X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded1-3. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction ‘snapshots’ are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source4. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes5. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (~200 nm to 2 μm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes6. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.

X-ray lasers offer new capabilities in understanding the structure of biological systems, complex materials and matter under extreme conditions1–4. Very short and extremely bright, coherent X-ray pulses can be used to outrun key damage processes and obtain a single diffraction pattern from a large macromolecule, a virus or a cell before the sample explodes and turns into plasma1. The continuous diffraction pattern of non-crystalline objects permits oversampling and direct phase retrieval2. Here we show that high-quality diffraction data can be obtained with a single X-ray pulse from a non-crystalline biological sample, a single mimivirus particle, which was injected into the pulsed beam of a hard-X-ray free-electron laser, the Linac Coherent Light Source5. Calculations indicate that the energy deposited into the virus by the pulse heated the particle to over 100,000 K after the pulse had left the sample. The reconstructed exit wavefront (image) yielded 32-nm full-period resolution in a single exposure and showed no measurable damage. The reconstruction indicates inhomogeneous arrangement of dense material inside the virion. We expect that significantly higher resolutions will be achieved in such experiments with shorter and brighter photon pulses focused to a smaller area. The resolution in such experiments can be further extended for samples available in multiple identical copies.

Fourth generation accelerator-based light sources, such as VUV and X-ray Free Electron Lasers (FEL), deliver ultra-brilliant (∼1012–1013 photons per bunch) coherent radiation in femtosecond (∼10–100 fs) pulses and, thus, require novel focal plane instrumentation in order to fully exploit their unique capabilities. As an additional challenge for detection devices, existing (FLASH, Hamburg) and future FELs (LCLS, Menlo Park; SCSS, Hyogo and the European XFEL, Hamburg) cover a broad range of photon energies from the EUV to the X-ray regime with significantly different bandwidths and pulse structures reaching up to MHz micro-bunch repetition rates. Moreover, hundreds up to trillions of fragment particles, ions, electrons or scattered photons can emerge when a single light flash impinges on matter with intensities up to 1022 W/cm2. In order to meet these challenges, the Max Planck Advanced Study Group (ASG) within the Center for Free Electron Laser Science (CFEL) has designed the CFEL-ASG MultiPurpose (CAMP) chamber. It is equipped with specially developed photon and charged particle detection devices dedicated to cover large solid-angles. A variety of different targets are supported, such as atomic, (aligned) molecular and cluster jets, particle injectors for bio-samples or fixed target arrangements. CAMP houses 4π solid-angle ion and electron momentum imaging spectrometers (“reaction microscope”, REMI, or “velocity map imaging”, VMI) in a unique combination with novel, large-area, broadband (50 eV–25 keV), high-dynamic-range, single-photon-counting and imaging X-ray detectors based on the pnCCDs. This instrumentation allows a new class of coherent diffraction experiments in which both electron and ion emission from the target may be simultaneously monitored. This permits the investigation of dynamic processes in this new regime of ultra-intense, high-energy radiation—matter interaction. After an introduction into the salient features of the CAMP chamber and the properties of the redesigned REMI/VMI spectrometers, the new 1024×1024 pixel format pnCCD imaging detector system will be described in detail. Results of tests of four smaller format (256×512) devices of identical performance, conducted at FLASH and BESSY, will be presented and the concept as well as the anticipated properties of the full, large-scale system will be elucidated. The data obtained at both radiation sources illustrate the unprecedented performance of the X-ray detectors, which have a voxel size of 75×75×450 μm3 and a typical read-out noise of 2.5 electrons (rms) at an operating temperature of −50 °C

X-ray free-electron lasers provide unique opportunities for exploring ultrafast dynamics and for imaging the structures of complex systems. Understanding the response of individual atoms to intense X-rays is essential for most free-electron laser applications. First experiments have shown that, for light atoms, the dominant interaction mechanism is ionization by sequential electron ejection, where the highest charge state produced is defined by the last ionic state that can be ionized with one photon. Here, we report an unprecedentedly high degree of ionization of xenon atoms by 1.5 keV free-electron laser pulses to charge states with ionization energies far exceeding the photon energy. Comparing ion charge-state distributions and fluorescence spectra with state-of-the-art calculations, we find that these surprisingly high charge states are created via excitation of transient resonances in highly charged ions, and predict resonance enhanced absorption to be a general phenomenon in the interaction of intense X-rays with systems containing high-Z constituents

X-ray free-electron lasers have enabled new approaches to the structural determination of protein crystals that are too small or radiation-sensitive for conventional analysis1. For sufficiently short pulses, diffraction is collected before significant changes occur to the sample, and it has been predicted that pulses as short as 10 fs may be required to acquire atomic-resolution structural information1–4. Here, we describe a mechanism unique to ultrafast, ultra-intense X-ray experiments that allows structural information to be collected from crystalline samples using high radiation doses without the requirement for the pulse to terminate before the onset of sample damage. Instead, the diffracted X-rays are gated by a rapid loss of crystalline periodicity, producing apparent pulse lengths significantly shorter than the duration of the incident pulse. The shortest apparent pulse lengths occur at the highest resolution, and our measurements indicate that current X-ray free-electron laser technology5 should enable structural determination from submicrometre protein crystals with atomic resolution.

Protein crystallization in cells has been observed several times in nature. However, owing to their small size these crystals have not yet been used for X-ray crystallographic analysis. We prepared nano-sized in vivo–grown crystals of Trypanosoma brucei enzymes and applied the emerging method of free-electron laser-based serial femtosecond crystallography to record interpretable diffraction data. This combined approach will open new opportunities in structural systems biology.

We demonstrate the use of an X-ray free electron laser synchronized with an optical pump laser to obtain X-ray diffraction snapshots from the photoactivated states of large membrane protein complexes in the form of nanocrystals flowing in a liquid jet. Light-induced changes of Photosystem I-Ferredoxin co-crystals were observed at time delays of 5 to 10 μs after excitation. The result correlates with the microsecond kinetics of electron transfer from Photosystem I to ferredoxin. The undocking process that follows the electron transfer leads to large rearrangements in the crystals that will terminally lead to the disintegration of the crystals. We describe the experimental setup and obtain the first time-resolved femtosecond serial X-ray crystallography results from an irreversible photo-chemical reaction at the Linac Coherent Light Source. This technique opens the door to time-resolved structural studies of reaction dynamics in biological systems.

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