Tables for
Volume F
Crystallography of biological macromolecules
Edited by E. Arnold, D. M. Himmel and M. G. Rossmann

International Tables for Crystallography (2012). Vol. F, ch. 8.1, pp. 192-194   | 1 | 2 |

Section 8.1.5. Evolution of SR machines and experiments

J. R. Helliwella*

aDepartment of Chemistry, University of Manchester, M13 9PL, England
Correspondence e-mail:

8.1.5. Evolution of SR machines and experiments

| top | pdf | First-generation SR machines

| top | pdf |

The so-called first generation of SR machines were those which were parasitic on high-energy physics operations, such as DESY in Hamburg, SPEAR in Stanford, NINA in Daresbury and VEPP in Novosibirsk. These machines had high fluxes into the X-ray range and enabled pioneering experiments. Parratt (1959)[link] discussed the use of the CESR (Cornell Electron Storage Ring) for X-ray diffraction and spectroscopy in a very perceptive paper. Cauchois et al. (1963)[link] conducted L-edge absorption spectroscopy at Frascati and were the first to diffract SR with a crystal (quartz). The opening experimental work in the area of biological diffraction was by Rosenbaum et al. (1971)[link]. In protein crystallography, multiple-wavelength anomalous-dispersion effects (Fig.[link] were used from the onset (Phillips et al., 1976[link], 1977[link]; Phillips & Hodgson, 1980[link]; Webb et al., 1977[link]; Harmsen et al., 1976[link]; Helliwell, 1977[link], 1979[link]), and a reduction in radiation damage was seen for high-resolution data collection (Wilson et al., 1983[link]). Historical insights into the performances of those machines, from the current-day perspective, are described in detail, for example, by Huxley & Holmes (1997)[link] at DESY, Munro (1997)[link] at Daresbury, and Doniach et al. (1997)[link] at Stanford. A principal limitation was the problem of source movements, which degraded the focusing of the source onto a small crystal or single fibre and thus degraded the intrinsic spectral brightness of the beam; see, for example, Haslegrove et al. (1977)[link], who advocated machine shifts dedicated to SR as a working compromise with the high-energy physicists. Some possible applications that were discussed were unfulfilled until brighter sources became available. The two-wavelength crystallography phasing method of Okaya & Pepinsky (1956)[link] (see also Hoppe & Jakubowski, 1975[link]) and the three-wavelength method of Herzenberg & Lau (1967)[link], as well as the implementation of the algebraic method of Karle (1967[link], 1980[link], 1989[link], 1994[link]), awaited more stable beams, which had to be rapidly and easily tunable over a fine bandpass (ideally 10−4). Experiments to define the anomalous-dispersion coefficients, including dichroism effects, at a large number of wavelengths at several example absorption edges in a variety of crystal structures were conducted at SPEAR (Phillips et al., 1978[link]; Templeton et al., 1980[link], 1982[link]; Templeton & Templeton, 1985[link]). Large values of f′′ were identified at `white lines', i.e. regions of the elemental absorption with pronounced effects (e.g. see Fig[link]). Values of f′ over a continuum of wavelengths in a real compound (i.e., not a metal in the gas phase) (Fig.[link]) were explored in a profile approach (now called DAFS, diffraction anomalous fine structure) by Arndt et al. (1982)[link] at the newly commissioned SRS, the first dedicated second-generation SR source (see Section[link]).


Figure | top | pdf |

Anomalous dispersion. (a) f″ as represented by an absorption spectrum [Pt LIII edge for K2Pt(CN)4 as the example with 19 electrons for f″ at the peak of that `white line', with pre-edge and post-edge f″ electron values also indicated] (Helliwell, 1984[link]). Reproduced with the permission of the Institute of Physics. (b) f′ as estimated by a continuous polychromatic profile method. Reproduced with permission from Nature (Arndt et al., 1982[link]). Copyright (1982) MacMillan Magazines Limited. Second-generation dedicated machines

