A microfabricated fixed path length silicon sample holder improves background subtraction for cryoSAXS

Abstract

The application of small-angle X-ray scattering (SAXS) for high-throughput characterization of biological macromolecules in solution is limited by radiation damage. By cryocooling samples, radiation damage and required sample volumes can be reduced by orders of magnitude. However, the challenges of reproducibly creating the identically sized vitrified samples necessary for conventional background subtraction limit the widespread adoption of this method. Fixed path length silicon sample holders for cryoSAXS have been microfabricated to address these challenges. They have low background scattering and X-ray absorption, require only 640 nl of sample, and allow reproducible sample cooling. Data collected in the sample holders from a nominal illuminated sample volume of 2.5 nl are reproducible down to q ' 0.02 Å À1, agree with previous cryoSAXS work and are of sufficient quality for reconstructions that match measured crystal structures. These sample holders thus allow faster, more routine cryoSAXS data collection. Additional development is required to reduce sample fracturing and improve data quality at low q.

Quantifying radiation damage in biomolecular small-angle X-ray scattering

“…The best strategies for reducing radiation damage remain oscillating or flowing the sample through the beam, to spread out the absorbed energy over a large volume (lowering the dose), and the addition of small-molecule compounds to the buffer to reduce damage (Fischetti et al, 2003;Kuwamoto et al, 2004;Lipfert et al, 2006;Jeffries et al, 2015). Additionally, cryocooling samples to 100 K can greatly reduce damage to the samples (Meisburger et al, 2013;Hopkins et al, 2015). As X-ray sources get brighter, with the upgrade of third-generation sources and the construction of fourthgeneration sources, the need to prevent radiation damage will get more urgent.…”

“…These approaches can be employed in parallel and result in the limitations on sample volume and exposure time given above. Cryocooling samples to 100 K has been shown to reduce radiation damage rates in SAXS (Meisburger et al, 2013;Hopkins et al, 2015), but substantial methodological development is required before cryocooling can be accepted for routine use. Despite the importance of radiation damage as a limiting factor in SAXS, early efforts using laboratory X-ray sources (Zipper & Durchschlag, 1980a,b,c, 1981Zipper et al, 1980Zipper et al, , 1985Zipper & Kriechbaum, 1986) have been followed by only two systematic, quantitative studies at synchrotron sources (Kuwamoto et al, 2004;Jeffries et al, 2015).…”

Development of tools to automate quantitative analysis of radiation damage in SAXS experiments

“…In an analogous manner to cryo-cooling in macromolecular crystallography (MX) (Garman, 1999), cryo-cooling samples down to 100 K for SAXS (cryoSAXS) has been reported to increase the dose tolerance of SAXS samples by at least two orders of magnitude (Meisburger et al, 2013). Despite developments to improve the experimental apparatus for cryoSAXS (Hopkins et al, 2015), it still requires specialized equipment and a certain level of technical expertise, which prevents it from currently being a commonly accessible technique . Additives such as glycerol, ethylene glycol, sucrose and sodium ascorbate can be added to the SAXS sample to increase the dose tolerance of the sample (Grishaev, 2012;Kuwamoto et al, 2004).…”

Density and electron density of aqueous cryoprotectant solutions at cryogenic temperatures for optimized cryoprotection and diffraction contrast

“…Previous cryo-SAXS measurements (Meisburger et al, 2013;Hopkins et al, 2015) used 45%(w/w) PEG 200 and 36%(w/w) propylene glycol solutions to prevent ice formation. At 40%(w/w), the monoalcohols give the largest electrondensity contrast Á, and forward scattering I(q!0) / (Á) 2 roughly double that of a 40%(w/w) glycerol solution.…”

“…Ice formation is also a critical problem in cryogenic temperature X-ray imaging of, for example, hydrated cells (Huang et al, 2009;Rodriguez et al, 2015;Lima et al, 2009), and in cryo-electron microscopy (cryo-EM; Costello, 2006), especially in highresolution single-particle cryo-EM, where diffraction images of enormous numbers of molecules must be combined to generate high-resolution structures. Even when crystalline ice ISSN 2059-7983 does not form, thermal contraction or expansion on cooling to the glass phase can damage samples (Juers & Matthews, 2004;Kriminski et al, 2002;Rabin et al, 2006;Hopkins et al, 2015). Differential contraction between internal and external solvent and protein crystals, between regions of a cell or tissue having different solvent contents, between cryo-SAXS samples and their holders, and between thin-film X-ray imaging and cryo-EM samples and their supports can cause sample deformation, creep, fracturing and microscale disorder.…”