Crystallography in the news

December 1, 2016. A team at Cold Spring Harbor Laboratory (CSHL) revealed for the first time the structure of a portion of an important brain cell receptor, called the NMDA (N-methyl D-aspartate) receptor. The newly mapped portion of the NMDA receptor is responsible for recognizing zinc, an element common throughout the brain that can inhibit a class of NMDA receptors.

December 5, 2016. Researchers at the Department of Energy's SLAC National Accelerator Laboratory have captured for the first time how a protein complex — photosystem II — harvests energy from sunlight and uses it to split water into hydrogen and oxygen, a process that generates the oxygen in the atmosphere

December 7, 2016. A new imaging technique that takes X-ray snapshots of proteins as they twitch in electric fields could let scientists simply unravel which parts of protein give them their function. The team, led by Rama Ranganathan of UT Southwestern Medical Center, tested the technique on a common human protein, discovering new information about it. The research may prove useful for guiding rational protein and drug design.

December 7, 2016. The increasingly popular subject of raw diffraction data deposition is examined in a Topical Review in IUCrJ [Kroon-Batenburg, Helliwell, McMahon & Terwilliger (2017). IUCrJ, 4, DOI:10.1107/S2052252516018315]. Building on the 2015 workshop organised by the IUCr Diffraction Data Deposition Working Group (DDDWG), the authors bring the story up to date.

December 7, 2016. Researchers at the Skaggs School of Pharmacy and Pharmaceutical Sciences at University of California San Diego have now determined the 3D structure of CCR2 simultaneously bound to two inhibitors. Understanding how these molecules fit together may better enable pharmaceutical companies to develop anti-inflammatory drugs that bind and inhibit CCR2 in a similar manner.

December 8, 2016. A type of crystal-like structure that is vanishingly rare in nature – a quasicrystal – has been found in a fragment of a meteorite that struck Siberia in the Koryak Mountains. This type of quasicrystal has a structure that has never been seen before in nature or in the laboratory.

December 9, 2016. A new book on crystallography has been released entitled Basic Elements of Crystallography, Second Edition by Nevill Gonzalez Szwacki and Teresa Szwacka. The authors' purpose is "to illustrate rather than describe 'using many words' the structure of materials."

December 12, 2016. Scientists have puzzled over what prompts the intertwined double-helix DNA to open its two strands and then start replication. USC scientists believe they have solved the mystery. Replication is prompted by a ring of proteins that bond with the DNA at a special location known as "origin DNA." The ring tightens around the strands and melts them to open up the DNA, initiating replication.

December 13, 2016. Researchers from the Joint BioEnergy Institute "JBEI" and the Great Lakes Bioenergy Research Center "GLBRC" report the atomic-level structure of NOV1, a stilbene cleaving oxygenase (SCO) that breaks down a stilbene substrate into two smaller compounds.

December 15, 2016. Microseeding: A new way to overcome hemihedral twinning? Microseeding is one of several seeding techniques that are used to successfully separate nucleation events from crystal-growth events. In this technique, crystals are used as seeds and introduced into new drops which are equilibrated at lower levels of supersaturation. It has frequently been used to improve reproducibility in crystallization and can yield different crystal forms.

December 16, 2016. Quantifying radiation damage in SAXS experiments: as for most other macromolecular structural techniques, radiation damage is still a major factor hindering the success of experiments. The high solvent proportion of biological SAXS samples means that hydroxyl, hydroperoxyl radicals and hydrated electrons are produced in abundance by the radiolysis of water when it is irradiated with X-rays.

Product spotlight: AutoChem

AutoChem is the ultimate productivity tool for chemical crystallography, offering fast, fully automatic structure solution and refinement during data collection. Developed exclusively for Rigaku Oxford Diffraction by the authors of Olex2 (Durham University and OlexSys), AutoChem builds upon the success of our original AutoChem software. Seamlessly integrated as an optional plug-in for CrysAlis^Pro, AutoChem offers an advanced approach for automatic structure determination, with an even higher rate of success.

AutoChem can work with or without a chemical formula, intelligently using multiple solution programs and typically requiring only partial completeness to solve routine structures. In more difficult cases, AutoChem will make attempts in multiple space groups. A number of refinement options are available; atoms are modeled anisotropically where the data supports it and hydrogen atoms are included in calculated geometric positions. The structure is then re-labeled and refined to completion before a final structure report is generated. For more >

CrysAlis^Pro displays the structure and key refinement parameters, and provides a link to a full Rigaku Oxford Diffraction edition of Olex2 — complete with AutoChem plug-in — which can be launched at any time. Here the user can review all aspects of the refinement, step back to any stage of the process and apply changes as necessary.