| top | pdf |

The building of dedicated X-ray sources began with the SRS at Daresbury, which came online in 1980, having followed the NINA synchrotron (closed in 1976) and the associated Synchrotron Radiation Facility at Daresbury. Elsewhere in the world, LURE (Lemonnier et al., 1978[link]) and CHESS at Cornell were building up their SR macromolecular crystallography operations in the late 1970s and early 1980s, and the NSLS in Brookhaven and the Photon Factory (PF) in Japan were both under construction. The NSLS and the PF came online in 1983 and 1984, respectively. Thus, there was a rapid increase in the number of operating machines and beamlines worldwide in the X-ray region for protein crystallography. There were teething problems with the SRS with the radio-frequency cavity window problem, interrupting operation for many months in 1983, and at the NSLS in its early period due to vacuum-chamber problems. Pioneering experiments continued and blossomed. Seminal work ensued in virus crystallography [Rossmann & Erickson (1983)[link] at Hamburg and Daresbury; and Usha et al. (1984)[link] at LURE], Laue diffraction for time-resolved protein crystallography [Moffat et al. (1984)[link] at CHESS; Helliwell (1984[link], 1985[link]) at the SRS; Cruickshank et al. (1987[link], 1991[link]); Hajdu, Machin et al. (1987)[link]; Helliwell et al. (1989)[link]; Bourenkov et al. (1996)[link]; Neutze & Hajdu (1997)[link]], enzyme catalysis in the crystal [Hajdu, Acharya et al. (1987[link]) at the SRS], MAD [Phillips et al. (1977)[link]; Einspahr et al. (1985)[link]; Hendrickson (1985)[link]; Hendrickson et al. (1989)[link] at SPEAR, the SRS and the PF; Guss et al. (1988)[link] at SPEAR; Kahn et al. (1985)[link] at LURE; Korszun (1987)[link] at CHESS; Mukherjee et al. (1989)[link] and Peterson et al. (1996)[link] at the SRS; Hädener et al. (1999)[link] at the SRS and the ESRF, to cite a few experiments], protein crystallography involving isomorphous replacement with optimized anomalous scattering [Baker et al. (1990)[link] at the SRS; Dumas et al. (1995)[link] at LURE], small crystals [Hedman et al. (1985)[link] at the SRS] and diffuse scattering with SR [Doucet & Benoit (1987)[link]; Caspar et al. (1988)[link]; Glover et al. (1991)[link]]. Table[link] shows the impact of the SRS in protein (i.e. macromolecular) crystallography integrated over its whole lifetime.

Table| top | pdf |
Structures in the Protein Data Bank (PDB) for which data were collected at the SRS

The data presented here were compiled in December 2009 (see ) and are likely to be reasonably complete since the SRS closed operations in August 2008. The SRS has delivered 3.6% of the total of 38 650 macromolecular crystal structures determined using radiation from synchrotrons around the world as of December 2009. The ESRF third-generation source, in comparison, integrated over about half as many years, but about two to three times more beamlines, has delivered 15.6% of the structures, i.e. at a rate therefore about three to four times greater than the second-generation SRS.

Year10. known
1995 0 0 0 5 6 19 3
1996 0 0 0 6 11 33 0
1997 0 0 0 11 29 43 0
1998 0 0 0 26 32 35 0
1999 0 0 0 28 13 45 4
2000 0 1 0 28 17 60 3
2001 0 13 9 9 16 47 2
2002 0 13 21 7 7 59 2
2003 0 27 38 3 8 41 3
2004 3 40 42 5 2 36 2
2005 18 34 36 1 4 47 1
2006 22 32 22 1 1 23 0
2007 21 37 21 0 0 11 1
2008 51 15 15 2 0 20 1
2009 14 12 5 1 0 3 0
Total 129 224 209 133 146 522 22 Third-generation high spectral brightness machines

