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| 2. |
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| 3. |
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| 4. |
- Cryan, J P, et al.
(author)
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Molecular frame Auger electron energy spectrum from N2
- 2012
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In: Journal of Physics B. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 45:5, s. 055601-
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Journal article (peer-reviewed)abstract
- Here we present the first angle-resolved, non-resonant (normal) Auger spectra for impulsively aligned nitrogen molecules. We have measured the angular pattern of Auger electron emission following K -shell photoionization by 1.1 keV photons from the Linac Coherent Light Source (LCLS). Using strong-field-induced molecular alignment to make molecular frame measurements is equally effective for both repulsive and quasi-bound final states. The capability to resolve Auger emission angular distributions in the molecular frame of reference provides a new tool for spectral assignments in congested Auger electron spectra that takes advantage of the symmetries of the final diction states. Based on our experimental results and theoretical predictions, we propose the assignment of the spectral features in the Auger electron spectrum.
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| 5. |
- Fuchs, M.a b, et al.
(author)
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Nonlinear X-ray compton scattering
- 2014
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Conference paper (other academic/artistic)abstract
- We use XFEL pulses to observe the most fundamental nonlinear X-ray-matter interaction: nonlinear Compton scattering. In contrast to theoretical predictions, we measure an anonymous and yet to be explained red-shift in the observed photon energy.
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| 6. |
- Nass, K., et al.
(author)
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In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors
- 2020
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1
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Journal article (peer-reviewed)abstract
- Sleeping sickness is a fatal disease caused by the protozoan parasite Trypanosoma brucei (Tb). Inosine-5'-monophosphate dehydrogenase (IMPDH) has been proposed as a potential drug target, since it maintains the balance between guanylate deoxynucleotide and ribonucleotide levels that is pivotal for the parasite. Here we report the structure of TbIMPDH at room temperature utilizing free-electron laser radiation on crystals grown in living insect cells. The 2.80 angstrom resolution structure reveals the presence of ATP and GMP at the canonical sites of the Bateman domains, the latter in a so far unknown coordination mode. Consistent with previously reported IMPDH complexes harboring guanosine nucleotides at the second canonical site, TbIMPDH forms a compact oligomer structure, supporting a nucleotide-controlled conformational switch that allosterically modulates the catalytic activity. The oligomeric TbIMPDH structure we present here reveals the potential of in cellulo crystallization to identify genuine allosteric co-factors from a natural reservoir of specific compounds. Trypanosoma brucei inosine-5 '-monophosphate dehydrogenase (IMPDH) is an enzyme in the guanine nucleotide biosynthesis pathway and of interest as a drug target. Here the authors present the 2.8 angstrom room temperature structure of TbIMPDH determined by utilizing X-ray free-electron laser radiation and crystals that were grown in insect cells and find that ATP and GMP are bound at the canonical sites of the Bateman domains.
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| 7. |
- Hajkova, V., et al.
(author)
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X-ray laser-induced ablation of lead compounds
- 2011
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In: DAMAGE TO VUV, EUV, AND X-RAY OPTICS III. - : SPIE.
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Conference paper (peer-reviewed)abstract
- The recent commissioning of a X-ray free-electron laser triggered an extensive research in the area of X-ray ablation of high-Z, high-density materials. Such compounds should be used to shorten an effective attenuation length for obtaining clean ablation imprints required for the focused beam analysis. Compounds of lead (Z=82) represent the materials of first choice. In this contribution, single-shot ablation thresholds are reported for PbWO(4) and PbI(2) exposed to ultra-short pulses of extreme ultraviolet radiation and X-rays at FLASH and LCLS facilities, respectively. Interestingly, the threshold reaches only 0.11 J/cm(2) at 1.55 nm in lead tungstate although a value of 0.4 J/cm(2) is expected according to the wavelength dependence of an attenuation length and the threshold value determined in the XUV spectral region, i.e., 79 mJ/cm(2) at a FEL wavelength of 13.5 nm. Mechanisms of ablation processes are discussed to explain this discrepancy. Lead iodide shows at 1.55 nm significantly lower ablation threshold than tungstate although an attenuation length of the radiation is in both materials quite the same. Lower thermal and radiation stability of PbI(2) is responsible for this finding.
