Armin Wagner

Transmission electron microscopy requires electron-transparent specimens, typically below 200 nm thick. For cellular and tissue samples this is typically achieved by focused ion-beam (FIB) thinning to form lamellae. Milling times scale with specimen thickness, and high-pressure-frozen specimens more than 10 µm thick can take up to 2 hours per lamella. We present a pre-processing approach in which bulk material is removed by ultrashort-pulse laser ablation prior to milling, rapidly generating large trenches in vitrified grids under cryogenic conditions and leaving material to be finished by conventional milling to yield electron-transparent lamellae. Laser ablation completes in seconds (4 seconds per pattern), compared with minutes to tens of minutes for FIB trench milling, and introduces negligible damage to the final lamellae. By replacing the most time-intensive, contamination-sensitive bulk-removal steps with seconds-long laser trenching, this open-source approach reduces time-to-lamellae, increasing throughput and preserves compatibility with standard cryo-FIB/SEM polishing and cryo-ET data-collection pipelines.

Emerging human pathogenic RNA viruses such as Lassa virus (LASV) and closely related viruses such as Hantavirus and Andes virus continue to be a major health threat globally. Treatment options for infections are severely limited. The widely conserved cap-snatching endonuclease of LASV (LASVendoN) is therefore used as an interesting drug target for our X-ray compound-screening experiments. Considering recent improvements in instrumentation and serial crystallography method development, different approaches may be used to facilitate pharmaceutical compound screening. Current-generation X-ray free-electron laser (XFEL) sources hold promise for obtaining higher quality diffraction data and achieving a high sample throughput using fixed-target serial femtosecond X-ray crystallography. We collected serial fixed-target X-ray diffraction data at Linac Coherent Light Source and at the synchrotron source PETRA III for comparison and solved the crystal structures of 2,4-dioxo-4-phenylbutanoic acid (DPBA) and baloxavir acid (BXA) binding to the active site of LASVendoN. These solved structures represent a reasonable starting point for drug development. In addition to room-temperature diffraction data, conventional single-crystal diffraction data were recorded at 100 K for comparison. To analyse the sample throughput in a compound-screening experiment at an XFEL, we further present data for the bacterial fosfomycin-resistance protein A with six ligands previously identified in a synchrotron screening experiment. In summary, the XFEL and synchrotron data-collection approaches have proven to be useful for compound screening with minor differences in achievable data quality and resolution. The individual experimental setup, detector and potentially the use of beam sweeping at XFELs at close-to-physiological temperatures combined with reasonable sample consumption and minimized radiation damage are considered to be advantageous for high-throughput drug development.

Preventing collisions during automated sample exchange is critical for synchrotron beamlines, particularly for complex cryogenic in-vacuum endstations where recovery from hardware damage may take days. GoniOwl , a compact convolutional neural network (CNN) model, classifies sample-pin presence on the goniometer from a live camera feed on the long-wavelength macromolecular crystallography beamline I23 at Diamond Light Source. Trained on over 8700 manually verified images spanning two years of routine operation and augmented for robustness to illumination changes, camera shifts and occlusions, the model achieves >99% accuracy with millisecond-level inference. A confidence-gating mechanism routes uncertain predictions to a fail-safe path requiring operator confirmation, ensuring suitability for machine-protection control. Integrated via Experimental Physics and Industrial Control System ( EPICS ) process variables, GoniOwl runs in real time within the automated sample-change sequence. In shadow-mode deployment, the CNN matched or exceeded both the legacy histogram method and operator confirmations, which each achieved 96% accuracy. A closed-loop disagreement-audit workflow automatically collects divergent cases for targeted retraining and verification. The approach is readily transferable to other beamline environments where camera-based vision systems can provide an additional software machine protection layer.

Experiment proposals at synchrotron facilities serve as the primary gateway for instrument access. They currently lack the standardized and granular topic metadata necessary for tasks such as classification and review, and, broadly speaking, reuse. This paper defines and tests the feasibility of a real-time topic classification service for experiment proposals using an open-source machine-learning model and domain experts for the evaluation phase. We applied the OpenAlex topic classification model to 5384 experiment proposals and selected 209 of them to each be independently evaluated by three domain experts to assess the performance and utility of the model. Analysis of the evaluations reveals a general consensus among the reviewers regarding the model's predictions, with a Krippendorff's alpha of 0.572. We also find that 74.2% of the proposals had at least one topic that was unanimously deemed relevant, which suggests that the model performs well enough to be used in a live setting with real-time verification. However, we do not recommend using it in automated environments without human oversight, given the proposal-based precision score of 56.0%. By aligning the data infrastructure of photon and neutron facilities with the OpenAlex ecosystem, we also lay the groundwork for the eventual inclusion of proposals and experiment reports into OpenAlex, which is necessary for a complete record of a research activity.

Despite the theoretical advantages of phosphorus single-wavelength anomalous diffraction (P-SAD) for nucleic acid phasing, its application remains limited due to high atomic displacement parameters and an unfavourable ratio of unique reflections to anomalous scatterers. In this study, we report the crystal structure of an RNA complex composed of four strands, which was solved by experimental phasing after AlphaFold 3 failed to produce reliable models. Bromine single-wavelength anomalous diffraction (Br-SAD) data were collected at 0.916 Å on beamline I04 at Diamond Light Source, while phosphorus anomalous data were obtained at 3.024 Å on beamline I23. The structure was successfully phased using bromine anomalous scattering, and phosphorus anomalous peaks corroborated the backbone positions and validated the model. Attempts to phase the structure directly from phosphorus data failed, consistent with theoretical predictions that successful SAD phasing requires a significantly higher reflection-to-scatterer ratio. The final models reveal an RNA complex stabilized by Watson–Crick and Hoogsteen base pairing, forming a pseudo-helical complex instead of the anticipated hairpin stem-loop, likely reflecting crystallization artefacts. This work demonstrates the complementary use of bromine and phosphorus anomalous signals in RNA crystallography.