| top | pdf |

As early as 1979, there were discussions on planning a proposal for a high spectral brightness, insertion-device-driven European synchrotron-radiation (ESR) source. A wide variety of discussion documents and workshops, and the ESR Project (ESRP) led by B. Buras and based in Geneva at CERN, culminated in the so-called `Red Book' in 1987, the ESRF Foundation Phase Report (1987)[link], totalling some 1000 pages of machine, beamline and experimental specifications and costs. This, then, was the progenitor of the third-generation sources, characterized by their high energy and high spectral brightness, tailored to optimized undulator emission in the 1 Å range. Actually, the ESRF machine energy was initially set at 5 GeV, but increased to 6 GeV to optimize the production of 14.4 keV photons to better match the nuclear scattering experiments proposed initially by Mossbauer in 1975. Proposals for the US machine, the Advanced Photon Source at 7 GeV, and the Japanese 8 GeV SPring-8 machine followed, with the higher machine energy enhancing the X-ray tuning range of undulators. Thus, MAD tuning-based techniques were facilitated with these machines and studies involving yet-smaller samples (crystals, single fibres or tiny liquid aliquots) or very large unit cells were enabled. As a result, micron-sized protein crystals as well as huge multi-macromolecular biological structures (of large viruses, for example) also became routinely accessible. New national SR machines

| top | pdf |

Today a variety of enhanced national SR machines have been built. In Switzerland there is the SLS, in the UK there is DIAMOND and in France there is SOLEIL. These machines are more tailored to the bulk of a country's user needs, distinct from the special provisions at the ESRF. The different countries' SR needs, of course, have many aspects in common, with some historical biases. The new sources are, in essence, characterized by high spectral brightness, i.e., low emittance. The 2 GeV SR source ELETTRA in Trieste, the MAXII machine in LUND and the Brazilian Light Source are already operational. In many ways, national sources like the SRS, LURE, DORIS and so on fuelled the case and specification for the ESRF. Now the developments at the ESRF, including high harmonic emission of undulators via magnet shimming (Elleaume, 1989[link]) and narrow-gap undulator operation (Elleaume, 1998[link]), are fuelling ideas and the specification of what is possible in the new national SR sources. X-ray free-electron lasers (XFELs)

| top | pdf |

In terms of the evolution of X-ray sources, X-ray FELs are being constructed at DESY in Hamburg (Brinkmann et al., 1997[link]), at SLAC (Winick, 1995[link]) and at Spring8. Compared to SR, one will have a transversely fully coherent beam, a larger average spectral brightness and, in particular, pulse lengths of ~10 fs full width at half-maximum with eight to ten orders of magnitude larger peak spectral brightness. Such a machine is based on a linear accelerator (linac)-driven XFEL utilizing a linear collider installation (e.g., for a high-energy physics centre-of-mass energy capability of 500 GeV). For this machine there is a `switchyard' distributing the electrons in a beam to different undulators from which the X-rays are generated in the range 0.1 to ~12 keV. The anticipated r.m.s. opening angle would be 1 mrad and the source diameter would be 20 µm. This source of X-rays would then compete in time resolution with laser-pulse-generated X-ray beams [see Helliwell & Rentzepis (1997)[link] for a survey of that work and a comparison with synchrotron radiation] and would also have higher pulse flux. Coherent methods in the X-ray sciences have been extensively reviewed by Nugent (2009[link]).


