Crystallography in the News

January 1, 2019. ThePrint celebrates one of India's greatest physicists on the 125th anniversary of his birth. Bose-Einstein statistics, Bose-Einstein Condensate, Bosons — these are terms that even casual observers of physics have heard regardless of whether they actually know about them or not. These nomenclatures, based upon Satyendra Nath Bose's surname (along with Einstein's in the first two cases), both commemorate and signify his immense contribution to physics.

January 3, 2019. A giant toadstool that swallows vitamins and nutrients in the intestines and kidneys: this is what the receptor that absorbs vitamin B12 in the small intestine looks like. For the first time, researchers have an insight into an as yet unknown biology that has survived hundreds of millions of years during the evolution of life.

January 7, 2019. Scientists at the MRC-MBU in Cambridge, U.K., have discovered how a key transport protein, called the mitochondrial ADP/ATP carrier, transports adenosine triphosphate (ATP), the chemical fuel of the cell. This work will help researchers understand how mutations can affect the function of these proteins, resulting in a range of neuromuscular, metabolic and developmental diseases.

January 7, 2019. Every so often, medicinal chemists need reminding that those beautiful X-ray crystallography structures of ligands bound to target proteins are not quite what they seem. Here's a post on that from a while back, and this new paper quantifies one of the issues.

January 10, 2019. In addition to visualizing the stunning order and symmetry of a virus particle on an atomic scale, structural models help researchers understand how viruses assemble, infect and propagate within their host. However, according to a new study by a group of researchers at Purdue University in Indiana, US, published in the journal Proceedings of the National Academy of Sciences, some aspects of these models may not be entirely realistic.

January 17, 2019. A study into a common bacterial toxin found in the human gut has yielded valuable information that could assist in the development of new antibiotics. Researchers at the John Innes Centre working alongside colleagues in Moscow and Poland made the findings in a study looking at the machinery that synthesises the toxin Microcin B17.

January 17, 2019. In biology, folded proteins are responsible for most advanced functions. These complex proteins are the result of evolution or design by scientists. Now scientists have discovered a new class of complex folding molecules that emerge spontaneously from simple building blocks.

January 21, 2019. Rosalind Franklin, eminent mid-century scientist and heroine of Photograph 51, is driven by The Work. It's a phrase she utters several times throughout the quasi-biographical play, delivered with a gravity that suggests capital letters. Franklin's capital-W Work was X-ray crystallography.

January 22, 2019. A study published in the journal Chem and undertaken by researchers at the Institute for Research in Biomedicine (IRB Barcelona) is the first to achieve stable simulations of DNA crystals. This accomplishment has allowed the scientists to explain the importance of the chemical additives used experimentally to achieve suitable crystallization conditions and stable crystals in the laboratory.

Product Spotlight

XtaLAB Synergy-R
The XtaLAB Synergy-R is the most powerful small molecule diffractometer available. It includes a high-flux, low-maintenance microfocus rotating anode, the PhotonJet-R, with a high-precision kappa goniometer and Rigaku's own Hybrid Photon Counting (HPC) X-ray detector the HyPix-6000HE. The PhotonJet-R X-ray source is comprised of a MicroMax-007 HF rotating anode and a newly designed optic. It is available with either Cu or Mo anodes.

This single crystal X-ray diffractometer has been specially designed to fully integrate the rotating anode X-ray source with all system components and software, making it a sleek, simple to use diffractometer without compromising the X-ray intensity.

For labs with high-throughput requirements, increasing the flux reduces data collection time and thus increases the number of samples that can be studied in your laboratory. For extremely small samples, additional flux will extend the minimum size limits for crystals that you can study.

Benefits

• Fast workflow due to complete integration of software and hardware
• Excels at the most challenging applications, e.g. MOFs or incommensurate structures
• Extremely high performance due to bright source, noise-free detector and fast goniometer speeds
• Provides unparalleled throughput
• Compact design to fit in your laboratory

Features

• True shutterless data collection
• Noise-free HPC X-ray detector for better measurement of weak data
• 4-circle kappa goniometer with high accuracy and speed

Lab in the Spotlight

RIKEN Center for Emergent Matter Science
Materials Characterization Support Team

Team Leader: Daisuke Hashizume (D.Sci.)
2-1 Hirosawa, Wako, Saitama
351-0198 Japan

The Materials Characterization Support Team provides research support in structural chemistry and materials science by means of X-ray crystal structure analysis, electron microscopy, and elemental analysis to the Rikagaku Kenkyūjyo (RIKEN) Center for Emergent Matter Science. The laboratory boasts a molybdenum rotating anode with a Saturn CCD for charge density data collection, a SmartLab for general purpose XRD and a brand new XtaLAB Synergy-i. The team is led by Daisuke Hashizume and supported by a number of scientists. Manabu Hoshino just joined the group as a visiting scientist. In addition to supporting other groups in RIKEN the team has been using X-ray diffraction to study bonding in compounds with unusual chemical bonds.