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| 8. |
- Echelmeier, A., et al.
(author)
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Segmented flow generator for serial crystallography at the European X-ray free electron laser
- 2020
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In: Nature Communications. - : Nature Research. - 2041-1723. ; 11:1
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Journal article (peer-reviewed)abstract
- Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) allows structure determination of membrane proteins and time-resolved crystallography. Common liquid sample delivery continuously jets the protein crystal suspension into the path of the XFEL, wasting a vast amount of sample due to the pulsed nature of all current XFEL sources. The European XFEL (EuXFEL) delivers femtosecond (fs) X-ray pulses in trains spaced 100 ms apart whereas pulses within trains are currently separated by 889 ns. Therefore, continuous sample delivery via fast jets wastes >99% of sample. Here, we introduce a microfluidic device delivering crystal laden droplets segmented with an immiscible oil reducing sample waste and demonstrate droplet injection at the EuXFEL compatible with high pressure liquid delivery of an SFX experiment. While achieving ~60% reduction in sample waste, we determine the structure of the enzyme 3-deoxy-D-manno-octulosonate-8-phosphate synthase from microcrystals delivered in droplets revealing distinct structural features not previously reported.
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| 9. |
- Rolles, D., et al.
(author)
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Femtosecond x-ray photoelectron diffraction on gas-phase dibromobenzene molecules
- 2014
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In: Journal of Physics B: Atomic, Molecular and Optical Physics. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 47:12
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Journal article (peer-reviewed)abstract
- We present time-resolved femtosecond photoelectron momentum images and angular distributions of dissociating, laser-aligned 1,4-dibromobenzene (C6H4Br2) molecules measured in a near-infrared pump, soft-x-ray probe experiment performed at an x-ray free-electron laser. The observed alignment dependence of the bromine 2p photoelectron angular distributions is compared to density functional theory calculations and interpreted in terms of photoelectron diffraction. While no clear time-dependent effects are observed in the angular distribution of the Br(2p) photoelectrons, other, low-energy electrons show a pronounced dependence on the time delay between the near-infrared laser and the x-ray pulse.
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| 10. |
- Frasinski, L. J., et al.
(author)
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Dynamics of Hollow Atom Formation in Intense X-Ray Pulses Probed by Partial Covariance Mapping
- 2013
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In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 111:7, s. 073002-
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Journal article (peer-reviewed)abstract
- When exposed to ultraintense x-radiation sources such as free electron lasers (FELs) the innermost electronic shell can efficiently be emptied, creating a transient hollow atom or molecule. Understanding the femtosecond dynamics of such systems is fundamental to achieving atomic resolution in flash diffraction imaging of noncrystallized complex biological samples. We demonstrate the capacity of a correlation method called partial covariance mapping'' to probe the electron dynamics of neon atoms exposed to intense 8 fs pulses of 1062 eV photons. A complete picture of ionization processes competing in hollow atom formation and decay is visualized with unprecedented ease and the map reveals hitherto unobserved nonlinear sequences of photoionization and Auger events. The technique is particularly well suited to the high counting rate inherent in FEL experiments.
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| 11. |
- Mucke, Melanie, et al.