ESRF Foundation Phase Report (1987). Grenoble: ESRF.
Arndt, U. W., Greenhough, T. J., Helliwell, J. R., Howard, J. A. K., Rule, S. A. & Thompson, A. W. (1982). Optimised anomalous dispersion crystallography: a synchrotron X-ray polychromatic simultaneous profile method. Nature (London), 298, 835–838.
Baker, P. J., Farrants, G. W., Stillman, T. J., Britton, K. L., Helliwell, J. R. & Rice, D. W. (1990). Isomorphous replacement with optimized anomalous scattering applied to protein crystallography. Acta Cryst. A46, 721–725.
Bourenkov, G. P., Popov, A. N. & Bartunik, H. D. (1996). A Bayesian approach to Laue diffraction analysis and its potential for time-resolved protein crystallography. Acta Cryst. A52, 797–811.
Brinkmann, R., Materlik, G., Rossbach, J., Schneider, J. R. & Wilk, B. H. (1997). An X-ray FEL laboratory as part of a linear collider design. Nucl. Instrum. Methods, 393, No. 1–3, 86–92.
Caspar, D. L. D., Clarage, J., Salunke, D. M. & Clarage, M. (1988). Liquid-like movements in crystalline insulin. Nature (London), 352, 659–662.
Cauchois, Y., Bonnelle, C. & Missoui, G. (1963). Rayonnement electromagnetique – premiers spectres X du rayonnement d'orbite du synchrotron de Frascati. C. R. Acad. Sci. Paris, 257, 409–412.
Cruickshank, D. W. J., Helliwell, J. R. & Moffat, K. (1987). Multiplicity distribution of reflections in Laue diffraction. Acta Cryst. A43, 656–674.
Cruickshank, D. W. J., Helliwell, J. R. & Moffat, K. (1991). Angular distribution of reflections in Laue diffraction. Acta Cryst. A47, 352–373.
Doniach, S., Hodgson, K., Lindau, I., Pianetta, P. & Winick, H. (1997). Early work with synchrotron radiation at Stanford. J. Synchrotron Rad. 4, 380–395.
Doucet, J. & Benoit, J. P. (1987). Molecular dynamics by analysis of the X-ray diffuse scattering from lysozyme crystals. Nature (London), 325, 643–646.
Dumas, C., Duquerroy, S. & Janin, J. (1995). Phasing with mercury at 1 Å wavelength. Acta Cryst. D51, 814–818.
Einspahr, H., Suguna, K., Suddath, F. L., Ellis, G., Helliwell, J. R. & Papiz, M. Z. (1985). The location of manganese and calcium ion cofactors in pea lectin crystals by use of anomalous dispersion and tuneable synchrotron X-radiation. Acta Cryst. B41, 336–341.
Elleaume, P. (1989). Special synchrotron radiation sources. Part 1: conventional insertion devices. Synchrotron Radiat. News, 1, 18–23.
Elleaume, P. (1998). Two-plane focusing of 30 keV undulator radiation. J. Synchrotron Rad. 5, 1–5.
Glover, I. D., Harris, G. W., Helliwell, J. R. & Moss, D. S. (1991). The variety of X-ray diffuse scattering from macromolecular crystals and its respective components. Acta Cryst. B47, 960–968.
Guss, J. M., Merritt, E. A., Phizackerley, R. P., Hedman, B., Murata, M., Hodgson, K. O. & Freeman, H. C. (1988). Phase determination by multiple wavelength X-ray diffraction – crystal structure of a basic blue copper protein from cucumbers. Science, 241, 806–811.
Hajdu, J., Acharya, K. R., Stuart, D. I., McLaughlin, P. J., Barford, D., Oikonomakos, N. G., Klein, H. & Johnson, L. N. (1987). Catalysis in the crystal – synchrotron radiation studies with glycogen phosphorylase. EMBO J. 6, 539–546.
Hajdu, J., Machin, P. A., Campbell, J. W., Greenhough, T. J., Clifton, I. J., Zurek, S., Gover, S., Johnson, L. N. & Elder, M. (1987). Millisecond X-ray diffraction and the first electron density map from Laue photographs of a protein crystal. Nature (London), 329, 178–181.
Harmsen, A., Leberman, R. & Schultz, G. E. (1976). Comparison of protein crystal diffraction patterns and absolute intensities from synchrotron and conventional X-ray sources. J. Mol. Biol. 104, 311–314.
Haslegrove, J. C., Faruqi, A. R., Huxley, H. E. & Arndt, U. W. (1977). The design and use of a camera for low-angle X-ray diffraction experiments with synchrotron radiation. J. Phys. E, 10, 1035–1044.
