Anomalous scattering in structural chemistry and biology

The uses of X-ray anomalous scattering in crystal structure analysis have undergone a major expansion due to the refinement and ease of availability of the necessary X-ray instrumentation and methods. The structural chemistry and biology fields span a similar suite of technical needs but with widely differing molecular systems. The innate synergies between the two research fields brought two of the authors (JRH and VK) together at an Erice Summer School on Synchrotron Radiation in Crystallography in 1985 and took them into a collaboration spanning already 20 years. The authors’ wide perspectives are therefore, if not unique, perhaps rather rare. Thus the breadth of coverage of this review is unusual. However, there are two excellent books on anomalous scattering and its uses that have been published covering the periods up to 1975 and 1994 [S. Ramaseshan, S.C. Abrahams (Eds). Anomalous Scattering, Munksgaard, Copenhagen (1975); G. Materlik, C.J. Sparks, K. Fischer (Eds). Resonant Anomalous X-ray Scattering: Theory and Applications, North Holland, Amsterdam (1994)]. As the number of examples of applications in structural biology are now so many it has only been possible to select some illustrative examples but with surveys of trends. In addition though, the development of the methodologies is described in more detail. The structural chemistry applications in, for example, microporous materials, superconductors and magnetic materials is expanding fast but still at a stage where we could attempt to provide a detailed coverage of results, which we have done. Anomalous scattering results on locating metal atoms can also be compared with other technique results and so sections on X-ray Absorption Spectroscopy (XAS), Diffraction Anomalous Fine Structure (DAFS), neutron diffraction and Nuclear Magnetic Resonance (NMR) applications are described where they relate to metal atom location and local structure. Finally anomalous scattering has also been very useful to help develop the modern synchrotron Laue method for quantitative crystal structure analysis, which is also briefly described. ¶Dedicated to Professor Durward W. J. Cruickshank, FRS, Emeritus Professor of Chemistry, The University of Manchester, on the occasion of his 82nd Birthday, 7 March 2006. Durward is an inspiration to us all as a scientist with many fine contributions spanning nearly 60 years, as well as a friend, mentor and colleague to several of us for many years. Contents Introduction 246 1. Brief resume of anomalous scattering 252 1.1. Principles 252 1.2. Different nomenclatures in use for the anomalous scattering coefficients 255 1.3. Some crystal symmetry and diffraction data measurement key facts 258 1.4. Absolute structure: the key definitions 260 2. Some historical notes: the absolute configuration of (R, R)-(1)-tartaric acid was determined by J. M. Bijvoet and colleagues (1951) 262 3. The use of anomalous scattering in structural chemistry 264 3.1. Introduction to site-specific, neighbouring element and valence contrast experiments 264 3.2. Overview of neighbouring element and valence contrast experiments 265 3.3. Applications of anomalous scattering to particular classes of materials 277 3.4. Potential applications of anomalous dispersion in powder diffraction structure solution de novo 290 3.5. The determination of the absolute configuration or hand of smaller molecules using crystallography 292 4. The use of anomalous scattering in structural biology 293 4.1. Previous reviews of the uses of anomalous scattering in protein crystallography especially SR 293 4.2. The location of the anomalous scatterers 296 4.3. MIR, SIROAS and MAD phasing 296 4.4. The recent growth of Single-wavelength Anomalous Dispersion(SAD) phasing 299 4.5. Identification of metals in metalloproteins (Mn, Zn, Cu, Ca) and ions (Cl − , ) in proteins including case studies 307 4.6. Instrumentation case study: line 10 at the SRS 309 5. Use of anomalous scattering derived structural details to help develop the Laue method 311 6. Complementary methods 314 6.1. XAS 314 6.2. Diffraction Anomalous Fine Structure Analysis (The DAFS method) 317 6.3. Neighbouring atom contrast by neutron diffraction methods 319 6.4. Magnetic resonance spectroscopy 320 7. Concluding remarks 323 Acknowledgements 324 References 325 Subject index 333