(author)
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Covariance mapping of two-photon double core hole states in C2H2 and C2H6 produced by an x-ray free electron laser
- 2015
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In: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 17
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Journal article (peer-reviewed)abstract
- Few-photon ionization and relaxation processes in acetylene (C2H2) and ethane (C2H6) were investigated at the linac coherent light source x-ray free electron laser (FEL) at SLAC, Stanford using a highly efficient multi-particle correlation spectroscopy technique based on a magnetic bottle. The analysis method of covariance mapping has been applied and enhanced, allowing us to identify electron pairs associated with double core hole (DCH) production and competing multiple ionization processes including Auger decay sequences. The experimental technique and the analysis procedure are discussed in the light of earlier investigations of DCH studies carried out at the same FEL and at third generation synchrotron radiation sources. In particular, we demonstrate the capability of the covariance mapping technique to disentangle the formation of molecular DCH states which is barely feasible with conventional electron spectroscopy methods.
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| 12. |
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| 13. |
- Thomas, H., et al.
(author)
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Explosions of Xenon Clusters in Ultraintense Femtosecond X-Ray Pulses from the LCLS Free Electron Laser
- 2012
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In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 108:13
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Journal article (peer-reviewed)abstract
- Explosions of large Xe clusters (< N > similar to 11 000) irradiated by femtosecond pulses of 850 eV x-ray photons focused to an intensity of up to 1017 W/cm(2) from the Linac Coherent Light Source were investigated experimentally. Measurements of ion charge-state distributions and energy spectra exhibit strong evidence for the formation of a Xe nanoplasma in the intense x-ray pulse. This x-ray produced Xe nanoplasma is accompanied by a three-body recombination and hydrodynamic expansion. These experimental results appear to be consistent with a model in which a spherically exploding nanoplasma is formed inside the Xe cluster and where the plasma temperature is determined by photoionization heating.
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| 14. |
- Zhaunerchyk, Vitali, et al.
(author)
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Using covariance mapping to investigate the dynamics of multi-photon ionization processes of Ne atoms exposed to X-FEL pulses
- 2013
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In: Journal of Physics B. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 46:16, s. 164034-
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Journal article (peer-reviewed)abstract
- We report on a detailed investigation into the electron emission processes of Ne atoms exposed to intense femtosecond x-ray pulses, provided by the Linac Coherent Light Source Free Electron Laser (FEL) at Stanford. The covariance mapping technique is applied to analyse the data, and the capability of this approach to disentangle both linear and nonlinear correlation features which may be hidden on coincidence maps of the same data set is demonstrated. Different correction techniques which enable improvements on the quality of the spectral features extracted from the covariance maps are explored. Finally, a method for deriving characteristics of the x-ray FEL pulses based on covariance mapping in combination with model simulations is presented.
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| 15. |
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| 16. |
- Frank, Matthias, et al.
(author)
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Femtosecond X-ray diffraction from two-dimensional protein crystals
- 2014
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In: IUCrJ. - 2052-2525. ; 1:2, s. 95-100
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Journal article (peer-reviewed)abstract
- X-ray diffraction patterns from two-dimensional (2-D) protein crystals obtained using femtosecond X-ray pulses from an X-ray free-electron laser (XFEL) are presented. To date, it has not been possible to acquire transmission X-ray diffraction patterns from individual 2-D protein crystals due to radiation damage. However, the intense and ultrafast pulses generated by an XFEL permit a new method of collecting diffraction data before the sample is destroyed. Utilizing a diffract-before-destroy approach at the Linac Coherent Light Source, Bragg diffraction was acquired to better than 8.5 Å resolution for two different 2-D protein crystal samples each less than 10 nm thick and maintained at room temperature. These proof-of-principle results show promise for structural analysis of both soluble and membrane proteins arranged as 2-D crystals without requiring cryogenic conditions or the formation of three-dimensional crystals.
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| 17. |
- Laksmono, Hartawan, et al.