Hedman, B., Hodgson, K. O., Helliwell, J. R., Liddington, R. & Papiz, M. Z. (1985). Protein micro-crystal diffraction and the effects of radiation damage with ultra high flux synchrotron radiation. Proc. Natl Acad. Sci. USA, 82, 7604–7607.
Helliwell, J. R. (1977). Application of synchrotron radiation to protein crystallography: preliminary experiments on 6PDGH crystals using the NINA synchrotron, Daresbury, UK. DPhil thesis, University of Oxford, Appendix 1.
Helliwell, J. R. (1979). Optimisation of anomalous scattering and structural studies of proteins using synchrotron radiation. In Proceedings of the Study Weekend. Applications of SR to the Study of Large Molecules of Chemical and Biological Interest, edited by R. B. Cundall & I. H. Munro, pp. 1–6. DL/SCI/R13. Warrington: Daresbury Laboratory.
Helliwell, J. R. (1984). Synchrotron X-radiation protein crystallography: instrumentation, methods and applications. Rep. Prog. Phys. 47, 1403–1497.
Helliwell, J. R. (1985). Protein crystallography with synchrotron radiation. J. Mol. Struct. 130, 63–91.
Helliwell, J. R., Habash, J., Cruickshank, D. W. J., Harding, M. M., Greenhough, T. J., Campbell, J. W., Clifton, I. J., Elder, M., Machin, P. A., Papiz, M. Z. & Zurek, S. (1989). The recording and analysis of synchrotron X-radiation Laue diffraction photographs. J. Appl. Cryst. 22, 483–497.
Helliwell, J. R. & Rentzepis, P. M. (1997). Editors. Time-resolved Diffraction. Oxford University Press.
Hendrickson, W. A. (1985). Analysis of protein structure from diffraction measurements at multiple wavelengths. Trans. Am. Crystallogr. Assoc. 21, 11–21.
Hendrickson, W. A., Pahler, A., Smith, J. L., Satow, Y., Merritt, E. A. & Phizackerley, R. P. (1989). Crystal structure of core streptavadin determined from multi-wavelength anomalous diffraction of synchrotron radiation. Proc. Natl Acad. Sci. USA, 86, 2190–2194.
Herzenberg, A. & Lau, H. S. M. (1967). Anomalous scattering and the phase problem. Acta Cryst. 22, 24–28.
Hoppe, W. & Jakubowski, V. (1975). The determination of phases of erythrocruorin using the two-wavelength method with iron as anomalous scatterer. In Anomalous Scattering, edited by S. Ramaseshan & S. C. Abrahams, pp. 437–461. Copenhagen: Munksgaard.
Huxley, H. E. & Holmes, K. C. (1997). Development of synchrotron radiation as a high-intensity source for X-ray diffraction. J. Synchrotron Rad. 4, 366–379.
Hädener, A., Matzinger, P. K., Battersby, A. R., McSweeney, S., Thompson, A. W., Hammersley, A. P., Harrop, S. J., Cassetta, A., Deacon, A., Hunter, W. N., Nieh, Y. P., Raftery, J., Hunter, N. & Helliwell, J. R. (1999). Determination of the structure of seleno-methionine-labelled hydroxymethylbilane synthase in its active form by multi-wavelength anomalous dispersion. Acta Cryst. D55, 631–643.
Kahn, R., Fourme, R., Bosshard, R., Chiadmi, M., Risler, J. L., Dideberg, O. & Wery, J. P. (1985). Crystal structure study of opsanus-tau parvalbumin by multi-wavelength anomalous dispersion. FEBS Lett. 170, 133–137.
Karle, J. (1967). Anomalous scatterers in X-ray diffraction and the use of several wavelengths. Appl. Opt. 6, 2132–2135.
Karle, J. (1980). Some anomalous dispersion developments for the structure investigation of macromolecular systems in biology. Int. J. Quantum Chem. Symp. 7, 357–367.
Karle, J. (1989). Macromolecular structure from anomalous dispersion. Phys. Today, 42, 22–29.
Karle, J. (1994). Developments in anomalous scattering for structure determination. In Resonant Anomalous X-ray Scattering, edited by G. Materlik, C. J. Sparks & K. Fischer, pp. 145–158. Amsterdam: North Holland.
Korszun, Z. R. (1987). The tertiary structure of azurin from pseudomonas-denitrificans as determined by Cu resonant diffraction using synchrotron radiation. J. Mol. Biol. 196, 413–419.
