Rigaku Oxford Diffraction in the News

The 29th European crystallographic meeting (ECM) was held August 23 – 28, 2015 in beautiful Rovinj, Croatia. As part of the festivities, Rigaku Oxford Diffraction held a raffle for an iWatch. Participants were required to attend the drawing wearing special Rigaku Oxford Diffraction sunglasses.

Crystallography in the news

September 1, 2015. Last summer, Saint Louis University scientists, led by Dr. Nicola Pozzi, made a breakthrough discovery about the way in which blood clots. Through X-ray crystallography, they solved the molecular structure of prothrombin, an important blood-clotting protein, revealing an unexpected, flexible role for a "linker" region that may be the key to developing better life-saving drugs.

September 3, 2015. A Caltech team, in the laboratory of Stephen Mayo, recently created for the first time a synthetic structure made of both protein and DNA. The ability to custom design biological materials combining protein and DNA opens up technological possibilities that were unimaginable just a few decades ago.

September 4, 2015. Book review for X-ray Crystallography, a revised edition of Bill Clegg's popular student text first published in 1998. As with the first edition, the focus is firmly on the use of X-ray crystallography in chemistry, with routine structure determination using in-house equipment being the chief subject.

September 9, 2015. The revolution will not be crystallized: a new method sweeps through structural biology. Cryo-electron microscopy is kicking up a storm by revealing the hidden machinery of the cell.

September 9, 2015. The GPCR Consortium announced the addition of four members from the pharmaceutical industry: Pfizer, Inc., H. Lundbeck A/S, Boehringer Ingelheim, and Taisho Pharmaceutical Co., Ltd. The GPCR Consortium was initiated in 2014 with the purpose of helping coordinate and manage the generation of high-resolution structure-function studies of G-protein coupled receptors (GPCRs).

September 13, 2015. NASA has spent decades promoting the notion that it is doing cutting edge biotech research in space when in fact one of its core efforts uses out of date technology. Neither a Nature issue celebrating the hundredth anniversary of crystallography in 2014 or a Science magazine feature in 2016 mention microgravity/space-based crystallography research. New methods offer even more precise structural information, with no apparent need for the trip to and from space.

September 14, 2015. A report now shows that a technique called microED (microelectron diffraction) can determine the structures of biomolecules at atomic resolution by probing crystals with only about one-millionth the volume of those needed for X-ray crystallography.

September 14, 2015. Prof. Wladek Minor of the Department of Molecular Physiology and Biological Physics at the University of Virginia is working to overcome one of the greatest challenges in his field: the management of astounding amounts of raw data. Much of the older data – the raw X-ray diffraction results – is in danger of being lost, destroyed or forgotten. But Minor is changing that, and he's doing so with only $20,000 worth of hardware acquired with a National Institutes of Health grant.

Product spotlight: Rigaku Reagents Labware

Rigaku Reagents now introduces tools for cryocrystallography, an important technique to mitigate the extent of X-ray damage to crystals and to allow easier transport of samples between crystallization drops and your favorite diffraction facility. This technique requires special tools to freeze and manipulate crystals at liquid nitrogen temperatures, and Rigaku Reagents has everything you need to plan your experiments.

For more information, please visit RigakuReagents.com. Also, make sure to check out our crystallization screens, including our Wizard cryo screen series for optimizing cryoprotectant conditions.

Lab spotlight: Kajander Lab

Tommi Kajander, Ph.D., Team Leader
Structural Biology and Biophysics
Institute of Biotechnology
University of Helsinki

The Kajander group research focuses on structural biology of neuronal contacts in the brain, mainly the leucine rich repeat adhesion proteins and other receptor and membrane proteins continuing on the subject of repeat proteins and structural biology of protein complexes.

Currently the other important research themes are membrane integral proteins and protein expression and engineering as tools for structural biology.

They also run the Biocenter Finland Helsinki Crystallization Core facility.

The research group of Tommi Kajander has an open position for a post doctoral researcher to work on structure and protein engineering and design of neuronal membrane proteins and their homologs.

Useful link: EMAN2.1

EMAN2 is the successor to EMAN1. It is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes. EMAN's original purpose was performing single particle reconstructions (3-D volumetric models from 2-D cryo-EM images) at the highest possible resolution, but the suite now also offers support for single particle cryo-ET, and tools useful in many other subdisciplines such as helical reconstruction, 2-D crystallography and whole-cell tomography. EMAN2 is capable of processing very large data sets (>100,000 particle) very efficiently (up to 20x faster than EMAN1).

Expanding the horizons of G protein-coupled receptor structure-based ligand discovery and optimization using homology models. Cavasotto, Claudio N.; Palomba, Damián. Chemical Communications. 9/14/2015, Vol. 51 Issue 71, p13576-13594. 19p. DOI: 10.1039/c5cc05050b.

Anesthetics target interfacial transmembrane sites in nicotinic acetylcholine receptors. Forman, Stuart A.; Chiara, David C.; Miller, Keith W. Neuropharmacology. Sep2015, Vol. 96 Issue Part B, p169-177. 9p. DOI: 10.1016/j.neuropharm.2014.10.002.

