Time-resolved protein nanocrystallography using an X-ray free-electron laser

Aquila, Andrew; Hunter, Mark S.; Doak, R. Bruce; Kirian, Richard A.; Fromme, Petra; White, Thomas A.; Andreasson, Jakob; Arnlund, David; Bajt, Saša; Barends, Thomas R. M.; Barthelmeß, Miriam; Bogan, Michael J.; Bostedt, Christoph; Bottin, Hervé; Bozek, John D.; Caleman, Carl; Coppola, N.; Davidsson, Jan; DePonte, Daniel P.; Elser, Veit; Epp, Sascha W.; Erk, Benjamin; Fleckenstein, H.; Foucar, L.; Frank, Matthias; Fromme, Raimund; Graafsma, H.; Grotjohann, Ingo; Gumprecht, Lars; Hajdu, János; Hampton, Christina Y.; Hartmann, Andreas; Hartmann, R.; Hau‐Riege, Stefan P.; Hauser, Günter; Hirsemann, H.; Holl, P.; Holton, James M.; Hömke, André; Johansson, Linda C.; Kimmel, Nils; Kassemeyer, Stephan; Krasniqi, Faton; Kühnel, K. U.; Liang, Mao; Lomb, Lukas; Malmerberg, Erik; Marchesini, Stefano; Martin, Andrew V.; Maia, Filipe R. N. C.; Messerschmidt, Marc; Nass, Karol; Reich, Christian; Neutze, Richard; Rolles, Daniel; Rudek, Benedikt; Rudenko, Artem; Schlichting, Ilme; Schmidt, Carlo; Schmidt, Kevin; Schulz, Joachim; Seibert, M.; Shoeman, Robert L.; Sierra, Raymond G.; Soltau, H.; Starodub, D.; Stellato, Francesco; Stern, Stephan; Strüder, L.; Tı̂mneanu, Nicuşor; Ullrich, J.; Wang, Xiaoyu; Williams, Garth J.; Weidenspointner, G.; Weierstall, Uwe; Wunderer, C.; Barty, Anton; Spence, John C. H.; Chapman, Henry N.

doi:10.1364/oe.20.002706

Cited by 228 publications

(171 citation statements)

References 29 publications

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“…3,4 This method is opening new doors in structural biology, yielding atomic resolution structures from micrometer-sized crystals and smaller, radiation sensitive protein crystals, [5][6][7][8][9][10] as well as, enabling experiments to study fast structural protein dynamics. [11][12][13][14][15] Considering the destructive nature of the pulses, data collection is optimized by a serial approach, where a new crystal is placed in the beam for each X-ray pulse. The Linac Coherent Light Source (LCLS) FEL has the fastest repetition rate of all currently operational hard X-ray FELs at 120 Hz, but a much faster 4.5 MHz bunch mode will be implemented at a) Current address: Department of Physics, Arizona State University, P.O.…”

Section: Introductionmentioning

confidence: 99%

Ceramic micro-injection molded nozzles for serial femtosecond crystallography sample delivery

Beyerlein

Adriano

Heymann

et al. 2015

Review of Scientific Instruments

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Serial femtosecond crystallography (SFX) using X-ray Free-Electron Lasers (XFELs) allows for room temperature protein structure determination without evidence of conventional radiation damage. In this method, a liquid suspension of protein microcrystals can be delivered to the X-ray beam in vacuum as a micro-jet, which replenishes the crystals at a rate that exceeds the current XFEL pulse repetition rate. Gas dynamic virtual nozzles produce the required micrometer-sized streams by the focusing action of a coaxial sheath gas and have been shown to be effective for SFX experiments. Here, we describe the design and characterization of such nozzles assembled from ceramic micro-injection molded outer gas-focusing capillaries. Trends of the emitted jet diameter and jet length as a function of supplied liquid and gas flow rates are measured by a fast imaging system. The observed trends are explained by derived relationships considering choked gas flow and liquid flow conservation. Finally, the performance of these nozzles in a SFX experiment is presented, including an analysis of the observed background.

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Section: Introductionmentioning

confidence: 99%

Ceramic micro-injection molded nozzles for serial femtosecond crystallography sample delivery

Beyerlein

Adriano

Heymann

et al. 2015

Review of Scientific Instruments

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“…Similar experiments were carried out to investigate the charge-order parameters in stripe-ordered La 1.75 Sr 0.25 NiO 4 nickelate crystals (Chuang et al, 2013). For serial femtosecond crystallography, laser pump X-ray probe schemes have been developed (Aquila et al, 2012) and these allowed the study of the light-activated S 3 state of photosystem II using double activation by green laser light (Kupitz et al, 2014). Other recent time-resolved experiments at FELs have addressed the ultrafast lattice dynamics in nanometre-thick Si crystal layers by time-resolved Bragg coherent X-ray diffraction (Tanaka et al, 2013) and the ultrafast structural dynamics in VO 2 nanowires (Newton et al, 2014), both at SACLA, and have probed the structure of water below the homogeneous ice nucleation temperature at ultra-fast timescales (Sellberg et al, 2014) at LCLS.…”

Section: Free-electron Lasersmentioning

confidence: 99%

The potential of future light sources to explore the structure and function of matter

