Crystallography in the News

September 1, 2018. Victoria Shennan, a Scottish artist, collaborated with Dr. Linda Long, a biochemist at Exeter University who has developed a method to generate music that represents the three-dimensional structure of proteins. Using the data from X-ray crystallography, the computer assigns note sequences to specific 3D features of the protein.

September 6, 2018. According to a new study, the distribution of prime numbers is similar to the positioning of atoms inside some crystalline materials. When scientists, led by Salvatore Torquato, Professor of Chemistry and the Princeton Institute for the Science and Technology of Materials, at Princeton University compared the pattern of prime numbers along a lengthy line of numbers with the atomic patterns revealed when crystals are blasted with X-rays, they were surprised by the similarities.

September 6, 2018. One of the major known causes of amyotrophic lateral sclerosis (ALS) is a mutation in the gene encoding SOD1 that cause the protein to fold in the wrong way, and aggregated SOD1 has been found in the motor neurons of both familial and sporadic ALS patients. Researchers at the Umeå University in Sweden have now discovered how the rogue protein can "transmit" its morbidity to other normal proteins.

September 6, 2018. Maria Selmer's research group at Uppsala University used X-ray crystallography to show how an antibiotic resistance enzyme (AadA) is able to recognise and inactivate two chemically different antibiotics (streptomycin and spectinomycin).

September 10, 2018. A research collaboration between Department of Molecular Biology and Genetics at Aarhus University and two American universities reveals that bacterial translational elongation factors (Ef-Tu) – and probably also other GTPases – structure and function are far more complex than previously assumed. In Søren Thirup's group, X-ray crystallographic analysis of E. coli EF-Tu has shown that EF-Tu bound to a variant of GTP, GDPNP, can also occur in the "off" state, which is characterized by a more open structure.

September 12, 2018. Ten outstanding articles have been shortlisted for this year's Max Perutz Science Writing Award, the Medical Research Council's annual writing competition. The award is named in honor of one of the UK's most outstanding scientists and communicators. Dr. Max Perutz. Max, who died in 2002, was awarded the 1962 Nobel Prize in Chemistry for his work using X-ray crystallography to study the structures of globular proteins.

September 12, 2018. A team of researchers at the University of Manchester has created the most tangled interlocked molecule ever. In their paper published in the journal Nature Chemistry, the group describes creating the knot and their hope that such knots will one day become useful.

September 13, 2018. Scientists at Monash University's Biomedicine Discovery Institute and the ARC Centre of Excellence in Advanced Molecular Imaging, working with the Australian Synchrotron, have answered a key question about how a dangerous bacterium, Clostridium perfringens, shares its genetic information.

September 16, 2018. Rutgers University leaders formally opened their new $115 million science building. The Chemistry and Chemical Biology building was funded largely by New Jersey's Building Our Future Bond Act. The four-story facility in Piscataway has everything students and researchers need to perform state-of-the-art research, school authorities said. It has a humidity and temperature-controlled climate, a microscopy suite, and nuclear magnetic resonance spectroscopy and X-ray crystallography laboratories.

September 16, 2018. Sabrina Davies, a Ph.D. student at the University of Western Australia, was part of a team that used X-ray crystallography to identify a compound, karrikin, that causes plants to germinate. The work has implications for food security in the future.

September 17, 2018. Chemists from RUDN University (Moscow) carried out detailed analysis of the nature of intermolecular bonds between nitrogen and chlorine in the molecules of azo dyes and defined their photochromic properties. The scientists also clarified the importance of hydrogen and halogen intermolecular bonds in the stabilization of dyes structure. The research can be useful for all the types of azo dyes applications.

Product Spotlight

XtaLAB Synergy-S

With your success utmost in our minds, we have developed the XtaLAB Synergy-S X-ray diffractometer for single crystal X-ray diffraction. Using a combination of leading edge components and user-inspired software tied together through a highly parallelized architecture, the XtaLAB Synergy-S produces fast, precise data in an intelligent fashion.

The system is based around the PhotonJet-S series of microfocus X-ray sources that incorporate continuously variable divergence slits. These third-generation sources have been designed to maximize X-ray photons at the sample by using a combination of new optics, new, longer life, tubes and an improved alignment system. PhotonJets are available in Cu, Mo or Ag wavelengths in either a single or dual source configuration.

The XtaLAB Synergy-S single crystal X-ray diffractometer comes with kappa goniometer that incorporates fast motor speeds and a unique telescopic two-theta arm to provide total flexibility for your diffraction experiment. The system is also equipped with your choice of HPC X-ray detector, including the HyPix-6000HE, PILATUS3 R 200K, PILATUS3 R 300K or EIGER 1M.