The use of polyoxometalates in protein crystallography – An attempt to widen a well-known bottleneck. Bijelic, Aleksandar; Rompel, Annette. Coordination Chemistry Reviews. Sep2015, Vol. 299, p22-38. 17p. DOI: 10.1016/j.ccr.2015.03.018.

3D reconstruction of two-dimensional crystals. Stahlberg, Henning; Biyani, Nikhil; Engel, Andreas. Archives of Biochemistry & Biophysics. Sep2015, Vol. 581, p68-77. 10p. DOI: 10.1016/j.abb.2015.06.006.

General and specific lipid–protein interactions in Na,K-ATPase. Cornelius, F.; Habeck, M.; Kanai, R.; Toyoshima, C.; Karlish, S.J.D. BBA – Biomembranes. Sep2015, Vol. 1848 Issue 9, p1729-1743. 15p. DOI: 10.1016/j.bbamem.2015.03.012.

The influence of cholesterol on membrane protein structure, function, and dynamics studied by molecular dynamics simulations. Grouleff, Julie; Irudayam, Sheeba Jem; Skeby, Katrine K.; Schiøtt, Birgit. BBA - Biomembranes. Sep2015, Vol. 1848 Issue 9, p1783-1795. 13p. DOI: 10.1016/j.bbamem.2015.03.029.

Crystal shape engineering of anatase TiO₂ and its biomedical applications. Yang, Shuang; Huang, Nian; Jin, Yong Mei; Zhang, Hui Qing; Su, Yong Hua; Yang, Hua Gui. CrystEngComm. 9/21/2015, Vol. 17 Issue 35, p6617-6631. 15p. DOI: 10.1039/c5ce00804b.

Crystal structure analysis of ornithine transcarbamylase from Thermus thermophilus – HB8 provides insights on the plasticity of the active site. Sundaresan, Ramya; Ebihara, Akio; Kuramitsu, Seiki; Yokoyama, Shigeyuki; Kumarevel, Thirumananseri; Ponnuraj, Karthe. Biochemical & Biophysical Research Communications. Sep2015, Vol. 465 Issue 2, p174-179. 6p. DOI: 10.1016/j.bbrc.2015.07.096.

Pharmaceutical salts of ciprofloxacin with dicarboxylic acids. Surov, Artem O.; Manin, Alex N.; Voronin, Alexander P.; Drozd, Ksenia V.; Simagina, Anna A.; Churakov, Andrei V.; Perlovich, German L. European Journal of Pharmaceutical Sciences. Sep2015, Vol. 77, p112-121. 10p. DOI: 10.1016/j.ejps.2015.06.004.

Crystal Structure of Insulin-Regulated Aminopeptidase with Bound Substrate Analogue Provides Insight on Antigenic Epitope Precursor Recognition and Processing. Mpakali, Anastasia; Saridakis, Emmanuel; Harlos, Karl; Yuguang Zhao; Papakyriakou, Athanasios; Kokkala, Paraskevi; Georgiadis, Dimitris; Stratikos, Efstratios. Journal of Immunology. 9/15/2015, Vol. 195 Issue 6, p2842-2851. 10p. DOI: 10.4049/jimmunol.1501103.

Crystal structures of the PsbS protein essential for photoprotection in plants. Fan, Minrui; Li, Mei; Liu, Zhenfeng; Cao, Peng; Pan, Xiaowei; Zhang, Hongmei; Zhao, Xuelin; Zhang, Jiping; Chang, Wenrui. Nature Structural & Molecular Biology. Sep2015, Vol. 22 Issue 9, p729-735. 7p. DOI: 10.1038/nsmb.3068.

Structure of α,ω-bis-(pentane-2,4-dione-3-ylmethylsulfanyl)alkanes and even/odd crystallization effects. Khalilov, Leonard M.; Tulyabaev, Arthur R.; Mescheryakova, Ekaterina S.; Akhmadiev, Nail S.; Timirov, Yulai I.; Skaldin, Oleg A.; Akhmetova, Vnira R. Journal of Crystal Growth. Sep2015, Vol. 426, p214-220. 7p. DOI: 10.1016/j.jcrysgro.2015.06.008.

The crystal structure of Helicobacter pylori HP1029 highlights the functional diversity of the sialic acid-related DUF386 family. Vallese, Francesca; Percudani, Riccardo; Fischer, Wolfgang; Zanotti, Giuseppe. FEBS Journal. Sep2015, Vol. 282 Issue 17, p3311-3322. 12p. DOI: 10.1111/febs.13344.

Insights into the crystal structure of a polyoxomolybdate(VI) anion stabilized by ammonium cation: Inputs from X-ray diffraction and Hirshfeld surface analysis. Wu, X.; Ma, A.; Wang, F.; Liu, J.; Kumar, A. Russian Journal of Coordination Chemistry. Sep2015, Vol. 41 Issue 9, p624-628. 5p. DOI: 10.1134/S1070328415090079.