The enterobacterial common antigen (ECA) is conserved in Gram-negative bacteria of the Enterobacterales order although its function is debated. ECA biogenesis depends on the Wzx/Wzy-dependent strategy whereby the newly synthesized lipid-linked repeat units, lipid III, are transferred across the inner membrane by the lipid III flippase WzxE. WzxE is part of the Wzx family and required in many glycan assembly systems, but an understanding of its molecular mechanism is hindered due to a lack of structural evidence. Here, we present the first X-ray structures of WzxE from Escherichia coli in complex with nanobodies. Both inward- and outward-facing conformations highlight two pairs of arginine residues that move in a reciprocal fashion, enabling flipping. One of the arginine pairs coordinated to a glutamate residue is essential for activity along with the C-terminal arginine rich tail located close to the entrance of the lumen. This work helps understand the translocation mechanism of the Wzx flippase family.

Analytical absorption corrections are employed in scaling diffraction data for highly absorbing samples, such as those used in long-wavelength crystallography, where empirical corrections pose a challenge. AnACor2.0 is an accelerated software package developed to calculate analytical absorption corrections. It accomplishes this by ray-tracing the paths of diffracted X-rays through a voxelized 3D model of the sample. Due to the computationally intensive nature of ray-tracing, the calculation of analytical absorption corrections for a given sample can be time consuming. Three experimental datasets (insulin at λ = 3.10 Å, thermolysin at λ = 3.53 Å and thaumatin at λ = 4.13 Å) were processed to investigate the effectiveness of the accelerated methods in AnACor2.0. These methods demonstrated a maximum reduction in execution time of up to 175× compared with previous methods. As a result, the absorption factor calculation for the insulin dataset can now be completed in less than 10 s. These acceleration methods combine sampling, which evaluates subsets of crystal voxels, with modifications to standard ray-tracing. The bisection method is used to find path lengths, reducing the complexity from O(n) to O(log₂ n). The gridding method involves calculating a regular grid of diffraction paths and using interpolation to find an absorption correction for a specific reflection. Additionally, optimized and specifically designed CUDA implementations for NVIDIA GPUs are utilized to enhance performance. Evaluation of these methods using simulated and real datasets demonstrates that systematic sampling of the 3D model provides consistently accurate results with minimal variance across different sampling ratios. The mean difference of absorption factors from the full calculation (without sampling) is at most 2%. Additionally, the anomalous peak heights of sulfur atoms in the Fourier map show a mean difference of only 1% compared with the full calculation. This research refines and accelerates the process of analytical absorption corrections, introducing innovative sampling and computational techniques that significantly enhance efficiency while maintaining accurate results.

Metal ions have important roles in supporting the catalytic activity of DNA-regulating enzymes such as topoisomerases (topos). Bacterial type II topos, gyrases and topo IV, are primary drug targets for fluoroquinolones, a class of clinically relevant antibacterials requiring metal ions for efficient drug binding. While the presence of metal ions in topos has been elucidated in biochemical studies, accurate location and assignment of metal ions in structural studies have historically posed significant challenges. Recent advances in X-ray crystallography address these limitations by extending the experimental capabilities into the long-wavelength range, exploiting the anomalous contrast from light elements of biological relevance. This breakthrough enables us to confirm experimentally the locations of Mg²⁺in the fluoroquinolone-stabilizedStreptococcus pneumoniaetopo IV complex. Moreover, we can unambiguously identify the presence of K⁺and Cl^-ions in the complex with one pair of K⁺ions functioning as an additional intersubunit bridge. Overall, our data extend current knowledge on the functional and structural roles of metal ions in type II topos.

AlphaFold2 has revolutionized structural biology by offering unparalleled accuracy in predicting protein structures. Traditional methods for determining protein structures, such as X-ray crystallography and cryo-electron microscopy, are often time-consuming and resource-intensive. AlphaFold2 provides models that are valuable for molecular replacement, aiding in model building and docking into electron density or potential maps. However, despite its capabilities, models from AlphaFold2 do not consistently match the accuracy of experimentally determined structures, need to be validated experimentally and currently miss some crucial information, such as post-translational modifications, ligands and bound ions. In this paper, the advantages are explored of collecting X-ray anomalous data to identify chemical elements, such as metal ions, which are key to understanding certain structures and functions of proteins. This is achieved through methods such as calculating anomalous difference Fourier maps or refining the imaginary component of the anomalous scattering factor f′′. Anomalous data can serve as a valuable complement to the information provided by AlphaFold2 models and this is particularly significant in elucidating the roles of metal ions.

Twisted gastrulation (TWSG1) is an evolutionarily conserved secreted glycoprotein which controls signaling by Bone Morphogenetic Proteins (BMPs). TWSG1 binds BMPs and their antagonist Chordin to control BMP signaling during embryonic development, kidney regeneration and cancer. We report crystal structures of TWSG1 alone and in complex with a BMP ligand, Growth Differentiation Factor 5. TWSG1 is composed of two distinct, disulfide-rich domains. The TWSG1 N-terminal domain occupies the BMP type 1 receptor binding site on BMPs, whereas the C-terminal domain binds to a Chordin family member. We show that TWSG1 inhibits BMP function in cellular signaling assays and mouse colon organoids. This inhibitory function is abolished in a TWSG1 mutant that cannot bind BMPs. The same mutation in the Drosophila TWSG1 ortholog Tsg fails to mediate BMP gradient formation required for dorsal-ventral axis patterning of the early embryo. Our studies reveal the evolutionarily conserved mechanism of BMP signaling inhibition by TWSG1.