Serial femtosecond crystallography is an emerging and promising method for determining protein structures, making use of the ultrafast and bright X-ray pulses from X-ray free-electron lasers. The upcoming X-ray laser sources will produce well above 1000 pulses per second and will pose a new challenge: how to quickly determine successful crystal hits and avoid a high-rate data deluge. Proposed here is a hit-finding scheme based on detecting photons from plasma emission after the sample has been intercepted by the X-ray laser. Plasma emission spectra are simulated for systems exposed to high-intensity femtosecond pulses, for both protein crystals and the liquid carrier systems that are used for sample delivery. The thermal radiation from the glowing plasma gives a strong background in the XUV region that depends on the intensity of the pulse, around the emission lines from light elements (carbon, nitrogen, oxygen). Sample hits can be reliably distinguished from the carrier liquid based on the characteristic emission lines from heavier elements present only in the sample, such as sulfur. For buffer systems with sulfur present, selenomethionine substitution is suggested, where the selenium emission lines could be used both as an indication of a hit and as an aid in phasing and structural reconstruction of the protein.

Center for Free Electron Laser Science Deutsches Elektronen Synchrotron Notkestraße 85 DE 226 07 Hamburg Germany

Condensed Matter Physics Department of Physics Chalmers University of Technology SE 412 96 Göteborg Sweden

Department of Cell and Molecular Biology Uppsala University Box 596 SE 751 24 Uppsala Sweden

Department of Physics and Astronomy Uppsala University Box 516 SE 751 20 Uppsala Sweden

ELI Beamlines Institute of Physics Czech Academy of Science Na Slovance 2 CZ 182 21 Prague Czech Republic

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