Perspectives for imaging single protein molecules with the present design of the European XFEL

The Single Particles, Clusters and Biomolecules & Serial Femtosecond Crystallography (SPB/SFX) instrument at the European XFEL is located behind the SASE1 undulator and aims to support imaging and structure determination of biological specimen between about 0.1 μm and 1 μm size. The instrument is designed to work at photon energies from 3 keV up to 16 keV. Here, we propose a cost-effective proof-of-principle experiment, aiming to demonstrate the actual feasibility of a single molecule diffraction experiment at the European XFEL. To this end, we assume self-seeding capabilities at SASE1 and we suggest to make use of the baseline European XFEL accelerator complex-with the addition of a slotted-foil setup-and of the SPB/SFX instrument. As a first step towards the realization of an actual experiment, we developed a complete package of computational tools for start-to-end simulations predicting its performance. Single biomolecule imaging capabilities at the European XFEL can be reached by exploiting special modes of operation of the accelerator complex and of the SASE1 undulator. The output peak power can be increased up to more than 1.5 TW, which allows to relax the requirements on the focusing efficiency of the optics and to reach the required fluence without changing the present design of the SPB/SFX instrument. Explicit simulations are presented using the 15-nm size RNA Polymerase II molecule as a case study. Noisy diffraction patterns were generated and they were processed to generate the 3D intensity distribution. We discuss requirements to the signal-to-background ratio needed to obtain a correct pattern orientation. When these are fulfilled, our results indicate that one can achieve diffraction without destruction with about 0.1 photons per Shannon pixel per shot at 4 Å resolution with 10(13) photons in a 4 fs pulse at 4 keV photon energy and in a 0.3 μm focus, corresponding to a fluence of 10(14) photons/μm(2). We assume negligible structured background. At this signal level, one needs only about 30 000 diffraction patterns to recover full 3D information. At the highest repetition rate manageable by detectors at European XFEL, one will be able to accumulate these data within a fraction of an hour, even assuming a relatively low hit probability of about a percent.