence the title. Some of the chapters have already been published in Crystallography Reviews.

Section 1 consists of a single chapter in which the author attempts to answer the question for the general public "What is crystal structure analysis?" Helliwell describes how the question was answered at several venues including his home institution, the University of Manchester, and the Prisoners' Education Trust.

I found the next section very interesting. Chapter 2 succinctly describes the first diffraction experiments by the Braggs before and during WWI while Chapter 3 provides retrospectives by W.H. Bragg, W. L. Bragg, P. P. Ewald and D. C. Phillips on the work described in Chapter 2.

Section III is titled "Aspects of Crystallography Research" and consists of 4 chapters. Chapter 4 is a transcript of the author's Lonsdale Lecture at the 2011 British Crystallographic Association. I found the short biography of Kathleen Lonsdale at the beginning enlightening. I knew of her importance with respect to the early crystal structures of organics and the creation of the original International Tables for Crystallography, but I did not know the details of her life's story. The lecture then describes the history of the use of synchrotron radiation by the crystallographic community.

The next two chapters cover more specific topics: a comparison of several programs for predicting protonation versus X-ray diffraction results and the structural of crustacyanin. The last chapter in this section is a short prospective on the future of crystallography.

The last section and chapter looks at how crystallography has been a part, and will continue be a part, of the eight Millennium Development Goals set forth by the UN in 2000. One of the goals is to promote gender equality and empower women. The author points out that, compared to other sciences, crystallography has more balance. Many of the goals are related to the alleviation of human pain and suffering—clearly crystallography excels through a better understanding of the world around us.

Review by Joseph D. Ferrara, Ph.D.
Chief Science Officer, Rigaku


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