High-resolution protein structure determination by serial femtosecond crystallography

Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules.

Fractal morphology, imaging and mass spectrometry of single aerosol particles in flight

The morphology of micrometre-size particulate matter is of critical importance in fields ranging from toxicology to climate science, yet these properties are surprisingly difficult to measure in the particles' native environment. Electron microscopy requires collection of particles on a substrate; visible light scattering provides insufficient resolution; and X-ray synchrotron studies have been limited to ensembles of particles. Here we demonstrate an in situ method for imaging individual sub-micrometre particles to nanometre resolution in their native environment, using intense, coherent X-ray pulses from the Linac Coherent Light Source free-electron laser. We introduced individual aerosol particles into the pulsed X-ray beam, which is sufficiently intense that diffraction from individual particles can be measured for morphological analysis. At the same time, ion fragments ejected from the beam were analysed using mass spectrometry, to determine the composition of single aerosol particles. Our results show the extent of internal dilation symmetry of individual soot particles subject to non-equilibrium aggregation, and the surprisingly large variability in their fractal dimensions. More broadly, our methods can be extended to resolve both static and dynamic morphology of general ensembles of disordered particles. Such general morphology has implications in topics such as solvent accessibilities in proteins, vibrational energy transfer by the hydrodynamic interaction of amino acids, and large-scale production of nanoscale structures by flame synthesis.

Nanoplasma dynamics of single large xenon clusters irradiated with superintense x-ray pulses from the linac coherent light source free-electron laser

The plasma dynamics of single mesoscopic Xe particles irradiated with intense femtosecond x-ray pulses exceeding 10(16)  W/cm2 from the Linac Coherent Light Source free-electron laser are investigated. Simultaneous recording of diffraction patterns and ion spectra allows eliminating the influence of the laser focal volume intensity and particle size distribution. The data show that for clusters illuminated with intense x-ray pulses, highly charged ionization fragments in a narrow distribution are created and that the nanoplasma recombination is efficiently suppressed.

Femtosecond dark-field imaging with an X-ray free electron laser

The emergence of femtosecond diffractive imaging with X-ray lasers has enabled pioneering structural studies of isolated particles, such as viruses, at nanometer length scales. However, the issue of missing low frequency data significantly limits the potential of X-ray lasers to reveal sub-nanometer details of micrometer-sized samples. We have developed a new technique of dark-field coherent diffractive imaging to simultaneously overcome the missing data issue and enable us to harness the unique contrast mechanisms available in dark-field microscopy. Images of airborne particulate matter (soot) up to two microns in length were obtained using single-shot diffraction patterns obtained at the Linac Coherent Light Source, four times the size of objects previously imaged in similar experiments. This technique opens the door to femtosecond diffractive imaging of a wide range of micrometer-sized materials that exhibit irreproducible complexity down to the nanoscale, including airborne particulate matter, small cells, bacteria and gold-labeled biological samples.

CrystFEL: a software suite for snapshot serial crystallography

In order to address the specific needs of the emerging technique of `serial femtosecond crystallography', in which structural information is obtained from small crystals illuminated by an X-ray free-electron laser, a new software suite has been created. The constituent programs deal with viewing, indexing, integrating, merging and evaluating the quality of the data, and also simulating patterns. The specific challenges addressed chiefly concern the indexing and integration of large numbers of diffraction patterns in an automated manner, and so the software is designed to be fast and to make use of multi-core hardware. Other constituent programs deal with the merging and scaling of large numbers of intensities from randomly oriented snapshot diffraction patterns. The suite uses a generalized representation of a detector to ease the use of more complicated geometries than those familiar in conventional crystallography. The suite is written in C with supporting Perl and shell scripts, and is available as source code under version 3 or later of the GNU General Public License.

