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Item type:Publication, Access status: with files , FDIP : a Fast Diffraction Image Processing library for X-ray crystallography experiments(Multidisciplinary Digital Publishing Institute (MDPI), 2024-02-05); ; ; ; Serial crystallography (SX) is a cutting-edge technique in structural biology, involving the systematic collection of X-ray diffraction data from numerous randomly oriented microcrystals. To extract comprehensive three-dimensional information about the studied system, SX utilises thousands of measured diffraction patterns. As such, SX takes advantages of the properties of modern X-ray sources, including Free Electron Lasers (FELs) and third and fourth generation synchrotrons, as well as contemporary high-repetition-rate detectors. Efficient analysis of the extensive datasets generated during SX experiments demands fast and effective algorithms. The FDIP library offers meticulously optimised functions tailored for preprocessing data obtained in SX experiments. This encompasses tasks such as background subtraction, identification and masking of parasitic streaks, elimination of unwanted powder diffraction (e.g., from ice or salt crystals), and pinpointing useful Bragg peaks in each diffraction pattern. The library is equipped with a user-friendly graphical interface for facile parameter adjustment tailored to specific datasets. Compatible with popular SX processing software like OnDA, Cheetah, CrystFEL, and Merge3D, the FDIP library enhances the capabilities of these tools for streamlined and precise serial crystallography analyses.Publicationtype: Journal Article30 100 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease(American Association for the Advancement of Science (Assoc.), 2021-04-02); ; ; ; The coronavirus disease (COVID-19) caused by SARS-CoV-2 is creating tremendous human suffering. To date, no effective drug is available to directly treat the disease. In a search for a drug against COVID-19, we have performed a high-throughput X-ray crystallographic screen of two repurposing drug libraries against the SARS-CoV-2 main protease (Mpro), which is essential for viral replication. In contrast to commonly applied X-ray fragment screening experiments with molecules of low complexity, our screen tested alreadyapproved drugs and drugs in clinical trials. From the three-dimensional protein structures, we identified 37 compounds that bind to Mpro. In subsequent cell-based viral reduction assays, one peptidomimetic and six nonpeptidic compounds showed antiviral activity at nontoxic concentrations. We identified two allosteric binding sites representing attractive targets for drug development against SARS-CoV-2.Publicationtype: Journal ArticleScopus© Citations 214 186 281 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: without files , Time-resolved serial femtosecond crystallography at the European XFEL(2020-01-01); ; ; ; The European XFEL (EuXFEL) is a 3.4-km long X-ray source, which produces femtosecond, ultrabrilliant and spatially coherent X-ray pulses at megahertz (MHz) repetition rates. This X-ray source has been designed to enable the observation of ultrafast processes with near-atomic spatial resolution. Time-resolved crystallographic investigations on biological macromolecules belong to an important class of experiments that explore fundamental and functional structural displacements in these molecules. Due to the unusual MHz X-ray pulse structure at the EuXFEL, these experiments are challenging. Here, we demonstrate how a biological reaction can be followed on ultrafast timescales at the EuXFEL. We investigate the picosecond time range in the photocycle of photoactive yellow protein (PYP) with MHz X-ray pulse rates. We show that difference electron density maps of excellent quality can be obtained. The results connect the previously explored femtosecond PYP dynamics to timescales accessible at synchrotrons. This opens the door to a wide range of time-resolved studies at the EuXFEL.Publicationtype: Journal Article190 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , pinkIndexer – a universal indexer for pink-beam X-ray and electron diffraction snapshotsA crystallographic indexing algorithm,pinkIndexer, is presented for the analysisof snapshot diffraction patterns. It can be used in a variety of contexts includingmeasurements made with a monochromatic radiation source, a polychromaticsource or with radiation of very short wavelength. As such, the algorithm isparticularly suited to automated data processing for two emerging measurementtechniques for macromolecular structure determination: serial pink-beam X-raycrystallography and serial electron crystallography, which until now lackedreliable programs for analyzing many individual diffraction patterns fromcrystals of uncorrelated orientation. The algorithm requires approximateknowledge of the unit-cell parameters of the crystal, but not the wavelengthsassociated with each Bragg spot. The use ofpinkIndexeris demonstrated byobtaining 1005 lattices from a published pink-beam serial crystallography dataset that had previously yielded 140 indexed