35 research outputs found
Coherent diffractive imaging of lipid vesicles and synaptic vesicles by femtosecond x-ray FEL pulses
No full textStructure and polydispersity of single lipid vesicles by small-angle X-ray scattering at European XFEL
No full textDirect Observation of the Exciton-Polaron in Single CsPbBr<sub>3</sub> Quantum Dots
No full textThe Outstanding optoelectronic properties of lead halide perovskites have been related to the formation of polarons. Nevertheless, the observation of the atomistic deformation brought about by one electron–hole pair in these materials has remained elusive. Here, we measure the transient structure of single CsPbBr3 quantum dots (QDs) after resonant excitation in the single exciton limit using serial femtosecond crystallography (SFX). By reconstructing the three-dimensional (3D) differential diffraction pattern and building on density functional theory (DFT) calculations, we assign the lattice distortion after photoexcitation to the combined presence of a delocalized electron and a localized hole, forming a mixed large/small exciton-polaron. This result creates a clear picture of the polaronic deformation in CsPbBr3 QDs and demonstrates the exceptional sensitivity of SFX to lattice distortions in few-nanometer crystallites. We plan to use this experimental platform for future studies of electron–lattice interactions
New insights into the function and molecular mechanisms of Ferredoxin-NADP+ reductase from Brucella ovis
No full textBacterial ferredoxin(flavodoxin)-NADP+ reductases (FPR) primarily catalyze the transfer of reducing equivalents from NADPH to ferredoxin (or flavodoxin) to provide low potential reducing equivalents for the oxidoreductive metabolism. In addition, they can be implicated in regulating reactive oxygen species levels. Here we assess the functionality of FPR from B. ovis to understand its potential roles in the bacteria physiology. We prove that this FPR is active with the endogenous [2Fe–2S] Fdx ferredoxin, exhibiting a KMFdx in the low micromolar range. At the molecular level, this study provides with the first structures of an FPR at room temperature obtained by serial femtosecond crystallography, envisaging increase in flexibility at both the adenine nucleotide moiety of FAD and the C-terminal tail. The produced microcrystals are in addition suitable for future mix-and-inject time-resolved studies with the NADP+/H coenzyme either at synchrotrons or XFELs. Furthermore, the study also predicts the ability of FPR to simultaneously interact with Fdx and NADP+/H
De novo determination of mosquitocidal Cry11Aa and Cry11Ba structures from naturally-occurring nanocrystals
No full textCry11Aa and Cry11Ba are the two most potent toxins produced by mosquitocidal Bacillus thuringiensis subsp. israelensis and jegathesan, respectively. The toxins naturally crystallize within the host; however, the crystals are too small for structure determination at synchrotron sources. Therefore, we applied serial femtosecond crystallography at X-ray free electron lasers to in vivo-grown nanocrystals of these toxins. The structure of Cry11Aa was determined de novo using the single-wavelength anomalous dispersion method, which in turn enabled the determination of the Cry11Ba structure by molecular replacement. The two structures reveal a new pattern for in vivo crystallization of Cry toxins, whereby each of their three domains packs with a symmetrically identical domain, and a cleavable crystal packing motif is located within the protoxin rather than at the termini. The diversity of in vivo crystallization patterns suggests explanations for their varied levels of toxicity and rational approaches to improve these toxins for mosquito control
Real-time analysis of liquid jet sample delivery stability for an X-ray free-electron laser using machine vision
No full textAutomated evaluation of optical microscopy images of liquid jets, commonlyused for sample delivery at X-ray free-electron lasers (XFELs), enables real-time tracking of the jet position and liquid jet hit rates, defined here as theproportion of XFEL pulses intersecting with the liquid jet. This method utilizesmachine vision for preprocessing, feature extraction, segmentation and jetdetection as well as tracking to extract key physical characteristics (such as thejet angle) from optical microscopy images captured during experiments. Todetermine the effectiveness of these tools in monitoring jet stability andenhancing sample delivery efficiency, we conducted XFEL experiments withvarious sample compositions (pure water, buffer and buffer with crystals),nozzle designs and jetting conditions. We integrated our real-time analysisalgorithm into the Karabo control system at the European XFEL. The resultsindicate that the algorithm performs well in monitoring the jet angle andprovides a quantitative characterization of liquid jet stability through opticalimage analysis conducted during experiment
Automatic bad pixel mask maker for X-ray pixel detectors with application to serial crystallography
