Day 2, Tuesday 22 August: The salt of the earth

Dr Clare Sansom, Department of Biological Sciences,  Birkbeck College, London, UK

What links the history of crystallography, Gandhi, the Indian chemical industry and the Guinness Book of Records? Unless you keep an exceptionally strict diet, you have probably eaten some today. It is common salt, which most people will remember from high school by its chemical name: sodium chloride. This humble compound was the subject of the fascinating session that kicked off the IUCr Congress parallel programme. This programme has been designed to highlight aspects of crystallography and structural science that don’t fit into the rigid structure of plenaries, keynotes and micro-symposia that comprise the main event. ‘The salt of the earth’ fitted that bill extremely well.

Common salt was chosen as a session topic to celebrate, of all things, a world record: the largest model crystal structure ever built. Robert Krickl, a freelance science communicator from Vienna, Austria, spent a year of his life building a 3’ x 3’ x 3’ model of a salt crystal, with its constituent sodium and chloride ions represented by red and white balls. One third of this structure will be sitting in the HICC foyer throughout the meeting. Krickl gave the first talk, and he began by explaining the inspiration behind his model. He moved into science communication following a PhD in crystallography communication and had made something of a name for himself with travelling exhibitions by the International Year of Crystallography (IYCr) in 2014. Asked then to ‘do something about it’ he was single-handedly responsible for Austria’s second place in the table of countries’ involvement in IYCr, touring the country with an exhibition and giving presentations at 182 schools. His plan to build the largest-ever model crystal structure was announced at the very end of the IYCr closing ceremony.

The choice of sodium chloride was an obvious one for Krickl; his model was built in 2015, exactly 100 years after the father-and-son team of W.H. and W.L Bragg were awarded the Nobel Prize for determining the crystal structure of this compound. A century later Krickl set about the task of acquiring the 38880 coloured balls and over 10km of sticks that he needed. The final model has repaid all his hard work, intellectually if not yet financially. If you look into it from different angles you will see an astonishing range of beautiful, symmetrical patterns. It can be disassembled so small parts can be displayed in museums or taken into schools. And the 25th IUCr congress in 2020 will be held in Prague, only about 300km from Vienna. Krickl might take his complete structure there; or, perhaps, he could challenge delegates to build a more complex model there.

Each of the four talks that followed explored a different aspect of salt: in the history of India and of crystallography, in contemporary science and in industry. Dinkar Joshi, an expert on the life of Mahatma Gandhi, described the history of salt taxes in India under the British Empire as a background to Gandhi’s famous ‘salt march’ of 1930. At the time, Indian salt was taxed to encourage Indians to buy imported salt that had been brought in as ballast for ships. Gandhi had written to the Viceroy with 11 demands, one of which concerned the salt tax; when he received no reply, he chose the salt issue for his ‘satyagraha’ (civil resistance) because of its importance to all Indians. Twenty-eight marchers, ranging in age from Gandhi himself at 61 to his teenage grandson, marched for 24 days to gather salt illegally at the coastal village of Dandi in Gujarat; the rest is history.

Mike Glazer from the University of Oxford, UK, vice-president of the IUCr explained the role that sodium chloride had played in the Braggs’ discoveries. It was not the first compound to produce a diffraction pattern (of sorts) in a beam of X-rays; that honour had gone to copper sulphate, a few years earlier. It was, however, the first to produce a diffraction pattern that was good enough for a correct structure to be determined. Interestingly, potassium chloride (KCl), which has the same structure, produced a different type of diffraction pattern because potassium and chloride ions have the same number of electrons and were therefore ‘seen’ as equivalent by the X-rays. The Braggs’ structure showed sodium chloride to be a ‘pure’ ionic compound, less than 20 years after the discovery of the electron. This was much to the chagrin of some chemists who had expected to see ‘molecules’ in the structure: but the rest, again, is history.

The final two talks brought the subject up to date. First, Artem Oganov, a solid state chemist with positions in both New York and Moscow, explained some of the properties that common salt’s ‘3D chessboard’ type cubic structure give to the many other compounds that share it. He took examples from centuries of solid state chemistry, taking the story right up to the present day and his own work. Among the structures he mentioned was a novel form of boron named gamma boron, in which small and large clusters of atoms replace the sodium and chloride ions on a cubic lattice; this is one of the hardest substances known. And finally, Amitava Das, director of an Indian government lab in Bhavnagar, described the vitally important role that common salt plays in the Indian chemical industry and thus in the country’s economy.

