From Wiley via Jisc Publications RouterHistory: received 2021-07-26, accepted 2021-08-11, pub-electronic 2021-08-13Article version: VoRPublication status: PublishedExtremely bright synchrotron radiation sources give extremely strong intensities at the sample. Lawrence Bright et al (2021) [J. Synchrotron Rad. (2021), 28, https://doi.org/10.1107/S160057752100669X] dive into the details for materials science. I offer a Commentary including a historical context

Helliwell, John R.

ChesterRep

scientific commentariesJ. Synchrotron Rad. (2021). 28 https://doi.org/10.1107/S1600577521008328 1 of 3Respect the synchrotron beam strength: how tomodel it, measure it and mitigate it for variousscientific fieldsJohn R. Helliwell*‡Science and Engineering Research Council (now Science and Technology Facilities Council), Daresbury Laboratory,Warrington WA4 4AD, United Kingdom. *Correspondence e-mail: john.helliwell@manchester.ac.ukIt was 1983 when I was a beamline scientist at the UK’s SRS responsible for ProteinCrystallography Stations 7.2 (bending magnet) and 9.6 (superconducting high fieldwiggler, 5 T) and I was on the European Synchrotron Radiation Project (ESRP) WorkingGroup for Biology chaired by Dr Joan Bordas. We had just received the spectral emissionspecifications from the ESRP Project Leader Professor Bronislaw Buras based at CERNin Geneva. The spectral brightnesses and fluxes of the various ESRP sources, especiallythe undulators, showed colossal gains over what we had at the SRS. At SRS 9.6 I hadalready insisted to the engineers involved on having a straight-through beam option. Themelting of lead by the white beam (Fig. 1) was a vivid effect to show us what we had at ourdisposal. It was one of the first ever synchrotron source wigglers. Duly concerned Imeasured the temperature rise in a sample of water in one of our standard protein crystalmounting glass capillaries, which (from memory) was about 1C. The details of my testwere very similar to those given in Fig. 11 of Cheng & Caffrey (1996) who used CHESS13.6 keV X-rays of 2  1010 photons s1 into a beam of size 0.3 mm and who reported a0.16 K temperature rise. Therefore beam heating even on a second-generation sourcewiggler was not to be an anxiety for us as facility provider.But, the beam strengths from the first ever third-generation source were far more (byup to 1000 more photons per second per mm2 into beam sizes of about 100 mm, insteadof SRS 9.6 of 1  1011 12 keV photons into a focus with our optics of 1 mm 0.5 mm). Another major feature of the ESRP specifications was that this was a 5 GeVring (ESRF was implemented at 6 GeV so that the undulator emission was bettermatched to the requested Mossbauer experiments). There were to be copious quantitiesof higher-energy photon fluxes to be available, i.e. we could consider quite easily workingwith 0.5 Å X-ray wavelength instead of typically 0.9 Å wavelength on SRS 9.6 and1.488 Å on SRS 7.2 (both instruments were fully tunable for the anomalous dispersion-based studies).Daresbury despatched me to work with Roger Fourme at the LURE synchrotron toconsider these machine specifications in detail, namely their potential and yet also thepossible problematic barriers to exploitation. I slept in the LURE users’ dormitory cabinwhich I had sole use of as it was a shutdown; I recall that eating in Orsay on a Sundayevening did not offer much by way of opportunity. Ultimately I presented our report(Helliwell & Fourme, 1983) to Professor Buras at CERN. We were actually very opti-mistic for macromolecular crystallography at the future ESRF. The calculations (Helli-well, 1984) showed that, in the worst case, the adiabatic model for the sample beamheating was serious but manageable. Specifically we proposed a new sample mounting toeffect the best possible heat conduction away from the protein crystal. This comprised acrystal attached by grease to a copper stalk and surrounded by helium (Fig. 2). The greasewould also protect the crystal from dehydration. Copper and helium were chosen fortheir high thermal conductivity. Later, at Daresbury and at other synchrotron sources weadopted the cryo-cooling methodology of Haas & Rossmann (1970), encouraged espe-cially by Hakon Hope and Ada Yonath for realizing successful ribosome crystallographymeasurements (Hope, 1988). Room-temperature diffraction measurements fell out offashion and our crystal sample mounting protocol dimmed from view.New third-generation sources steadily appeared, as have a succession of lower emit-tance, higher spectral brightness, machine upgrades. After 17 years a new sample heatingISSN 1600-5775Received 26 July 2021Accepted 11 August 2021‡ Current address: Department of Chemistry,University of Manchester, Manchester M13 9PL,UK.Keywords: extremely bright SR sources;materials science; macromolecularcrystallography.publication appeared (Kuzay et al., 2001) and they even gaveme a mention in their Contents’ page Synopsis, although notquite how I would appreciate it:‘Improved thermal models that include convection are developedwhich replace Helliwell’s adiabatic approximation. Temperaturerises of 6 K are calculated for a cryocooled 100 micron thickcrystal and of 18 K for a room-temperature air-cooled 1 mm thickcrystal for an 8 keV 1013 photons s1 mm2 beam. Theimportance of internal heat conduction within the crystal is alsocarefully examined.’Apparently I was to be replaced rather than built upon.I presented the different aspects of the Helliwell & Fourme(1983) ESRP internal report in the journals’ literature firstly inHelliwell (1984). The beam heating calculations had of courseprovided a basic ‘worst case’ adiabatic model. Kuzay et al.