The Materials Science beamline at the Swiss Light Source has been operational since 2001. In late 2010, the original wiggler source was replaced with a novel insertion device, which allows unprecedented access to high photon energies from an undulator installed in a medium-energy storage ring. In order to best exploit the increased brilliance of this new source, the entire front-end and optics had to be redesigned. In this work, the upgrade of the beamline is described in detail. The tone is didactic, from which it is hoped the reader can adapt the concepts and ideas to his or her needs.

At low emittance synchrotron sources it has become possible to perform structure determinations from the measurement of multiple microcrystals which were previously considered too small for diffraction experiments. Conventional mounting techniques do not fulfill the requirements of these new experiments. They significantly contribute to background scattering and it is difficult to locate the crystals, making them incompatible with automated serial crystallography. We have developed a micro-fabricated sample holder from single crystalline silicon with micropores, which carries up to thousands of crystals and significantly reduces the background scattering level. For loading, the suspended microcrystals are pipetted onto the chip and excess mother liquor is subsequently soaked off through the micropores. Crystals larger than the pore size are retained and arrange themselves according to the micropore pattern. Using our chip we were able to collect 1.5 Å high resolution diffraction data from protein microcrystals with sizes of 4 micrometers and smaller.

Recent success at X-ray free-electron lasers has led to serial crystallography experiments staging a comeback at synchrotron sources as well. With crystal lifetimes typically in the millisecond range and the latest-generation detector technologies with high framing rates up to 1 kHz, fast sample exchange has become the bottleneck for such experiments. A micro-patterned chip has been developed from single-crystalline silicon, which acts as a sample holder for up to several thousand microcrystals at a very low background level. The crystals can be easily loaded onto the chip and excess mother liquor can be efficiently removed. Dehydration of the crystals is prevented by keeping them in a stream of humidified air during data collection. Further sealing of the sample holder, for example with Kapton, is not required. Room-temperature data collection from insulin crystals loaded onto the chip proves the applicability of the chip for macromolecular crystallography. Subsequent structure refinements reveal no radiation-damage-induced structural changes for insulin crystals up to a dose of 565.6 kGy, even though the total diffraction power of the crystals has on average decreased to 19.1% of its initial value for the same dose. A decay of the diffracting power by half is observed for a dose ofD1/2= 147.5 ± 19.1 kGy, which is about 1/300 of the dose before crystals show a similar decay at cryogenic temperatures.

21We have developed a method for serial X-ray crystallography at X-ray free electron lasers (XFELs), 22 which allows for full use of the current 120 Hz repetition rate of the Linear Coherent Light Source 23 (LCLS). Using a micro-patterned silicon chip in combination with the high-speed Roadrunner 24 goniometer for sample delivery we were able to determine the crystal structures of a picornavirus, 25 bovine enterovirus 2 (BEV2), and the cytoplasmic polyhedrosis virus type 18 polyhedrin. Total data 26 collection times were less than 14 and 10 minutes, respectively. Our method requires only micrograms 27 of sample and will therefore broaden the applicability of serial femtosecond crystallography to 28 challenging projects for which only limited amounts of samples are available. By synchronizing the 29 sample exchange to the XFEL repetition rate it further allows for the most efficient use of the limited 30 beamtime available at XFELs and a significant increase in sample throughput at these facilities. 31 32 Introduction 33

We report a method for achieving advanced photon diagnostics of x-ray free-electron lasers (XFELs) under a quasi-noninvasive condition by using a beam-splitting scheme. Here, we used a transmission grating to generate multiple branches of x-ray beams. One of the two primary diffracted branches (+1st-order) is utilized for spectral measurement in a dispersive scheme, while the other (−1st-order) is dedicated for arrival timing diagnostics between the XFEL and the optical laser pulses. The transmitted x-ray beam (0th-order) is guided to an experimental station. To confirm the validity of this timing-monitoring scheme, we measured the correlation between the arrival timings of the −1st and 0th branches. The observed error was as small as 7.0 fs in root-mean-square. Our result showed the applicability of the beam branching scheme to advanced photon diagnostics, which will further enhance experimental capabilities of XFEL.