Weckert¹

2014

Acta Cryst Sect A

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Structural studies in general, and crystallography in particular, have benefited and still do benefit dramatically from the use of synchrotron radiation. Lowemittance storage rings of the third generation provide focused beams down to the micrometre range that are sufficiently intense for the investigation of weakly scattering crystals down to the size of several micrometres. Even though the coherent fraction of these sources is below 1%, a number of new imaging techniques have been developed to exploit the partially coherent radiation. However, many techniques in nanoscience are limited by this rather small coherent fraction. On the one hand, this restriction limits the ability to study the structure and dynamics of non-crystalline materials by methods that depend on the coherence properties of the beam, like coherent diffractive imaging and X-ray correlation spectroscopy. On the other hand, the flux in an ultra-small diffraction-limited focus is limited as well for the same reason. Meanwhile, new storage rings with more advanced lattice designs are under construction or under consideration, which will have significantly smaller emittances. These sources are targeted towards the diffraction limit in the X-ray regime and will provide roughly one to two orders of magnitude higher spectral brightness and coherence. They will be especially suited to experiments exploiting the coherence properties of the beams and to ultra-small focal spot sizes in the regime of several nanometres. Although the length of individual X-ray pulses at a storage-ring source is of the order of 100 ps, which is sufficiently short to track structural changes of larger groups, faster processes as they occur during vision or photosynthesis, for example, are not accessible in all details under these conditions. Linear accelerator (linac) driven free-electron laser (FEL) sources with extremely short and intense pulses of very high coherence circumvent some of the limitations of present-day storage-ring sources. It has been demonstrated that their individual pulses are short enough to outrun radiation damage for single-pulse exposures. These ultra-short pulses also enable time-resolved studies 1000 times faster than at standard storage-ring sources. Developments are ongoing at various places for a totally new type of X-ray source combining a linac with a storage ring. These energy-recovery linacs promise to provide pulses almost as short as a FEL, with brilliances and multi-user capabilities comparable with a diffraction-limited storage ring. Altogether, these new X-ray source developments will provide smaller and more intense X-ray beams with a considerably higher coherent fraction, enabling a broad spectrum of new techniques for studying the structure of crystalline and non-crystalline states of matter at atomic length scales. In addition, the short X-ray pulses of FELs will enable the study of fast atomic dynamics and non-equilibrium states of matter.

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“…An appealing alternative, made possible by recent advances in light source technology, is X-ray nanocrystallography, which is able to image structures resistant to large crystallization, such as membrane proteins, by substituting a large ensemble of easier to build nanocrystals, typically <1 μm, often delivered to the beam via a liquid jet (1)(2)(3)(4)(5)(6) (Fig. 1).…”

mentioning

confidence: 99%

“…Furthermore, these techniques only narrow down orientation to a list of possibilities when the diffraction pattern has less symmetry than the lattice, leading to an ambiguity in the image orientation, known as the indexing ambiguity. Current methods of processing the diffraction data are largely based on averaging out the data variance over several images (1)(2)(3)(4)(5)(6)(7)(8). However, if the data are processed without resolving the indexing ambiguity then they will appear to be perfectly twinned, i.e., averaged over multiple orientations.…”

mentioning

confidence: 99%

Algorithmic framework for X-ray nanocrystallographic reconstruction in the presence of the indexing ambiguity

Donatelli¹,

Sethian²

2013

Proc. Natl. Acad. Sci. U.S.A.

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X-ray nanocrystallography allows the structure of a macromolecule to be determined from a large ensemble of nanocrystals. However, several parameters, including crystal sizes, orientations, and incident photon flux densities, are initially unknown and images are highly corrupted with noise. Autoindexing techniques, commonly used in conventional crystallography, can determine orientations using Bragg peak patterns, but only up to crystal lattice symmetry. This limitation results in an ambiguity in the orientations, known as the indexing ambiguity, when the diffraction pattern displays less symmetry than the lattice and leads to data that appear twinned if left unresolved. Furthermore, missing phase information must be recovered to determine the imaged object's structure. We present an algorithmic framework to determine crystal size, incident photon flux density, and orientation in the presence of the indexing ambiguity. We show that phase information can be computed from nanocrystallographic diffraction using an iterative phasing algorithm, without extra experimental requirements, atomicity assumptions, or knowledge of similar structures required by current phasing methods. The feasibility of this approach is tested on simulated data with parameters and noise levels common in current experiments.A lthough conventional X-ray crystallography has been used extensively to determine atomic structure, it is limited to objects that can be formed into large crystal samples ð>10 μmÞ. An appealing alternative, made possible by recent advances in light source technology, is X-ray nanocrystallography, which is able to image structures resistant to large crystallization, such as membrane proteins, by substituting a large ensemble of easier to build nanocrystals, typically <1 μm, often delivered to the beam via a liquid jet (1-6) ( Fig. 1). However, the beam power required to retrieve sufficient information destroys the crystal, hence ultrafast pulses (≤70 fs) are required to collect data before damage effects alter the signal. Using nanocrystals introduces several challenges. Due to the small crystal size, Bragg peaks are smeared out, and there is noticeable signal between peaks. Typically, only partial peak reflections are measured, resulting in reduced intensities. Variations in crystal size and incident photon flux density, unknown orientations, shot noise, and background signal from the liquid and detector add additional uncertainty to the data.If crystal orientations were known, noise and variation in the peak measurements could be averaged out, and the data could be inverted to retrieve the object's electron density. Although autoindexing techniques can be used to determine crystal orientation up to lattice symmetry from the location of a sufficient number of Bragg peaks, they typically face difficulties in the presence of partial and non-Bragg reflections common in nanocrystal diffraction images. Furthermore, these techniques only narrow down orientation to a list of possibilities when the diffraction pattern has less ...

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Time-resolved protein nanocrystallography using an X-ray free-electron laser

Cited by 228 publications

References 29 publications

Ceramic micro-injection molded nozzles for serial femtosecond crystallography sample delivery

Ceramic micro-injection molded nozzles for serial femtosecond crystallography sample delivery

The potential of future light sources to explore the structure and function of matter

Algorithmic framework for X-ray nanocrystallographic reconstruction in the presence of the indexing ambiguity

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