MicroMax-007 HF with Saturn CCD for charge density studies (left), and XtaLAB Synergy-i and SmartLab for conventional small molecule experiments and general purpose XRD, respectively (right).

Electron donation from σ (C−C) orbital to Si atom visualized by accurate X-ray analysis.

Useful Links

Here are two links Gerard Bricogne posted just before the new year for newly improved STARANISO and PDBpeep servers, respectively situated at

The STARANISO Server

and

The STARANISO/PDBpeep Server

Ab initio phasing of the diffraction of crystals with translational disorder. Morgan, Andrew J.; Ayyer, Kartik; Barty, Anton; Ekeberg, Tomas; Oberthuer, Dominik; White, Thomas A.; Yefanov, Oleksandr; Chapman, Henry N.; Chen, Joe P. J. Acta Crystallographica. Section A, Foundations & Advances. Jan2019, Vol. 75 Issue 1, p25-40. 16p. DOI: 10.1107/S2053273318015395.

Aspherical scattering factors for SHELXL – model, implementation and application. Wandtke, Claudia M.; Sheldrick, George M.; Lübben, Jens; Ruf, Michael; Hübschle, Christian B.; Dittrich, Birger. Acta Crystallographica. Section A, Foundations & Advances. Jan2019, Vol. 75 Issue 1, p50-62. 13p. DOI: 10.1107/S2053273318013840.

Reaction mechanism of the bioluminescent protein mnemiopsin1 revealed by X-ray crystallography and QM/MM simulations. Molakarimi, Maryam; Gorman, Michael A.; Mohseni, Ammar; Pashandi, Zaiddodine; Taghdir, Majid; Naderi-Manesh, Hossein; Sajedi, Reza H.; Parker, Michael W. Journal of Biological Chemistry. 1/4/2019, Vol. 294 Issue 1, p20-27. 8p. DOI: 10.1074/jbc.RA118.006053.

Crystal structure of a Thermus aquaticus diversity-generating retroelement variable protein. Handa, Sumit; Shaw, Kharissa L.; Ghosh, Partho. PLoS ONE. 1/10/2019, Vol. 14 Issue 01, p1-12. 12p. DOI: 10.1371/journal.pone.0205618.

Uncoordination mode of κ⁰-Janus scorpionate with La(III) and Ce(III) complexes: Synthesis, characterization, thermolysis and crystal structure determination. Kharbani, Donkupar; Khatua, Snehadrinarayan; Soh, Charlestine; Rymmai, E.K. Journal of Molecular Structure. Jan2019, Vol. 1176, p128-132. 5p. DOI: 10.1016/j.molstruc.2018.08.041.

Three monomeric compounds containing the dipyrimidine-2-thiolategold(I) anion. Neils, Thomas L.; Biros, Shannon M.; Staples, Richard J.; Wackerle, Brandon G.; Harrison, Robert B. Polyhedron. Jan2019, Vol. 157, p474-478. 5p. DOI: 10.1016/j.poly.2018.10.043.

An integrated remote data collection system for macromolecular crystallography beamline at SSRF. Wang, Qisheng; Sun, Bo; Zhou, Huan; Wang, Zhijun; Yu, Feng; He, Jianhua. Nuclear Instruments & Methods in Physics Research Section A. Jan2019, Vol. 914, p42-45. 4p. DOI: 10.1016/j.nima.2018.10.167.

VMXi: a fully automated, fully remote, high-flux in situ macromolecular crystallography beamline. Sanchez-Weatherby, Juan; Sandy, James; Mikolajek, Halina; Lobley, Carina M. C.; Mazzorana, Marco; Kelly, Jon; Preece, Geoff; Littlewood, Rich; Sørensen, Thomas L.-M. Journal of Synchrotron Radiation. Jan2019, Vol. 26 Issue 1, p291-301. 11p. DOI: 10.1107/S1600577518015114.

Total synthesis of diaportheone A. Tan, Mario A.; Züger, Patrik Peter; Roggo, Silvio. Tetrahedron Letters: International Organ for the Rapid Publication of Preliminary Communications in Organic Chemistry. Jan2019, Vol. 60 Issue 1, p52-54. 3p. DOI: 10.1016/j.tetlet.2018.11.055.

