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Radiation damage in small-molecule crystallography: fact not fiction - PubMed

  • ️Tue Jan 01 2019

Radiation damage in small-molecule crystallography: fact not fiction

Jeppe Christensen et al. IUCrJ. 2019.

Abstract

Traditionally small-molecule crystallographers have not usually observed or recognized significant radiation damage to their samples during diffraction experiments. However, the increased flux densities provided by third-generation synchrotrons have resulted in increasing numbers of observations of this phenomenon. The diversity of types of small-molecule systems means it is not yet possible to propose a general mechanism for their radiation-induced sample decay, however characterization of the effects will permit attempts to understand and mitigate it. Here, systematic experiments are reported on the effects that sample temperature and beam attenuation have on radiation damage progression, allowing qualitative and quantitative assessment of their impact on crystals of a small-molecule test sample. To allow inter-comparison of different measurements, radiation-damage metrics (diffraction-intensity decline, resolution fall-off, scaling B-factor increase) are plotted against the absorbed dose. For ease-of-dose calculations, the software developed for protein crystallography, RADDOSE-3D, has been modified for use in small-molecule crystallography. It is intended that these initial experiments will assist in establishing protocols for small-molecule crystallographers to optimize the diffraction signal from their samples prior to the onset of the deleterious effects of radiation damage.

Keywords: dose; global damage; radiation damage; small-molecule crystallography; specific damage.

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Figures

Figure 1
Figure 1

1D polymers extending down the b axis (into the page) and (a) hydrogen bonding of the hydrates in the channels formed between them. (b) A perpendicular view clearly indicating water channels. Carbon is shown in black, nitro­gen is shown in blue, oxygen is shown in red and nickel is shown in green.

Figure 2
Figure 2

Results from experiment 1. The effect of sample decay at 100 K on (a) diffraction limit and (b) normalized average intensity as a function of dose.

Figure 3
Figure 3

The change in R merge (diamonds) and traditional refinement atomic R-factor (triangles) values as a function of absorbed dose, where formula image and formula image formula image.

Figure 4
Figure 4

Thermal ellipsoid plots based on (a) the first i.e. 0.63 MGy and (b) the 14th i.e. 8.82 MGy scans. Carbon is shown in blue, nitro­gen is shown in purple, oxygen is shown in red and nickel is shown in green. (c) The graph shows the development of U eq for the nickel site as a function of dose.

Figure 5
Figure 5

Residual density plots based on data from (a) the first scan, i.e. 0.63 MGy, and from (b) the 12th scan, i.e. 7.56 MGy. Carbon is shown in grey, nitro­gen is shown in blue, oxygen is shown in red, hydrogen is shown in white and nickel is shown in dark blue/purple. Residual peaks are coloured brown and the numbered Q labels refer to a ranked peak height. Values for residuals in hydrogen positions are 0.48–0.63 e Å3 and 0.31–0.40 e Å3 for structures shown in (a) and (b), respectively.

Figure 6
Figure 6

The variation in suggested resolution limit (calculated from CC1/2) as a function of dose for experiment 1 (diamonds) and experiment 4 (squares). The two experiments were performed at the same beamline settings and the experimental resolution limit was 0.59 Å. Circles (a), (b) and (c) indicate datasets with similar resolution [(a) and (b)] or similar dose [(b) and (c)] (see discussion below).

Figure 7
Figure 7

Average integrated intensity (normalized to 100) for each scan for experiment 1 (diamonds) and experiment 4 (squares).

Figure 8
Figure 8

Comparison of structural models for the three data points [(a), (b) and (c)] indicated in Table 3 ▸. Carbon is shown in blue, nitro­gen is shown in purple, oxygen is shown in red and nickel is shown in green.

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Grants and funding

This work was funded by Engineering and Physical Sciences Research Council grants PR150005 and EP/G03706X/1. Suomen Kulttuurirahasto grant . Diamond Light Source grant MT15762 to Simon Coles.