High-efficiency x-ray gratings with asymmetric-cut multilayers

We present the fabrication and analysis of efficient and highly dispersive gratings for the x-ray and extreme ultraviolet (EUV) regime. We show that an asymmetric-cut multilayer structure can act as a near-perfect blazed grating. The precision and high line density are achieved by layer deposition of materials, which can be controlled to the angstrom level. We demonstrate this in the EUV regime with two structures made by cutting and polishing magnetron-sputtered multilayer mirrors of over 2000 bilayers thick, each with a period of 6.88 nm. These were cut at angles of 2.9° and 7.8° to the surface. Within the 3% bandwidth rocking curve of the multilayer, the angular dispersion of the diffracted wave was in agreement with the grating equation for elements with 7250 and 19,700 line pairs/mm, respectively. The dependence of the measured efficiency was in excellent agreement with a formulation of dynamical diffraction theory for multilayered structures. At a wavelength of 13.2 nm, the efficiency of the first-order diffraction was over 95% of the reflectivity of the uncut multilayer. We predict that such structures should also be effective at shorter x-ray wavelengths. Both the Laue (transmitting) and Bragg (reflecting) geometries are incorporated in our formalism, which is applied to the analysis of multilayer Laue lenses and focusing and dispersing Bragg optics.

Femtosecond free-electron laser x-ray diffraction data sets for algorithm development

We describe femtosecond X-ray diffraction data sets of viruses and nanoparticles collected at the Linac Coherent Light Source. The data establish the first large benchmark data sets for coherent diffraction methods freely available to the public, to bolster the development of algorithms that are essential for developing this novel approach as a useful imaging technique. Applications are 2D reconstructions, orientation classification and finally 3D imaging by assembling 2D patterns into a 3D diffraction volume.

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

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.

In vivo protein crystallization opens new routes in structural biology

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.

Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements

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 information^1-4. 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.

Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser

X-ray free-electron lasers deliver intense femtosecond pulses that promise to yield high resolution diffraction data of nanocrystals before the destruction of the sample by radiation damage. Diffraction intensities of lysozyme nanocrystals collected at the Linac Coherent Light Source using 2 keV photons were used for structure determination by molecular replacement and analyzed for radiation damage as a function of pulse length and fluence. Signatures of radiation damage are observed for pulses as short as 70 fs. Parametric scaling used in conventional crystallography does not account for the observed effects.

Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering

Single-particle experiments using X-ray Free Electron Lasers produce more than 10(5) snapshots per hour, consisting of an admixture of blank shots (no particle intercepted), and exposures of one or more particles. Experimental data sets also often contain unintentional contamination with different species. We present an unsupervised method able to sort experimental snapshots without recourse to templates, specific noise models, or user-directed learning. The results show 90% agreement with manual classification.

Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals

A complete set of structure factors has been extracted from hundreds of thousands of femtosecond single-shot X-ray microdiffraction patterns taken from randomly oriented nanocrystals. The method of Monte Carlo integration over crystallite size and orientation was applied to experimental data from Photosystem I nanocrystals. This arrives at structure factors from many partial reflections without prior knowledge of the particle-size distribution. The data were collected at the Linac Coherent Light Source (the first hard-X-ray laser user facility), to which was fitted a hydrated protein nanocrystal injector jet, according to the method of serial crystallography. The data are single 'still' diffraction snapshots, each from a different nanocrystal with sizes ranging between 100 nm and 2 µm, so the angular width of Bragg peaks was dominated by crystal-size effects. These results were compared with single-crystal data recorded from large crystals of Photosystem I at the Advanced Light Source and the quality of the data was found to be similar. The implications for improving the efficiency of data collection by allowing the use of very small crystals, for radiation-damage reduction and for time-resolved diffraction studies at room temperature are discussed.

