International
Tables for
Crystallography
Volume F
Crystallography of biological molecules
Edited by M. G. Rossmann and E. Arnold

International Tables for Crystallography (2006). Vol. F, ch. 8.1, pp. 158-161   | 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: john.helliwell@man.ac.uk

8.1.5. Evolution of SR machines and experiments

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8.1.5.1. First-generation SR machines

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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. 8.1.5.1)[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 (Wilson et al., 1983[link]) for high-resolution data collection. 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 brilliance 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 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 (<10−3). 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]). Values of f′ over a continuum of wavelengths in a real compound (i.e., not a metal in the gas phase) (Fig. 8.1.5.1b[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 8.1.5.2[link]).

[Figure 8.1.5.1]

Figure 8.1.5.1 | top | pdf |

Anomalous dispersion. (a) f″ as represented by an absorption spectrum [Pt LIII edge for K2Pt(CN)4 as the example] (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.

8.1.5.2. Second-generation dedicated machines

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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 r.f. 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; 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]].

8.1.5.3. Third-generation high-brilliance machines

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As early as 1979, there were discussions on planning a proposal for a high-brilliance, insertion-device-driven European synchrotron-radiation (ESR) source. A wide variety of discussion documents and workshops, and the ESR project 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 brilliance, 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 ultra-small 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 accessible.

8.1.5.4. New national SR machines

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Today a variety of enhanced national SR machines are being proposed and/or built. In the UK there is the DIAMOND 3 GeV machine and in France there is SOLEIL. The SLS in Switzerland, the country's first SR light source, is under construction. 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 brilliance, i.e., low emittance. The 2 GeV high-brilliance 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 these new national SR sources. Table 8.1.5.1[link] compares the parameters of the mature SRS of 1997 (from Munro, 1997[link]) with the proposed design for DIAMOND (Suller, 1994[link]). A shift of emphasis to high brilliance is again clear, as the applications of SR involving small samples dominate. Likewise, a 3 GeV machine energy is indicative of the need to include a provision of high photon energies for many applications, including, obviously, access to short-wavelength absorption edges. The extent to which undulators, for <3 GeV, will reach the hard X-ray region at high brilliance (e.g. around 1 Å wavelength) will depend on the minimum undulator magnet gaps realizable, along with magnet shimming to improve high harmonic emission. Moreover, longer wavelengths in protein crystallography are being explored on lower-energy SR machines (e.g. <3 GeV) at >1.5 Å, even 2.5 Å (Helliwell 1993[link], 1997a[link]; Polikarpov et al., 1997[link]; Teplyakov et al., 1998[link]), and even softer wavelengths are under active development to utilize the S K edge for anomalous dispersion (Stuhrmann & Lehmann, 1994[link]). Such developments interact closely with machine and beamline specifications. At very short (~0.5 Å) and ultra-short (~0.3 Å) wavelengths, a high machine energy yields copious flux output; pilot studies have been conducted in protein crystallography at CHESS (Helliwell et al., 1993[link]) and at the ESRF (Schiltz et al., 1997[link]).

Table 8.1.5.1| top | pdf |
A comparison of the parameter list for the 2 GeV SRS, 1997, and the new higher-energy machine for the UK, DIAMOND

S/C = superconducting magnet; MW = multipole wiggler (permanent magnet design).

 SRS DIAMOND
Storage ring energy 2 GeV 3 GeV §
Circumference 96 m 350 m
Beam emittance 110 nm rad 15 nm rad
Beam current after injection 300 mA 300 mA
Typical dipole beam source sizes (σ)    
 horizontal 900 µm 400 µm
 vertical 200 µm 150 µm
Critical energy    
 dipole 3.2 keV 20 keV (S/C)
 wiggler 13.3 keV (S/C) 10 keV (MW)
From Munro (1997)[link].
From Suller (1994)[link] and Suller (1998)[link].
§Up to 3.5 GeV.
A larger circumference is now proposed.

8.1.5.5. X-ray free electron laser (XFEL)

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In terms of the evolution of X-ray sources, mention should be made of the X-ray free electron laser (XFEL); it now seems feasible that this will yield wavelength output well below the visible region of the electromagnetic spectrum. At DESY in Hamburg (Brinkmann et al., 1997[link]) and at SLAC (Winick, 1995[link]), such considerations and developments are being pursued. Compared to SR, one would obtain a transversely fully coherent beam, a larger average brilliance and, in particular, pulse lengths of ~200 fs full width at half-maximum with eight to ten orders of magnitude larger peak brilliance. 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 brilliance.

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