(author)
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Anomalous Behavior of the Homogeneous Ice Nucleation Rate in No-Man's Land
- 2015
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In: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 6:14, s. 2826-2832
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Journal article (peer-reviewed)abstract
- We present an analysis of ice nucleation kinetics from near-ambient pressure water as temperature decreases below the homogeneous limit T-H by cooling micrometer-sized droplets (microdroplets) evaporatively at 10(3)-10(4) K/s and probing the structure ultrafast using femtosecond pulses from the Linac Coherent Light Source (LCLS) free-electron X-ray laser. Below 232 K, we observed a slower nucleation rate increase with decreasing temperature than anticipated from previous measurements, which we suggest is due to the rapid decrease in water's diffusivity. This is consistent with earlier findings that microdroplets do not crystallize at <227 K, but vitrify at cooling rates of 10(6)-10(7) K/s. We also hypothesize that the slower increase in the nucleation rate is connected with the proposed fragile-to-strong transition anomaly in water.
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| 18. |
- Milathianaki, D., et al.
(author)
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Femtosecond Visualization of Lattice Dynamics in Shock-Compressed Matter
- 2013
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 342:6155, s. 220-223
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Journal article (peer-reviewed)abstract
- The ultrafast evolution of microstructure is key to understanding high-pressure and strain-rate phenomena. However, the visualization of lattice dynamics at scales commensurate with those of atomistic simulations has been challenging. Here, we report femtosecond x-ray diffraction measurements unveiling the response of copper to laser shock-compression at peak normal elastic stresses of similar to 73 gigapascals (GPa) and strain rates of 10(9) per second. We capture the evolution of the lattice from a one-dimensional (1D) elastic to a 3D plastically relaxed state within a few tens of picoseconds, after reaching shear stresses of 18 GPa. Our in situ high-precision measurement of material strength at spatial (<1 micrometer) and temporal (<50 picoseconds) scales provides a direct comparison with multimillion-atom molecular dynamics simulations.
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| 19. |
- Ryan, Rebecca A., et al.
(author)
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Measurements of Long-range Electronic Correlations During Femtosecond Diffraction Experiments Performed on Nanocrystals of Buckminsterfullerene
- 2017
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In: Journal of Visualized Experiments. - : MyJove Corporation. - 1940-087X. ; :126
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Journal article (peer-reviewed)abstract
- The precise details of the interaction of intense X-ray pulses with matter are a topic of intense interest to researchers attempting to interpret the results of femtosecond X-ray free electron laser (XFEL) experiments. An increasing number of experimental observations have shown that although nuclear motion can be negligible, given a short enough incident pulse duration, electronic motion cannot be ignored. The current and widely accepted models assume that although electrons undergo dynamics driven by interaction with the pulse, their motion could largely be considered 'random'. This would then allow the supposedly incoherent contribution from the electronic motion to be treated as a continuous background signal and thus ignored. The original aim of our experiment was to precisely measure the change in intensity of individual Bragg peaks, due to X-ray induced electronic damage in a model system, crystalline C-60. Contrary to this expectation, we observed that at the highest X-ray intensities, the electron dynamics in C-60 were in fact highly correlated, and over sufficiently long distances that the positions of the Bragg reflections are significantly altered. This paper describes in detail the methods and protocols used for these experiments, which were conducted both at the Linac Coherent Light Source (LCLS) and the Australian Synchrotron (AS) as well as the crystallographic approaches used to analyse the data.
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| 20. |
- Aricescu, A R, et al.
(author)
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Eukaryotic expression: developments for structural proteomics.
- 2006
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In: Acta Crystallographica Section D: Biological Crystallography. - 1399-0047 .- 0907-4449. ; 62, s. 1114-1124
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Journal article (peer-reviewed)abstract
- The production of sufficient quantities of protein is an essential prelude to a structure determination, but for many viral and human proteins this cannot be achieved using prokaryotic expression systems. Groups in the Structural Proteomics In Europe (SPINE) consortium have developed and implemented high-throughput (HTP) methodologies for cloning, expression screening and protein production in eukaryotic systems. Studies focused on three systems: yeast (Pichia pastoris and Saccharomyces cerevisiae), baculovirus-infected insect cells and transient expression in mammalian cells. Suitable vectors for HTP cloning are described and results from their use in expression screening and protein-production pipelines are reported. Strategies for co-expression, selenomethionine labelling (in all three eukaryotic systems) and control of glycosylation (for secreted proteins in mammalian cells) are assessed.