For more about AutoChem and CrysAlis^Pro >

Lab in the spotlight

Professor Christine Joy McKenzie's research group
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark

The McKenzie group is interested in supramolecular inorganic nanochemistry. Inspired by the way in which living organisms utilize the unique chemical, structural and physical properties of the transition metal ions in metalloenzymes, the McKenzie group studies new molecular and supramolecular transition metal-containing materials. The organic ligands supporting the metal ions are designed to furnish specific metal binding sites so that:

(i) Some of nature's most impressive chemical tricks might be elucidated.

(ii) Materials with useful biomimetic catalytic and sensing functions are discovered.

The latter has far-reaching implications for the design of new materials with specific catalytic, optical or magnetic properties; in metal-containing drugs, in medical imaging and diagnostics, and in artificial photosynthesis.

Their research relies on organic, organometallic and inorganic synthesis and a battery of characterization and spectroscopic techniques, sometimes carried out in collaboration with other groups around the world. E.g. X-ray and synchrotron X-ray crystallography, NMR, ESR, Mössbauer IR, Raman, CD and VCD spectroscopy and ESI mass spectrometry, magnetochemistry and electrochemistry.

Useful link:

Literature on Crystallographic Theory and Methods

Dr. Phil Jeffrey (Princeton Univ.) has compiled an excellent list of literature references for macromolecular crystallography to help people fill in the gaps often left by automated software.

Iterative projection algorithms for ab initio phasing in virus crystallography. Lo, Victor L.; Kingston, Richard L.; Millane, Rick P. Journal of Structural Biology. Dec2016, Vol. 196 Issue 3, p407-413. 7p. DOI: 10.1016/j.jsb.2016.09.004.

The use of haptic interfaces and web services in crystallography: an application for a 'screen to beam' interface. Bruno, Andrew E.; Soares, Alexei S.; Owen, Robin L.; Snell, Edward H. Journal of Applied Crystallography. Dec2016, Vol. 49 Issue 6, p2082-2090. 8p. DOI: 10.1107/S160057671601431X.

Pushing the limits of crystallography. Wolny, Janusz; Buganski, Ireneusz; Kuczera, Pawel; Strzalka, Radoslaw. Journal of Applied Crystallography. Dec2016, Vol. 49 Issue 6, p2106-2115. 9p. DOI: 10.1107/S160057671601637X.

FOURIER2D and FOURIER3D: programs to demonstrate Fourier synthesis in crystallography. Glazer, A. M. Journal of Applied Crystallography. Dec2016, Vol. 49 Issue 6, p2276-2278. 2p. DOI: 10.1107/S1600576716016721.

Analysis of P-O-C, P-S-C and P-O-P angles: a database survey completed with four new X-ray crystal structures. Sabbaghi, Fahimeh; Pourayoubi, Mehrdad; Dušek, Michal; Eigner, Václav; Bayat, Sahar; Damodaran, Krishnan; Necas, Marek; Kuceráková, Monika. Structural Chemistry. Dec2016, Vol. 27 Issue 6, p1831-1844. 14p. DOI: 10.1007/s11224-016-0809-7.

2016 British Crystallographic Association (BCA) Spring Meeting, April 4???7, 2016. Rendle, David. Powder Diffraction. Dec2016, Vol. 31 Issue 4, p308-312. 5p. DOI: 10.1017/S0885715616000464.

Robust background modelling in DIALS. Parkhurst, James M.; Winter, Graeme; Waterman, David G.; Fuentes-Montero, Luis; Gildea, Richard J.; Murshudov, Garib N.; Evans, Gwyndaf. Journal of Applied Crystallography. Dec2016, Vol. 49 Issue 6, p1912-1921. 9p. DOI: 10.1107/S1600576716013595.

FAULTS: a program for refinement of structures with extended defects. Casas-Cabanas, Montse; Reynaud, Marine; Rikarte, Jokin; Horbach, Pavel; Rodríguez-Carvajal, Juan. Journal of Applied Crystallography. Dec2016, Vol. 49 Issue 6, p2259-2269. 10p. DOI: 10.1107/S1600576716014473.

CrystalCMP: an easy-to-use tool for fast comparison of molecular packing. Rohlícek, Jan; Skorepová, Eliška; Babor, Martin; Cejka, Jan. Journal of Applied Crystallography. Dec2016, Vol. 49 Issue 6, p2172-2183. 11p. DOI: 10.1107/S1600576716016058.

Effects of cooling rate in microscale and pilot scale freeze-drying – Variations in excipient polymorphs and protein secondary structure. Peters, Björn-Hendrik; Staels, Lotte; Rantanen, Jimi; Molnár, Ferdinand; De Beer, Thomas; Lehto, Vesa-Pekka; Ketolainen, Jarkko. European Journal of Pharmaceutical Sciences. Dec2016, Vol. 95, p72-81. 10p. DOI: 10.1016/j.ejps.2016.05.020.