Tri-material multilayer coatings with high reflectivity and wide bandwidth for 25 to 50 nm extreme ultraviolet light

Magnesium/silicon carbide (Mg/SiC) multilayers have been fabricated with normal incidence reflectivity in the vicinity of 40% to 50% for wavelengths in the 25 to 50 nm wavelength range. However many applications, for example solar telescopes and ultrafast studies using high harmonic generation sources, desire larger bandwidths than provided by high reflectivity Mg/SiC multilayers. We investigate introducing a third material, Scandium, to create a tri-material Mg/Sc/SiC multilayer allowing an increase the bandwidth while maintaining high reflectivity.

Absolute sensitivity calibration of extreme ultraviolet photoresists

One of the major challenges facing the commercialization of extreme ultraviolet (EUV) lithography remains simultaneously achieving resist sensitivity, line-edge roughness, and resolution requirement. Sensitivity is of particular concern owing to its direct impact on source power requirements. Most current EUV exposure tools have been calibrated against a resist standard with the actual calibration of the standard resist dating back to EUV exposures at Sandia National Laboratories in the mid 1990s. Here we report on an independent sensitivity calibration of two baseline resists from the SEMATECH Berkeley MET tool performed at the Advanced Light Source Calibrations and Standards beamline. The results show the baseline resists to be approximately 1.9 times faster than previously thought based on calibration against the long standing resist standard.

Metrologies for the phase characterization of attosecond extreme ultraviolet optics

Extreme ultraviolet (EUV) optics play a key role in attosecond science since only with higher photon energies is it possible to achieve the wide spectral bandwidth required for ultrashort pulses. Multilayer EUV mirrors have been proposed and are being developed to temporally shape (compress) attosecond pulses. To fully characterize a multilayer optic for pulse applications requires not only knowledge of the reflectivity, as a function of photon energy, but also the reflected phase of the mirror. We develop the metrologies to determine the reflected phase of an EUV multilayer mirror using the photoelectric effect. The proposed method allows one to determine the optic's impulse response and hence its pulse characteristics.

Design and performance of capping layers for extreme-ultraviolet multilayer mirrors

Multilayer lifetime has emerged as one of the major issues for the commercialization of extreme-ultraviolet lithography (EUVL). We describe the performance of an oxidation-resistant capping layer of Ru atop multilayers that results in a reflectivity above 69% at 13.2 nm, which is suitable for EUVL projection optics and has been tested with accelerated electron-beam and extreme-ultraviolet (EUV) light in a water-vapor environment. Based on accelerated exposure results, we calculated multilayer lifetimes for all reflective mirrors in a typical commercial EUVL tool and concluded that Ru-capped multilayers have approximately 40x longer lifetimes than Si-capped multilayers, which translates to 3 months to many years, depending on the mirror dose.

The Vascular Project: using data to improve processes and outcomes

Fiscal accountability by health care providers has become a theme in health care delivery systems; however, evaluation of outcomes on the basis of cost alone may minimize the importance of patient needs and the quality of the care delivered. Mechanisms related to resource identification and allocation has to be driven by internal data and information systems that consider clinical, financial, administrative, and patient satisfaction data. This article will define processes, outcomes and outcomes measurement, and management. Various nursing-sensitive outcomes will be presented and their establishment, tracking, interpretation, and effect on the delivery of patient care in a newly opened vascular unit will be highlighted.

No need for pain

In an attempt to promote as pain free an experience as possible for patients and to improve how pain is managed in all settings, this 500-bed teaching hospital embarked on a hospital-wide quality improvement (QI) initiative. Initial measurement of clinicians' knowledge and attitudes related to pain and surveys on patient satisfaction identified improvement opportunities. Highlights of these findings and the major interventions taken are described. Education of all clinical staff on the major principles of pain management became the primary focus. Major outcomes realized to date have been: (a) a significant increase (p = .01) in physicians and nurses discussing with their patients the importance of managing their pain, (b) development of processes for documenting pain as the fifth vital sign, and (c) a 26% decrease in the use of meperidine. The next steps will be comprehensive monitoring of the effectiveness of pain management by clinical service, increased patient and family education on pain, and development of a formalized pain management competency program for clinical staff.