No full textX-ray crystallography has witnessed a massive development over the past decade, driven by large increases in the intensity and brightness of X-ray sources and enabled by employing high-frame-rate X-ray detectors. The analysis of large data sets is done via automatic algorithms that are vulnerable to imperfections in the detector and noise inherent with the detection process. By improving the model of the behaviour of the detector, data can be analysed more reliably and data storage costs can be significantly reduced. One major requirement is a software mask that identifies defective pixels in diffraction frames. This paper introduces a methodology and program based upon concepts of machine learning, called robust mask maker (RMM), for the generation of bad-pixel masks for large-area X-ray pixel detectors based on modern robust statistics. It is proposed to discriminate normally behaving pixels from abnormal pixels by analysing routine measurements made with and without X-ray illumination. Analysis software typically uses a Bragg peak finder to detect Bragg peaks and an indexing method to detect crystal lattices among those peaks. Without proper masking of the bad pixels, peak finding methods often confuse the abnormal values of bad pixels in a pattern with true Bragg peaks and flag such patterns as useful regardless, leading to storage of enormous uninformative data sets. Also, it is computationally very expensive for indexing methods to search for crystal lattices among false peaks and the solution may be biased. This paper shows how RMM vastly improves peak finders and prevents them from labelling bad pixels as Bragg peaks, by demonstrating its effectiveness on several serial crystallography data sets
Shot-to-shot two-dimensional photon intensity diagnostics within megahertz pulse-trains at the European XFEL
No full textCharacterizing the properties of X-ray free-electron laser (XFEL) sources is a critical step for optimization of performance and experiment planning. The recent availability of MHz XFELs has opened up a range of new opportunities for novel experiments but also highlighted the need for systematic measurements of the source properties. Here, MHz-enabled beam imaging diagnostics developed for the SPB/SFX instrument at the European XFEL are exploited to measure the shot-to-shot intensity statistics of X-ray pulses. The ability to record pulse-integrated two-dimensional transverse intensity measurements at multiple planes along an XFEL beamline at MHz rates yields an improved understanding of the shot-to-shot photon beam intensity variations. These variations can play a critical role, for example, in determining the outcome of single-particle imaging experiments and other experiments that are sensitive to the transverse profile of the incident beam. It is observed that shot-to-shot variations in the statistical properties of a recorded ensemble of radiant intensity distributions are sensitive to changes in electron beam current density. These changes typically occur during pulse-distribution to the instrument and are currently not accounted for by the existing suite of imaging diagnostics. Modulations of the electron beam orbit in the accelerator are observed to induce a time-dependence in the statistics of individual pulses – this is demonstrated by applying radio-frequency trajectory tilts to electron bunch-trains delivered to the instrument. We discuss how these modifications of the beam trajectory might be used to modify the statistical properties of the source and potential future applications
Crystal structure of a bacterial photoactivated adenylate cyclase determined by serial femtosecond and serial synchrotron crystallography
No full textInternational audienceOaPAC is a recently discovered blue-light-using flavin adenosine dinucleotide (BLUF) photoactivated adenylate cyclase from the cyanobacterium Oscillatoria acuminata that uses adenosine triphosphate and translates the light signal into the production of cyclic adenosine monophosphate. Here, we report crystal structures of the enzyme in the absence of its natural substrate determined from room-temperature serial crystallography data collected at both an X-ray free-electron laser and a synchrotron, and we compare these structures with cryo-macromolecular crystallography structures obtained at a synchrotron by us and others. These results reveal slight differences in the structure of the enzyme due to data collection at different temperatures and X-ray sources. We further investigate the effect of the Y6W mutation in the BLUF domain, a mutation which results in a rearrangement of the hydrogen-bond network around the flavin and a notable rotation of the side chain of the critical Gln48 residue. These studies pave the way for picosecond–millisecond time-resolved serial crystallography experiments at X-ray free-electron lasers and synchrotrons in order to determine the early structural intermediates and correlate them with the well studied picosecond–millisecond spectroscopic intermediates
Focusing of X-ray free-electron laser pulses using multilayer Laue lenses
No full textAchieving the highest possible intensities of pulses at X-ray free-electron laser(XFEL)facilitiesentailsfocusingtheX-raybeamtothesmallestpossibledimensions. MultilayerLauelensesarevolumediffractiveopticsthatholdpromisetoachievehighintensitiesduetotheirhighnumericalapertureathardX-raywavelengths. Theselensesaremadebylayerdepositionandhence have a small aperture that is usually less than 100µm. Consequently, they must withstandhigh intensities and heat loads if used to focus pulses of high energies. Here, we demonstrate thefocusingofXFELpulsesusinglensesmadefromlayersofMo2CandSiC,whichwerechosenfortheirhighefficiencyandlowbeamheating. WeshowthatlensalignmentandcharacterisationcanbecarriedoutusingattenuatedXFELpulsesusingthemethodofptychographicX-rayspeckletracking, which also provides an approach for high-resolution projection imaging with XFELpulses. The approach also gives quantitative information about the distribution of intensityin the focal plane, which is analysed here using plots of the encircled energy describing theproportionofthebeamenergyconcentratedintoacertaindiameter,showingthepossibilitytoreach 1.8×1020 Wcm−2 at a photon energy of 16.9keV. No measurable change in the wavefrontaberrationsofthelensescouldbedetectedaftertheiruseinanexperimentformanydayswithunattenuated XFEL pulses, showing that the materials and mounting scheme presented heremake theselenses suitablefor sustained use at XFEL facilities