β-Strand Mimicry: Exploring Oligothienylpyridine Foldamers. Jouanne, Marie; Voisin-Chiret, Anne Sophie; Legay, R??mi; Coufourier, Sébastien; Rault, Sylvain; Sopkova-de Oliveira Santos, Jana. European Journal of Organic Chemistry. Dec2016, Vol. 2016 Issue 34, p5686-5696. 11p. DOI: 10.1002/ejoc.201600882.

Theoretical modeling of multiprotein complexes by iSPOT: Integration of small-angle X-ray scattering, hydroxyl radical footprinting, and computational docking. Huang, Wei; Ravikumar, Krishnakumar M.; Parisien, Marc; Yang, Sichun. Journal of Structural Biology. Dec2016, Vol. 196 Issue 3, p340-349. 10p. DOI: 10.1016/j.jsb.2016.08.001.

Use of small-angle X-ray scattering to resolve intracellular structure changes of Escherichia coli cells induced by antibiotic treatment. von Gundlach, A. R.; Garamus, V. M.; Willey, T. M.; Ilavsky, J.; Hilpert, K.; Rosenhahn, A. Journal of Applied Crystallography. Dec2016, Vol. 49 Issue 6, p2210-2216. 6p. DOI: 10.1107/S1600576716018562.

Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS). Perkins, Stephen J.; Wright, David W.; Zhang, Hailiang; Brookes, Emre H.; Chen, Jianhan; Irving, Thomas C.; Krueger, Susan; Barlow, David J.; Edler, Karen J.; Scott, David J.; Terrill, Nicholas J.; King, Stephen M.; Butler, Paul D.; Curtis, Joseph E. Journal of Applied Crystallography. Dec2016, Vol. 49 Issue 6, p1861-1875. 14p. DOI: 10.1107/S160057671601517X.

Lipid functionalized biopolymers: A review. Qurat-ul-Ain, null; Zia, Khalid Mahmood; Zia, Fatima; Ali, Muhammad; Rehman, Saima; Zuber, Mohammad. International Journal of Biological Macromolecules. Dec2016 Part A, Vol. 93, p1057-1068. 12p. DOI: 10.1016/j.ijbiomac.2016.09.071.

X-ray structural investigations of fusion intermediates: Lipid model systems and beyond. Salditt, Tim; Aeffner, Sebastian. Seminars in Cell & Developmental Biology. Dec2016, Vol. 60, p65-77. 13p. DOI: 10.1016/j.semcdb.2016.06.014.

Current strategies for protein production and purification enabling membrane protein structural biology. Pandey, Aditya; Shin, Kyungsoo; Patterson, Robin E.; Liu, Xiang-Qin; Rainey, Jan K. Biochemistry & Cell Biology. 2016, Vol. 94 Issue 6, p507-527. 21p. DOI: 10.1139/bcb-2015-0143.

Crystal Structure of the Salmonella Typhimurium Effector GtgE. Xu, Caishuang; Kozlov, Guennadi; Wong, Kathy; Gehring, Kalle; Cygler, Miroslaw. PLoS ONE. 12/6/2016, Vol. 11 Issue 12, p1-15. 15p. DOI: 10.1371/journal.pone.0166643.

Characterization and Crystal Structure of a Robust Cyclohexanone Monooxygenase. Romero, Elvira; Castellanos, J. Rub??n Gómez; Mattevi, Andrea; Fraaije, Marco W. Angewandte Chemie. 12/19/2016, Vol. 128 Issue 51, p16084-16087. 4p. DOI: 10.1002/ange.201608951.

Studies on the σ???hole bonds (halogen, chalcogen, pnicogen and carbon bonds) based on the orientation of crystal structure. Pandiyan, B. Vijaya; Deepa, P.; Kolandaivel, P. Molecular Physics. Dec2016, Vol. 114 Issue 24, p3629-3642. 14p. DOI: 10.1080/00268976.2016.1255796.

Book review

Born to Run by Bruce Springsteen, 2016, Simon and Schuster, New York, 528 pages, ISBN-13: 978-1501141515

In 1979 I first heard the WMMS broadcast of Springsteen???s 1978 concert at the Cleveland Agora. I knew that my life would never be the same.

Springsteen writes prose with the same rhythm he writes lyrics???with ferocity. This makes a lot of sense???he has been writing his autobiography in his music for decades. The author describes his childhood in the Italian-Irish town of Freehold, New Jersey in the shadow of the Catholic Church and an alcoholic father. He realized music would become his life when he first saw Elvis Presley on The Ed Sullivan Show in 1956. He describes in detail the arc of his career from his first band, The Merchants, to the stadium-filled concerts of the 80s and 90s with the E Street Band, the Super Bowl halftime show in 2009 and all the other tours. We learn about the members of the band, especially Clarence Clemons. Springsteen delves deep into the psyche of the American middle class and exposes his own demons. His is the story of one man who succeeded in his American Dream.

By the way, the WMMS concert I mentioned was recorded on a 24-track tape and can be listened to in all its glory at the Western Reserve Historical Society.

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