Benefits

• Extremely high performance due to bright source, noise-free X-ray detector and fast goniometer speeds
• Continuously variable divergence slit option lets you resolve reflections from long unit cells.
• Minimal downtime with longer X-ray tube lifetime - supported by online diagnostics and troubleshooting
• Compact design to fit in your laboratory

Features

• High source flux and increased goniometer speed to allow quicker, more agile experiments
• Unique telescopic two-theta arm to reach both longer and shorter crystal-to-detector distances
• Enhanced kappa goniometer design with symmetrical 2θ positioning
• Improved X-ray optic alignment mechanism for easy maintenance
• User-inspired cabinet design for improved workflow
• New electronically controlled brightness of cabinet and crystal lighting

School in the Spotlight

Zürich School of Crystallography 2018 in Tianjin, China

The highly regarded Zürich School of Crystallography (ZSC) this year took place in the School of Pharmaceutical Science and Technology (SPST) at Tianjin University from June 17 – 28. The school focusses on intensively training a small group of lucky participants. For this 8th school, 20 participants where handpicked from China, Hong Kong and Thailand. Regular tutors Tony Linden, Olivier Blacque, Hans-Beat Bürgi, Lukas Palatinus, Michael Wörle, Bernd Schweizer and Gervais Chapius were joined by Richard Cooper from Oxford, Ian Williams from HKUST and Junliang Sun from Peking University to train the participants. The ZSC endeavors to maintain a favorable student:tutor ratio of 2:1, ensuring each participant gets enough tutelage and leaves equipped with enough theory and practice to determine their own structures or recognize when to seek help.

With a structure of 2 hours of lectures followed by 2 hours of practical work, participants work through three sets of structures intended to familiarize them with structure determination and validation with the Olex² software package from OlexSys. While working through these problems, problem complexity is slowly increased to provide a challenging set of instructive problems to give participants a broad experience of crystallographic techniques and approaches.

The school made use of Rigaku equipment including a XtaLAB Synergy-S and a dual port XtaLAB Synergy Custom FR-X Rotating Anode system at the SPST as well as a SuperNova diffractometer at the School of Science. Through using these instruments, participants were able to gain hands-on experience with data collection procedures using their own samples on a range of instrumentation. Yan Zier from Rigaku Beijing China attended the school to assist with the brand new instruments.

This was the first Zurich School in China and the very successful outcome of the final two-hour written exam showed how really hard everybody worked. Feedback from students was very positive. Professors Jay Siegel, Kim Baldridge and SPST hosted the school with most of the local organisation effort made by Jun Xu.

Rigaku Oxford Diffraction was very pleased and proud to help financially support this unique school and to contribute with the expertise of our applications team.

If you are you interested in the next school, see
The Zürich School of Crystallography
University of Zürich, June 16 – 27, 2019
http://www.chem.uzh.ch/linden/zsc

Useful Link

DECOR

Amy Sarjeant, ACA Past President and GM at CCDC, pointed out this web site to me: https://decor.cst.temple.edu/ which is a wiki-style repository of teaching tools for crystallography established by Mike Zdilla at Temple.

A high-performance protein crystallization plate pre-embedded with crosslinked protein microcrystals as seeds. Hou, Hai; Shi, Miao; Chen, Zhong-Hao; Ahmad, Fiaz; Liu, Yue; Yan, Er-Kai; Luo, Chao; Li, Jing; Zhu, Cheng-Long; Deng, Xu-Dong; Yin, Da-Chuan. CrystEngComm. 2018, Vol. 20 Issue 33, p4713-4718. 6p. DOI: 10.1039/c8ce00807h.

The impact of cryosolution thermal contraction on proteins and protein crystals: volumes, conformation and order. Juers, Douglas H.; Farley, Christopher A.; Saxby, Christopher P.; Cotter, Rosemary A.; Cahn, Jackson K. B.; Holton-Burke, R. Conor; Harrison, Kaitlin; Wu, Zhenguo. Acta Crystallographica: Section D, Structural Biology. Sep2018, Vol. 74 Issue 9, p922-938. 16p. DOI: 10.1107/S2059798318008793.

MBP-binding DARPins facilitate the crystallization of an MBP fusion protein. Gumpena, Rajesh; Lountos, George T.; Waugh, David S. Acta Crystallographica: Section F, Structural Biology Communications. Sep2018, Vol. 74 Issue 9, p549-557. 8p. DOI: 10.1107/S2053230X18009901.

Crystallography and Its Impact on Carbonic Anhydrase Research. Lomelino, Carrie L.; Andring, Jacob T.; McKenna, Robert. International Journal of Medicinal Chemistry. 9/13/2018, p1-21. 21p. DOI: 10.1155/2018/9419521.