(2001) initiated the modelling of heat transfer from thesample, what I called an isothermal (i.e. steady state) model.We had of course immediately proposed an experimentalsolution, as mentioned above (Fig. 2). Further modellingstudies, and measurements, followed [such as Snell et al.(2007)]. All these, including Kuzay et al. (2001), restrictedthemselves to modelling the case of a cryocooled proteincrystal sample. An important exception was the extensivestudies by Cherezov et al. (2002) who were constrained in theirstructural studies of lipid membranes and mesophases toroom temperature.Lawrence Bright et al. (2021) now lead the way forconsidering materials science and their samples’ beam heating.They provide as context for their initiative a full citing of themacromolecular crystallography beam heating papers, to myknowledge [except the Cherezov et al. (2002) studies] and aselection of the radiation damage papers. This latter is a muchbigger literature thanks to the major efforts of the Interna-tional Symposia on Radiation Damage in MacromolecularCrystallography [see, for example, Garman & Weik (2015)].As part of the proposed ESRP and proposed New Rings at theStanford Synchrotron Radiation Laboratory initiative led byProfessors Keith Hodgson and Herman Winick, we also madeevaluations of overall and specific (disulfide bond breaking)radiation damage (Hedman et al., 1985; Helliwell, 1988).The context for Lawrence Bright et al. (2021) is that theESRF’s Extremely Bright Source (EBS) upgrade has beencompleted and even greater spectral source brightnesses dulyrealized at the turn of the year. They certainly respect theirnew ESRF EBS synchrotron beam strength. They offer theirown ways of how to model it and measure it with different testsamples relevant to materials science. They also offer ways tomitigate it. More than that, they suggest ways for experi-menters to validate their measurements, learning from thoseexperimental situations where experimenters should beconcerned. As for the macromolecular crystallographers, thepaper of Halle (2004) on cryo structural artefacts is encoura-ging us to more firmly establish when those artefacts might beserious. Our proposed sample mount (Fig. 2) may yet comeinto fashion. Also the helium gas would be in an enclosureallowing control of the crystal’s temperature to be at 37C,i.e. physiological for mammals. That temperature would notallow much headroom as the protein melting temperature formammalian proteins is around 60C. The alternative solutionto Fig. 2, imported from the XFEL facilities, of serial crys-tallography of course implicitly assumes that every sample isidentical. In a recent study I was thwarted in my detailedanalyses because I merged the cryodiffraction data of twoapparently identical crystals; I only made headway when Ianalysed them separately (Govada et al., 2021). Meanwhile,cryocrystallography continues to prove very effective insynchrotron facility measurement pipelines and with more andmore remote working, as well as mitigating beam heating.These cryo crystal structures, the vast majority in the ProteinData Bank, have also dominated the training set though forprediction of 3D structures using deep learning from aminoacid sequences (Helliwell, 2020).Finally, I note that in Lawrence Bright et al. (2021) theadiabatic approximation has enjoyed a revival with sixdetailed mentions, and with much more besides. Suffice to say,Lawrence Bright et al. (2021) is I think an important paper.ReferencesCheng, A. & Caffrey, M. (1996). Biophys. J. 70, 2212–2222.Cherezov, V., Riedl, K. M. & Caffrey, M. (2002). J. Synchrotron Rad.9, 333–341.scientific commentaries2 of 3 John R. Helliwell  Respect the synchrotron beam strength J. Synchrotron Rad. (2021). 28Figure 1A piece of lead, aligned horizontally, at the SRS 9.6 melts due to the whitebeam.Figure 2A strategy to control crystal sample heating was offered for room-temperature X-ray diffraction measurements at the exceptionally largeESRF X-ray intensities that were planned (Helliwell & Fourme, 1983).Garman, E. F. & Weik, M. (2015). J. Synchrotron Rad. 22, 195–200.Govada, L., Saridakis, E., Kassen, S. C., Bin-Ramzi, A., Morgan,R. M., Chain, B., Helliwell, J. R. & Chayen, N. E. (2021). IUCrJ, 8,678–683.Haas, D. J. & Rossmann, M. G. (1970). Acta Cryst. B26, 998–1004.Halle, B. (2004). Proc. Natl Acad. Sci. USA, 101, 4793–4798.Hedman, B., Hodgson, K. O., Helliwell, J. R., Liddington, R. & Papiz,M. Z. (1985). Proc. Natl Acad. Sci. USA, 82, 7604–7607.Helliwell, J. R. (1984). Rep. Prog. Phys. 47, 1403–1497.Helliwell, J. R. (1988). J. Cryst. Growth, 90, 259–272.Helliwell, J. R. (2020). IUCr Newsl. 28(4), 6.Helliwell, J. R. & Fourme, R. (1983). The ESRF as a facility forprotein crystallography: A report and design study. ESRP ReportIRI-4/83, pp. 1–36.Hope, H. (1988). Acta Cryst. B44, 22–26.Kuzay, T. M., Kazmierczak, M. & Hsieh, B. J. (2001). Acta Cryst. D57,69–81.Lawrence Bright, E., Giacobbe, C. & Wright, J. P. (2021). J.Synchrotron Rad. 28. https://doi.org/10.1107/S160057752100669X.Snell, E. H., Bellamy, H. D., Rosenbaum, G. & van der Woerd, M. J.(2007). J. Synchrotron Rad. 14, 109–115.scientific commentariesJ. Synchrotron Rad. (2021). 28 John R. Helliwell  Respect the synchrotron beam strength 3 of 3

Respect the synchrotron beam strength: how to model it, measure it and mitigate it for various scientific fields

https://chesterrep.openrepository.com/bitstream/10034/625572/2/S1600577521008328.pdf

Respect the synchrotron beam strength: how to model it, measure it and mitigate it for various scientific fields

Abstract

Similar works

Full text

Available Versions

ChesterRep