Lemonnier, M., Fourme, R., Rousseaux, F. & Kahn, R. (1978). X-ray curved-crystal monochromator system at the storage ring DCI. Nucl. Instrum. Methods, 152, 173–177.
Moffat, K., Szebenyi, D. & Bilderback, D. H. (1984). X-ray Laue diffraction from protein crystals. Science, 223, 1423–1425.
Mukherjee, A. K., Helliwell, J. R. & Main, P. (1989). The use of MULTAN to locate the positions of anomalous scatterers. Acta Cryst. A45, 715–718.
Munro, I. H. (1997). Synchrotron radiation research in the UK. J. Synchrotron Rad. 4, 344–358.
Neutze, R. & Hajdu, J. (1997). Femtosecond time resolution in X-ray diffraction experiments. Proc. Natl Acad. Sci. USA, 94, 5651–5655.
Nugent, K. (2009). Coherent methods in the X-ray sciences. Adv. Phys. 59, 1–99.
Okaya, Y. & Pepinsky, R. (1956). New formulation and solution of the phase problem in X-ray analysis of non-centric crystals containing anomalous scatterers. Phys. Rev. 103, 1645–1647.
Parratt, L. G. (1959). Use of synchrotron orbit-radiation in X-ray physics. Rev. Sci. Instrum. 30, 297–299.
Peterson, M. R., Harrop, S. J., McSweeney, S. M., Leonard, G. A., Thompson, A. W., Hunter, W. N. & Helliwell, J. R. (1996). MAD phasing strategies explored with a brominated oligonucleotide crystal at 1.65 Å resolution. J. Synchrotron Rad. 3, 24–34.
Phillips, J. C. & Hodgson, K. O. (1980). The use of anomalous scattering effects to phase diffraction patterns from macromolecules. Acta Cryst. A36, 856–864.
Phillips, J. C., Templeton, L. K., Templeton, D. H. & Hodgson, K. O. (1978). L-III edge anomalous X-ray scattering by cesium measured with synchrotron radiation. Science, 201, 257–259.
Phillips, J. C., Wlodawer, A., Goodfellow, J. M., Watenpaugh, K. D., Sieker, L. C., Jensen, L. H. & Hodgson, K. O. (1977). Applications of synchrotron radiation to protein crystallography. II. Anomalous scat­tering, absolute intensity and polarization. Acta Cryst. A33, 445–455.
Phillips, J. C., Wlodawer, A., Yevitz, M. M. & Hodgson, K. O. (1976). Applications of synchrotron radiation to protein crystallography: preliminary results. Proc. Natl Acad. Sci. USA, 73, 128–132.
Rosenbaum, G., Holmes, K. C. & Witz, J. (1971). Synchrotron radiation as a source for X-ray diffraction. Nature (London), 230, 434–437.
Rossmann, M. G. & Erickson, J. W. (1983). Oscillation photography of radiation-sensitive crystals using a synchrotron source. J. Appl. Cryst. 16, 629–636.
Templeton, D. H. & Templeton, L. K. (1985). X-ray dichroism and anomalous scattering of potassium tetrachloroplatinate(II). Acta Cryst. A41, 365–371.
Templeton, D. H., Templeton, L. K., Phillips, J. C. & Hodgson, K. O. (1980). Anomalous scattering of X-rays by cesium and cobalt measured with synchrotron radiation. Acta Cryst. A36, 436–442.
Templeton, L. K., Templeton, D. H., Phizackerley, R. P. & Hodgson, K. O. (1982). L3-edge anomalous scattering by gadolinium and samarium measured at high resolution with synchrotron radiation. Acta Cryst. A38, 74–78.
Usha, R., Johnson, J. E., Moras, D., Thierry, J. C., Fourme, R. & Kahn, R. (1984). Macromolecular crystallography with synchrotron radiation: collection and processing of data from crystals with a very large unit cell. J. Appl. Cryst. 17, 147–153.
Webb, N. G., Samson, S., Stroud, R. M., Gamble, R. C. & Baldeschwieler, J. D. (1977). A focusing monochromator for small-angle diffraction studies with synchrotron radiation. J. Appl. Cryst. 10, 104–110.
Wilson, K. S., Stura, E. A., Wild, D. L., Todd, R. J., Stuart, D. I., Babu, Y. S., Jenkins, J. A., Standing, T. S., Johnson, L. N., Fourme, R., Kahn, R., Gadet, A., Bartels, K. S. & Bartunik, H. D. (1983). Macromolecular crystallography with synchrotron radiation. II. Results. J. Appl. Cryst. 16, 28–41.
Winick, H. (1995). The linac coherent light source (LCLS): a fourth-generation light source using the SLAC linac. J. Electron Spectrosc. Relat. Phenom. 75, 1–8.

to end of page
to top of page