Identification of a novel tetrameric structure for human apolipoprotein-D. Kielkopf, Claudia S.; Low, Jason K.K.; Mok, Yee-Foong; Bhatia, Surabhi; Palasovski, Tony; Oakley, Aaron J.; Whitten, Andrew E.; Garner, Brett; Brown, Simon H.J. Journal of Structural Biology. Sep2018, Vol. 203 Issue 3, p205-218. 14p. DOI: 10.1016/j.jsb.2018.05.012.

Solubilisation behaviour of poorly water-soluble drugs during digestion of solid SMEDDS. Vithani, Kapilkumar; Hawley, Adrian; Jannin, Vincent; Pouton, Colin; Boyd, Ben J. European Journal of Pharmaceutics & Biopharmaceutics. Sep2018, Vol. 130, p236-246. 11p. DOI: 10.1016/j.ejpb.2018.07.006.

Oxyanion clusters with antielectrostatic hydrogen bonding (AEHB) in tetraalkylammonium hypodiphosphates. Emami, Marzieh; Slepokura, Katarzyna Anna; Trzebiatowska, Monika; Noshiranzadeh, Nader; Kinzhybalo, Vasyl. CrystEngComm. 9/21/2018, Vol. 20 Issue 35, p5209-5219. 11p. DOI: 10.1039/c8ce00880a.

Revisit of Reconstituted 30-nm Nucleosome Arrays Reveals an Ensemble of Dynamic Structures. Zhou, Bing-Rui; Jiang, Jiansheng; Ghirlando, Rodolfo; Norouzi, Davood; Sathish Yadav, K.N.; Feng, Hanqiao; Wang, Rui; Zhang, Ping; Zhurkin, Victor; Bai, Yawen. Journal of Molecular Biology. Sep2018:Part B, Vol. 430 Issue 18, p3093-3110. 18p. DOI: 10.1016/j.jmb.2018.06.020.

Crystal structure of gluconate bound iron(iii) complex: synthesis, characterization and redox properties of the complex in aqueous solution. Stewart, Christopher D.; Arman, Hadi; Benavides, Brenda; Musie, Ghezai T. New Journal of Chemistry. 9/21/2018, Vol. 42 Issue 18, p15088-15096. 9p. DOI: 10.1039/c8nj01886c.

Design and synthesis of a new class of 2,4-thiazolidinedione based macrocycles suitable for Fe³⁺ sensing. Sepay, Nayim; Mallik, Sumitava; Saha, Pranab C.; Mallik, Asok K. New Journal of Chemistry. 9/21/2018, Vol. 42 Issue 18, p15270-15276. 7p. DOI: 10.1039/c8nj01536h.

Ferrocene-based anilides: synthesis, structural characterization and inhibition of butyrylcholinesterase. Altaf, Ataf Ali; Hamayun, Muhammad; Lal, Bhajan; Tahir, Muhammad Nawaz; Holder, Alvin A.; Badshah, Amin; Crans, Debbie C. Dalton Transactions: An International Journal of Inorganic Chemistry. 9/14/2018, Vol. 47 Issue 34, p11769-11781. 13p. DOI: 10.1039/c8dt01726c.

Structural characterization, hydrolytic stability and dynamics of cis-Mo^VIO₂²⁺ hydroquinonate/phenolate complexes. Drouza, Chryssoula; Hadjithoma, Sofia; Nicolaou, Maria; Keramidas, Anastasios D. Polyhedron. Sep2018, Vol. 152, p22-30. 9p. DOI: 10.1016/j.poly.2018.06.008.

Mixed µ-azido-Schiff-base cyclometallated Pd (II) complexes as a template for novel palladacycles bearing bridging carbodiimido, tetrazolato ligands, and tetrazole-thiolato linkers. Jiang, Yuchun; Li, Manna; Liu, Daliang; Song, Xi-Ming; Chang, Xiaohong. Journal of Organometallic Chemistry. Sep2018, Vol. 871, p103-110. 8p. DOI: 10.1016/j.jorganchem.2018.06.009.

Structure and function of l-threonine-3-dehydrogenase from the parasitic protozoan Trypanosoma brucei revealed by X-ray crystallography and geometric simulations. Adjogatse, Eyram; Erskine, Peter; Wells, Stephen A.; Kelly, John M.; Wilden, Jonathan D.; Chan, A. W. Edith; Selwood, David; Coker, Alun; Wood, Steve; Cooper, Jonathan B. Acta Crystallographica: Section D, Structural Biology. Sep2018, Vol. 74 Issue 9, p861-876. 15p. DOI: 10.1107/S2059798318009208.