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| 21. |
- Boll, Rebecca, et al.
(author)
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Imaging molecular structure through femtosecond photoelectron diffraction on aligned and oriented gas-phase molecules
- 2014
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In: Faraday Discussions. - : Royal Society of Chemistry (RSC). - 1364-5498. ; 171, s. 57-80
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Journal article (peer-reviewed)abstract
- This paper gives an account of our progress towards performing femtosecond time-resolved photoelectron diffraction on gas-phase molecules in a pump-probe setup combining optical lasers and an X-ray free-electron laser. We present results of two experiments aimed at measuring photoelectron angular distributions of laser-aligned 1-ethynyl-4-fluorobenzene (C8H5F) and dissociating, laser-aligned 1,4-dibromobenzene (C6H4Br2) molecules and discuss them in the larger context of photoelectron diffraction on gas-phase molecules. We also show how the strong nanosecond laser pulse used for adiabatically laser-aligning the molecules influences the measured electron and ion spectra and angular distributions, and discuss how this may affect the outcome of future time-resolved photoelectron diffraction experiments.
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| 22. |
- Brändén, Gisela, 1975, et al.
(author)
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Coherent diffractive imaging of microtubules using an X-ray laser.
- 2019
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In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1
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Journal article (peer-reviewed)abstract
- X-ray free electron lasers (XFELs) create new possibilities for structural studies of biological objects that extend beyond what is possible with synchrotron radiation. Serial femtosecond crystallography has allowed high-resolution structures to be determined from micro-meter sized crystals, whereas single particle coherent X-ray imaging requires development to extend the resolution beyond a few tens of nanometers. Here we describe an intermediate approach: the XFEL imaging of biological assemblies with helical symmetry. We collected X-ray scattering images from samples of microtubules injected across an XFEL beam using a liquid microjet, sorted these images into class averages, merged these data into a diffraction pattern extending to 2nm resolution, and reconstructed these data into a projection image of the microtubule. Details such as the 4nm tubulin monomer became visible in this reconstruction. These results illustrate the potential of single-molecule X-ray imaging of biological assembles with helical symmetry at room temperature.
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| 23. |
- Ekeberg, Tomas, et al.
(author)
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Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser
- 2016
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In: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 3
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Journal article (peer-reviewed)abstract
- Free-electron lasers (FEL) hold the potential to revolutionize structural biology by producing X-ray pules short enough to outrun radiation damage, thus allowing imaging of biological samples without the limitation from radiation damage. Thus, a major part of the scientific case for the first FELs was three-dimensional (3D) reconstruction of non-crystalline biological objects. In a recent publication we demonstrated the first 3D reconstruction of a biological object from an X-ray FEL using this technique. The sample was the giant Mimivirus, which is one of the largest known viruses with a diameter of 450 nm. Here we present the dataset used for this successful reconstruction. Data-analysis methods for single-particle imaging at FELs are undergoing heavy development but data collection relies on very limited time available through a highly competitive proposal process. This dataset provides experimental data to the entire community and could boost algorithm development and provide a benchmark dataset for new algorithms.
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| 24. |
- Hattne, Johan, et al.
(author)
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Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers
- 2014
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In: Nature Methods. - 1548-7091 .- 1548-7105. ; 11:5, s. 545-548
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Journal article (peer-reviewed)abstract
- X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and without radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract meaningful high-resolution signals from fewer diffraction measurements.
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| 25. |
- Hattne, Johan, et al.
(author)
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Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers
- 2014
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In: Nature Methods. - : Springer Science and Business Media LLC. - 1548-7091 .- 1548-7105. ; 11:5, s. 545-548
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Journal article (peer-reviewed)abstract
- X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and without radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract meaningful high-resolution signals from fewer diffraction measurements.
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