The opening of the 24th congress and general assembly of the International Union of  Crystallography

The opening of the 24th congress and general assembly of the International Union of Crystallography was marked by a splendid programme that stressed, time and again, the international nature of our crystallographic community. When Professor Gautam Desiraju, the organising committee chair and immediate past president of the IUCr, quoted one of the discipline’s founding fathers, W. L. Bragg, in his welcome address: “At a scientific conference nationality disappears” he could have been summing up the whole event.

Certainly, this is the most diverse IUCr congress yet, as Desiraju explained. There are representatives of 73 countries here in Hyderabad, more than the 58 national members of the International Union. India is represented by over 500 delegates and the other BRICS countries – Brazil, Russia, China and South Africa – have all sent substantial delegations. The challenges and opportunities for scientists in these very different but in many ways surprisingly similar emerging countries will be discussed later in the week. Several countries including the Cameroon and Myanmar have sent a single delegate, but the most significant example of the ‘borderless’ nature of crystallography might be the 17 delegates from Bangladesh. Three of these are students who have joined the band of enthusiastic conference volunteers on equal terms with their domestic counterparts.

The IUCr President, Marvin Hackert of the University of Texas, Austin, gave a talk running through the history of the Union and its congresses. Like independent India, the IUCr was ‘born’ in 1947, and its international congress has taken place every third year since 1948. It has grown out of recognition since those early days but its basic roles are essentially unchanged: maintaining standards, publishing books and journals (including the International Tables) and promoting international collaboration. And a number of new initiatives have been started in or after the highly successful International Year of Crystallography in 2014. These include the LAAMP project – or the Lightsources for Africa, the (Southern) Americas and Middle East Project – to provide greater access to advanced synchrotron sources for scientists working in these disadvantaged regions. India already has two such sources, with others planned.

Paul Peter Ewald, a pioneering crystallographer known to students of structural science throughout the world for his ‘Ewald sphere’, was one of those principally involved in setting up the IUCr. Since 1986, his memory has been honoured by the award of the Ewald Prize at each congress to a distinguished crystallographer. The 2017 prize was therefore the eleventh in the series; it was awarded to Sir Tom Blundell from the University of Cambridge, UK, a pioneering structural biologist and a co-founder of Astex Pharmaceuticals.

Blundell’s prize lecture was a tour de force, a whirlwind summary of half a century at the forefront of structural biology. Time and again, he came back to the importance of collaboration, both between nationalities and between academic and industrial scientists. And time and again he came back to his mentor, Nobel laureate Dorothy Hodgkin. He joined Hodgkin’s lab as a student in 1964, the year in which she won the Chemistry Nobel, and became a member of the group that solved the 3D structure of insulin. He described giving his first plenary lecture at an international conference as a 27-year-old in 1969, showing delegates at the eighth IUCr congress the newly-solved structure of that vitally important biological molecule.

During his talk, he drew out four ‘lessons’ from Dorothy Hodgkin’s example and the insulin story, illustrating them with anecdotes from throughout his career.  Firstly, he explained that good science requires a long-term vision by citing the thirty years between the first insulin crystals and the first publishable 3D structure. There are lessons here for today’s grant agencies and journal editors. His second point stressed the value of international and interdisciplinary teams and his third the importance of writing up experimental methods: Protein Crystallography, the book he co-authored with Louise Johnson in 1976, was the first authoritative textbook on this subject.

Blundell devoted most time to the fourth ‘lesson’, on the value and quality of industrial science. He has collaborated with the pharma industry since the Seventies – then perhaps rather improbably as a left-wing firebrand of an Oxford City councillor. His was one of the groups that simultaneously solved the structure of HIV’s protease, paving the way for some of the most successful drugs for AIDS. In 1999 he and two ex-colleagues, Harren Jhoti and Chris Abell, founded Astex to pioneer the technique of fragment-based drug discovery. This company is now wholly owned by Otsuka Pharmaceuticals in Japan, and eighteen years after the program was launched, its first drug, riboclicib, has just received FDA approval for breast cancer. Dorothy Hodgkin herself would recognise this time-scale. Blundell is now taking the technologies pioneered at Astex back into academia for complex targets and neglected diseases, the latter with generous funding from the Gates Foundation. Despite passing the ‘official’ retirement age he still has plenty of plans for his international, interdisciplinary team, and for what his mentor might have called ‘useful’ crystallography; I will be reporting on more of both throughout the meeting.