Five benzoic acid derivatives: Crystallographic study using X-ray powder diffraction, electronic structure and molecular electrostatic potential calculation. Pramanik, Samiran; Dey, Tanusri; Mukherjee, Alok Kumar. Journal of Molecular Structure. Jan2019, Vol. 1175, p185-194. 10p. DOI: 10.1016/j.molstruc.2018.07.090.

Determination of protein crystallization kinetics by a through-flow small-angle X-ray scattering method. Poplewska, Izabela; Lyskowski, Andrzej; Kolodziej, Michal; Szalanski, Piotr; Piatkowski, Wojciech; Antos, Dorota. Chemical Engineering Research & Design: Transactions of the Institution of Chemical Engineers Part A. Jan2019, Vol. 141, p580-591. 12p. DOI: 10.1016/j.cherd.2018.11.030.

Structural Variability of EspG Chaperones from Mycobacterial ESX-1, ESX-3, and ESX-5 Type VII Secretion Systems. Tuukkanen, Anne T.; Freire, Diana; Chan, Sum; Arbing, Mark A.; Reed, Robert W.; Evans, Timothy J.; Zenkeviciute, Grasilda; Kim, Jennifer; Kahng, Sara; Sawaya, Michael R.; Chaton, Catherine T.; Wilmanns, Matthias; Eisenberg, David; Parret, Annabel H.A.; Korotkov, Konstantin V. Journal of Molecular Biology. Jan2019, Vol. 431 Issue 2, p289-307. 19p. DOI: 10.1016/j.jmb.2018.11.003.

Reducing dynamical electron scattering reveals hydrogen atoms. Clabbers, Max T. B.; Abrahams, Jan Pieter; Gruene, Tim; van Genderen, Eric. Acta Crystallographica. Section A, Foundations & Advances. Jan2019, Vol. 75 Issue 1, p82-93. 12p. DOI: 10.1107/S2053273318013918.

Book Review

The Skeptics Guide to the Universe: How to Know What's Really Real in a World Increasingly Full of Fake
By Dr. Steven Novella with Bob Novella, Cara Santa Maria, Jay Novella, and Evan Bernstein

The Skeptics Guide to the Universe is a wonderfully comprehensive work for anyone who already identifies as a skeptic or who wants to become a well-informed one. Podcast fans might recognize the title—it's shared with a weekly show hosted by Dr. Steven Novella and his team of co-authors.

The book will probably take longer to read than listening to an episode of the podcast—or even several. Coming in at almost 450 pages, The Skeptics Guide delivers just what its name implies: a guide to the universe for those of a more skeptical nature. The book is broken down into five sections: Core Concepts Every Skeptic Should Know, Adventures in Skepticism, Skepticism and the Media, Death by Pseudoscience, and Changing Yourself and the World.

The first section, Core Concepts Every Skeptic Should Know, is the longest and most densely packed with information. In the first 316 pages of the book, Novella lays the fundamental groundwork for skepticism. This section is subdivided into the following categories: Neuropsychological Humility and Mechanisms of Deception, Metacognition, Science and Pseudoscience, and Iconic Cautionary Tales from History.

Novella uses a lot of technical jargon, especially in these earlier chapters, and does an excellent job of explaining this jargon and illustrating each term through vivid examples, but if you don't pay attention in the first section, you will be lost in the latter part of the book. The first section feels like a very reader-friendly, well-written textbook on skepticism, while the latter sections are more like a work of popular science that could be titled Skepticism and the Real World.

It’s these later sections, especially Adventures in Skepticism, where the book really captures the reader's attention. Once Novella is done teaching the fundamentals, he applies them to entertaining and exciting real-world scenarios. Adventures in Skepticism brings each co-author to the fore, with an anecdotal adventure into skepticism. One told by Evan Bernstein involves ghost hunters Ed and Lorraine Warren. You might recognize their names from The Conjuring film franchise. Several films in the franchise, which includes spin-offs like Annabelle, focus on real cases the Warrens worked on—although the “realness” of the supernatural events depicted should probably be approached with a healthy dose of skepticism.

Given the author's role as host of a podcast of the same name, the structure of The Skeptics Guide makes sense. Treat each subdivision of the first section as its own section, and each subsequent shorter section (2-5) as their own—as individual episodes of a podcast if you will. Stop reading to pause and contemplate what you have read before diving into the next section, and you will probably have a more fruitful reading experience than someone who tries to read the whole book in one sitting.

Review by Jeanette S. Ferrara, MA