lattices. Additionally, in tests onexperimental serial crystallography diffraction data recorded with quasi-monochromatic X-rays and with electrons the algorithm indexed more patternsthan other programs tested.Publicationtype: Journal ArticleScopus© Citations 24 282 214 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Evaluation of serial crystallographic structure determination within megahertz pulse trains(American Institute of Physics (AIP), 2019-12-04); ; ; ; The new European X-ray Free-Electron Laser (European XFEL) is the first X-ray free-electron laser capable of delivering intense X-ray pulses with a megahertz interpulse spacing in a wavelength range suitable for atomic resolution structure determination. An outstanding but crucial question is whether the use of a pulse repetition rate nearly four orders of magnitude higher than previously possible results in unwanted structural changes due to either radiation damage or systematic effects on data quality. Here, separate structures from the first and subsequent pulses in the European XFEL pulse train were determined, showing that there is essentially no difference between structures determined from different pulses under currently available operating conditions at the European XFEL.Publicationtype: Journal ArticleScopus© Citations 27 152 194 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Membrane protein megahertz crystallography at the European XFEL(Nature Publishing Group, 2019-11-04); ; ; ; The world’s first superconducting megahertz repetition rate hard X-ray free-electron laser (XFEL), the European XFEL, began operation in 2017, featuring a unique pulse train structure with 886 ns between pulses. With its rapid pulse rate, the European XFEL may alleviate some of the increasing demand for XFEL beamtime, particularly for membrane protein serial femtosecond crystallography (SFX), leveraging orders-of-magnitude faster data collection. Here, we report the first membrane protein megahertz SFX experiment, where we determined a 2.9 Å-resolution SFX structure of the large membrane protein complex, Photosystem I, a > 1 MDa complex containing 36 protein subunits and 381 cofactors. We address challenges to megahertz SFX for membrane protein complexes, including growth of large quantities of crystals and the large molecular and unit cell size that influence data collection and analysis. The results imply that megahertz crystallography could have an important impact on structure determination of large protein complexes with XFELs.Publicationtype: Journal ArticleScopus© Citations 43 518 242 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , XGANDALF – extended gradient descent algorithm for lattice finding(Wiley-Blackwell, 2019-08-30); ; ; ; Serial crystallography records still diffraction patterns from single, randomly oriented crystals, then merges data from hundreds or thousands of them to form a complete data set. To process the data, the diffraction patterns must first be indexed, equivalent to determining the orientation of each crystal. A novel automatic indexing algorithm is presented, which in tests usually gives significantly higher indexing rates than alternative programs currently available for this task. The algorithm does not require prior knowledge of the lattice parameters but can make use of that information if provided, and also allows indexing of diffraction patterns generated by several crystals in the beam. Cases with a small number of Bragg spots per pattern appear to particularly benefit from the new approach. The algorithm has been implemented and optimized for fast execution, making it suitable for real-time feedback during serial crystallography experiments. It is implemented in an open-source C++ library and distributed under the LGPLv3 licence. An interface to it has been added to the CrystFEL software suite.Publicationtype: Journal ArticleScopus© Citations 71 500 227 - Some of the metrics are blocked by yourconsent settings
Item type:Publication, Access status: with files , Megahertz serial crystallography(Nature Publishing Group, 2018-10-02); ; ; ; The new European X-ray Free-Electron Laser is the first X-ray free-electron laser capable of delivering X-ray pulses with a megahertz inter-pulse spacing, more than four orders of magnitude higher than previously possible. However, to date, it has been unclear whether it would indeed be possible to measure high-quality diffraction data at megahertz pulse repetition rates. Here, we show that high-quality structures can indeed be obtained using currently available operating conditions at the European XFEL. We present two complete data sets, one from the well-known model system lysozyme and the other from a so far unknown complex of a β-lactamase from K. pneumoniae involved in antibiotic resistance. This result opens up megahertz serial femtosecond crystallography (SFX) as a tool for reliable structure determination, substrate screening and the efficient measurement of the evolution and dynamics of molecular structures using megahertz repetition rate pulses available at this new class of X-ray laser source.Publicationtype: Journal ArticleScopus© Citations 158 748 259