Dr Clare Sansom, Department of Biological Sciences,  Birkbeck College, London, UK

A pioneering X-ray technique that can analyse artefacts of any shape or texture in a non-destructive way has been developed by an international team of scientists. The method uses X-ray diffraction (XRD) in order to determine crystallographic phase information in artefacts with very high accuracy and without causing damage to the object being scanned [Hansford et al. (2017). Acta Cryst. A73, 293-311].

Using the technique, researchers can identify pigments in paintings and on painted objects – which could potentially be applied in the future to help to clamp down on counterfeit artwork and artefacts and verify authenticity.

The research suggests that the non-invasive technique could also eliminate the frequent need to compromise between archaeological questions that can be solved and the analytical methods available to do so.

Dr Graeme Hansford, from the University of Leicester, explained, “What makes this method really unique is that the shape and texture of the sample become immaterial. I expect future studies to make significant contributions to determining the provenance of a range of archaeological objects, and this data will ultimately provide vital context information for museum collections.

“In paintings, the type of pigment used frequently yields useful insights into methods of production and the organisation of ancient industries, as well as restricting the possible date of manufacture. This could help to determine if the provenance of an artefact is as purported.”

The research was supported by the UK’s Science and Technology Facilities Council.

Mechanochemistry is a widespread synthesis technique in all areas of chemistry. Various materials have been synthesized by this technique when the classical wet chemistry route is not satisfactory. Characterization of the reaction mixture is however much less accessible than in solutions.

Recently, in situ observations of mechanochemical reactions have been achieved by X-ray diffraction and Raman spectroscopy. Solid-state reactions can be directly tracked, revealing phase transitions and other material transformations during synthesis in a ball mill jar. This technique has become increasingly popular in different fields of mechanochemistry.

As the X-rays go through the entire jar, the diffraction patterns present a high background due to the scattering from the thick walls of the jar. Also, broad diffraction peaks are expected from the sample as a result of probing a large sample area covering the entire jar. An extra complexity arises from diffraction on the milling balls.

Tumanov et al. [(2017). J. Appl. Cryst. 50. doi:10.1107/S1600576717006744] reasoned that these issues can be resolved by modifying the geometry and material of the milling jar. But, making a jar with a complex geometry using traditional production techniques is complicated, especially at the stage of creating a prototype, when introducing changes into a design should be facile. For this reason they decided to use a 3D printer for the purpose. They show how this useful production tool can quickly make milling jars optimized for improved background, absorption and angular resolution in X-ray powder diffraction experiments; the jars are also more resistant to solvents compared with standard acrylic jars. 3D printing allows for low-cost fast production on demand.

Source files for printing the jars are available as supporting information for the paper.

Gorrec F, MRC Laboratory of Molecular Biology, Cambridge, UK

Technology developments, including innovative crystallization screens, are needed to obtain X-ray diffraction-quality crystals from increasingly challenging protein and other macromolecular samples. MORPHEUS crystallization screens are continuously developed to further enhance initial screening. MORPHEUS screens integrate small molecules frequently observed in the PDB to co-crystallize with proteins. These molecules are included to function as additives that act as protein stabilizers, crystal packing bridges, or any other role beneficial to protein crystallization.

Each MORPHEUS screen integrates 96 conditions, a minimal format for limiting amounts of sample. To limit the number of conditions employed, the potential ligands found in the PDB are combined into mixes. Other mixes of compounds are used, such as buffer systems and precipitant mixes that also act as convenient and effective cryoprotectants. The different types of compound mixes are combined using a fixed ratio to generate 3-D grid screens. The preparation of a screen and the optimization of conditions are amenable to automation.

A multitude of test crystallization screens are used against novel and challenging samples produced at the LMB before making choices about the formulation. The main goal is to produce exclusive crystallization hits that were not observed in other screens. MORPHEUS screens, I and II, are now used routinely in many laboratories, while MORPHEUS III is being developed. Before describing the developments related to the MORPHEUS screens, I will briefly present theoretical and pragmatic aspects of macromolecular crystallography that were taken into consideration during the early stages of MORPHEUS development. In the last section I will show how to optimize conditions following the 4-corner method.

A recording of this webinar is now available to view: https://www.youtube.com/watch?v=Gpb4SypWnQY

A complementary event is also available: https://www.youtube.com/watch?v=8cH0YNmDshY

Questions and answers raised during the webinar Formulation of the MORPHEUS protein crystallization screens

If you have any questions about the event please do not hesitate to contact Dr Jonathan Agbenyega, Business Development Manager, IUCr at ja@iucr.org