The Closing Mechanism of DNA Polymerase I at Atomic Resolution. IIIMiller, Bill R.; Beese, Lorena S.; Parish, Carol A.; Wu, Eugene Y. Structure. Sep2015, Vol. 23 Issue 9, p1609-1620. 12p. DOI: 10.1016/j.str.2015.06.016.

Complex wireframe DNA origami nanostructures with multi-arm junction vertices. Zhang, Fei; Jiang, Shuoxing; Wu, Siyu; Li, Yulin; Mao, Chengde; Liu, Yan; Yan, Hao. Nature Nanotechnology. Sep2015, Vol. 10 Issue 9, p779-784. 6p. DOI: 10.1038/nnano.2015.162.

Book review:

Foundations of Crystallography with Computer Applications, Second Edition by Maureen M. Julian

Taylor and Francis, LLC, 2015, 680 pages, ISBN 9781466552913

When I was handed this book at the ACA meeting this past July, I said to myself I've already done this. Nevertheless, I took the book and brought it home. I placed it next the first edition and immediately noticed it was nearly twice the thickness, 680 pages versus 368 pages, so I took both off the shelf and started looking for the differences.

This book is the first I have seen since Prince's Mathematical Techniques in Crystallography and Materials Science that actually provides computer code to teach crystallography. The code is specific to MatLab, so I could not test it myself, but I understand that MatLab is a common teaching tool on many campuses so that should not be a real hindrance. The code teaches students rudimentary programming, something all of us older crystallographers had to do and to which many younger crystallographers should be exposed.

The first chapter covers the basics of lattices in two and three dimensions, using hexamethylbenzene (HMB) and anhydrous alum as examples. The author was a postdoc of Kathleen Lonsdale's, hence the use of HMB as an example throughout the book. HMB is also triclinic, Ρ1, providing a simple general case.

The second chapter covers important concepts like fractional coordinates, placing atoms in the unit cell, calculating bond distances and angles, and crystallographic transformations. The book does not cover least squares or maximum likelihood refinement, so the calculation of errors is not described.

Chapter 3 provides a detailed description of two- and three-dimensional point groups, starting with the basic symmetry elements. Chapter 4 adds the lattice and translations to the concept of the point group, developing space groups in two and three dimensions. All seventeen 2D space groups and a number of 3D space groups are reviewed in detail. Further, a flowchart for dissecting space groups and how to read the International Tables for Crystallography, Volume A is given.

Chapter 5 covers the concept of the reciprocal lattice, along with the topics of making transformations between the direct and reciprocal lattice and the significance of vectors and planes in both types.

Chapter 6 introduces X-rays and how they interact with matter. Bragg's Law is derived. Chapter 7 derives the structure factor and electron density, as well as the scattering factor of an atom. The author discusses the effect of atom position on the amplitude and phase of a reflection. The concept of the Fourier relationship between electron density and structure factors would have benefitted from a code example. However, this chapter does provide example calculations of the structure factors for a number of simple structures (P, C, I and F) and of how systematic absences arise. The absences arising from glide planes and screw axes are described as well. Friedel's law is covered but not its breakdown.

What is new in this second edition is the addition of Chapter 8, which includes the introduction of the use of color to point and space group diagrams, and the next seven chapters. I have not seen the use of color thus far, red, blue and purple, but it really makes the diagrams and stereoprojections much more intuitive.

Each of the next seven chapters describe in great detail the structure of a material in one of the seven crystal systems: triclinic, monoclinic, orthorhombic, tetragonal, trigonal, hexagonal and cubic. The structures are all freely available so anyone can download the CIFs and play around with them. Each of these chapters can stand on its own in terms of the depth of the material covered; for example, Chapter 10 covers the structure of sucrose. The topics common to each of these chapters include: point group and space group properties, the direct and reciprocal lattices, atomic coordinates, analysis of the structure, powder diffraction, atomic scattering curves, and the structure factor. Each of the seven chapters has a special topic section—for sucrose the topics are proper point groups and space groups, and scanning electron microscopy.

Each of the fifteen chapters is bracketed by section objectives and an introduction at the beginning and definitions, exercises and a starter program (except in one case) at the end. This is not a complete book for a crystallography course, but it does provide an excellent tool for teaching the concepts of lattices and symmetry.

On the heavier side, I just finished and can recommend these two volumes on the American presidency: The Bully Pulpit by Dorothy Kearns Goodwin and One Man Against the World by Tim Weiner (rhymes with whiner). The former is a dual biography of Theodore Roosevelt and William Howard Taft, presidents at the turn of the last century. I was amazed by the fact that we seem to be reliving many of the social and political issues of that day: huge companies controlling large portions of the economy, bankers with too much power, independents running for office and so on.

One Man Against the World is the history of the Nixon presidency. This new work has the benefit of information provided by the declassification of thousands of documents and transcripts in 2011–13. It provides a clear view of Nixon's personality and how it drove the Vietnam war, the Watergate cover-up, rapprochement and détente. Sadly, those 18 minutes are still missing.

Joseph D. Ferrara, Ph.D.
Chief Science Officer