New insights into oximic ligands: Synthesis and characterization of 1D chains by the use of pyridine 2-amidoxime and polycarboxylates. Mylonas-Margaritis, Ioannis; Winterlich, Meghan; Efthymiou, Constantinos G.; Lazarides, Theodore; Mcardle, Patrick; Papatriantafyllopoulou, Constantina. Polyhedron. Sep2018, Vol. 151, p360-368. 9p. DOI: 10.1016/j.poly.2018.05.027.

Metallo-macrocycles from a library of flexible linkers: 1D cobalt(II) coordination polymers and a supramolecular pipe. Manna, Paulami; Ramathulasamma, Mukara; Bommakanti, Suresh; Das, Samar K. Polyhedron. Sep2018, Vol. 151, p394-400. 7p. DOI: 10.1016/j.poly.2018.05.047.

Sonication-assisted synthesis of a new cationic zinc nitrate complex with a tetradentate Schiff base ligand: Crystal structure, Hirshfeld surface analysis and investigation of different parameters influence on morphological properties. Mousavi, S.A.; Montazerozohori, M.; Masoudiasl, A.; Mahmoudi, G.; White, J.M. Ultrasonics Sonochemistry. Sep2018, Vol. 46, p26-35. 10p. DOI: 10.1016/j.ultsonch.2018.02.050.

Metal- and Multicarboxylate-Dependent Structural Diversity in Metal-Organic Frameworks with Acylamide-Based Ligand. Fan, Huitao; Zhong, Zhiguo; Liu, Shanshan; Li, Bo; Duan, Wenxin. Journal of Chemical Crystallography. Sep2018, Vol. 48 Issue 3, p125-130. 6p. DOI: 10.1007/s10870-018-0719-1.

Co-crystallization of a Versatile Building Block Benzoguanamine with Two Flexible Cyclohexanedicarboxylic Acids. Zheng, Ling Ling; Zhou, Ai Ju; Hu, Sheng. Journal of Chemical Crystallography. Sep2018, Vol. 48 Issue 3, p117-124. 8p. DOI: 10.1007/s10870-018-0718-2.

Crystal structure, optical properties, DFT analysis of new morpholine based Schiff base ligands and their copper(II) complexes: DNA, protein docking analyses, antibacterial study and anticancer evaluation. Dhahagani, Karuthamohamed; Kesavan, Mookkandi Palsamy; Gujuluva Gangatharan Vinoth, Kumar; Rajesh, Jegathalaprathaban; Ravi, Lokesh; Rajagopal, Gurusamy. Materials Science & Engineering: C. Sep2018, Vol. 90, p119-130. 12p. DOI: 10.1016/j.msec.2018.04.032.

Mosquito-larvicidal binary toxin receptor protein (Cqm1): crystallization and X-ray crystallographic analysis. Sharma, Mahima; Lakshmi, Ashwitha; Gupta, Gagan D.; Kumar, Vinay. Acta Crystallographica: Section F, Structural Biology Communications. Sep2018, Vol. 74 Issue 9, p571-577. 6p. DOI: 10.1107/S2053230X18010671.

Book Review

Biological Small Angle Scattering: Theory and Practice^*, Eaton E. Lattman, Thomas D. Grant and Edward H Snell, Oxford University Press, Oxford, 2018, 288 pages, ISBN: 978-019967087-1.

Although I've reviewed at least one other book on small angle scattering (SAS), this volume really addresses the current theory and practice with sufficient detail for a skilled scientist to successfully begin a study in biological small angle scattering. The book is divided into five parts.

Part 1, the introduction, conveys the basic reasons you might perform a SAS experiment and the results you might obtain: particle molecular mass, radius of gyration, pair distance distribution, compactness and molecular envelope.

Part 2 has three chapters. The first two provide a mathematical description of scattering theory and derive the equations for many of the results listed in the Part 1. The last chapter of Part 2 covers the topic of modeling from SAS data.

The first half of Part 3 delves into the issues of how to prepare samples for data collection, data collection, initial interpretation of results at the time of collection, and interpreting final results. The second half of Part 3 considers various aspects of instrumentation both at home and at the beamline, special experimental setups, and neutron scattering.

Part 4 looks at some interesting examples of the application of SAS to biological problems. Here, the authors provide initial findings from XFELs and describe an interesting concept that many will recognize as an application of the Shake-and-Bake algorithm to the SAS problem. The authors conclude with a short epilogue listing a number of references for operating various software packages.

Part 5 contains an appendix, a list of acronyms, a glossary, a list defining major variables, references, and an index.

^* I should disclose I have known two of the authors for many years, there is a picture of a Rigaku system on page 139 and I have no financial interest.

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