VMXi-Versatile Macromolecular Crystallography in situ
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Open Access
Abstract: Macromolecular crystallography provides mechanistic understanding of biological processes and can be applied in drug design. Nowadays, the use of robotic systems for crystal growth and diffraction analysis is widespread and high-throughput protein-to-structure pipelines for ligand and fragment screening are revolutionizing the field. However, the identification of crystals is still largely carried out through manual inspection, sometimes involving tens of thousands of images, which represents a bottleneck in an otherwise highly automated process. Here we describe AXIS, an AI-based Crystal Identification System combining the DINOv2 computer vision model, state-of-the-art transfer learning and MARCO, the largest crystallization dataset available to date, for automated crystal detection. AXIS can operate with both visible and UV light images and integrates a Lab-in-the-Loop approach combining ML and expert inputs for iterative learning and specialization. AXIS enables automated annotation of large crystallization image datasets with performance and accuracy comparable to that of human experts, and the Lab-in-the-Loop approach introduced here enables efficient adaptation to local conditions, facilitating widespread application, which has been a major limitation to date. AXIS can help to correct human errors in image annotation and removes critical bottlenecks, particularly in the context of extensive crystallization screens or high-throughput applications like fragment and ligand screening, unlocking the potential for higher levels of automation that are key in both fundamental and translational research.
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May 2026
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Open Access
Abstract: Serial crystallography relies on the reproducible production of high-density suspensions of microcrystals, yet sample optimization remains a resource-intensive bottleneck. While phase diagrams provide a theoretical framework for controlling crystal size and number, experimental mapping is traditionally hindered by relatively high sample consumption. We present an automated microbatch-under-oil crystallization approach that rapidly maps phase boundaries using only 15–60 µl (∼0.15–3.8 mg) of protein. While this workflow is ideally suited for refining existing hits, it serves as a standalone platform for characterizing the crystallization landscape of new protein targets. The power of this approach lies in the integration of three distinct strategies that exploit the stable chemical environment of microbatch-under-oil. Firstly, we utilize an ingenious diagonal sampling strategy that traverses the phase boundary parallel to the solubility curve by systematically varying protein-to-precipitant ratios, identifying primary nucleation zones with far greater efficiency than traditional orthogonal grids. Secondly, we employ a linked variation of multiple precipitants to reveal morphology-specific regions, such as the rod versus plate transitions crucial for time-resolved experiments. Finally, we incorporate automated seed-stock titration to precisely define the metastable zone, enabling the predictive rescue of nucleation-limited systems. The synergy of these three strategies enables the systematic decoupling of nucleation from growth, providing a rational route to optimize microcrystal density, size and lattice order. Crucially, by eliminating the evaporation-related variables inherent in vapor diffusion, this method ensures that the chemical coordinates identified during screening remain constant during scale-up to larger volumes. This workflow transforms empirical serial crystallography sample preparation into a rational, reproducible and highly efficient process applicable to both the optimization of known conditions and the de novo development of microcrystal suspensions, tailored to the rigorous demands of modern serial diffraction experiments.
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Mar 2026
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I22-Small angle scattering & Diffraction
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Diamond Proposal Number(s):
[15320]
Open Access
Abstract: Understanding the structure–function relationships in anisotropic fibre-symmetric materials is critical for both biological insight and bioinspired design. We present a generalized analytical model for X-ray diffraction intensity from nanofibrillar materials with fibre symmetry, accommodating arbitrary diffraction rings beyond prior axial and equatorial limits. This model integrates 3D orientation, strain heterogeneity and angular misalignment effects, and is validated using wide-angle X-ray diffraction (WAXD) from the Bouligand-structured cuticle of the mantis shrimp (Odontodactylus scyllarus). Using scanning synchrotron WAXD, we extract depth-averaged and sub-lamellar information on 3D fibre orientation and crystalline parameters from 2D scans. Model simulations and experimental fits show accurate reconstruction of the Bouligand texture and reveal spatial gradients in orientation, strain and angular dispersion. By fitting multiple reflections – axial (002), equatorial (110) and intermediate (013) – we improve the robustness in parameter extraction, especially in regions where the Ewald condition is partially satisfied. Our framework enhances the interpretation of WAXD in heterogeneous fibre-based materials and can be embedded into advanced tomographic or machine-learning workflows. This approach is applicable to a broad class of biological and synthetic composites, facilitating high-throughput structural characterization in scenarios where rotation is impractical or impossible.
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Dec 2025
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I24-Microfocus Macromolecular Crystallography
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Peter
Smyth
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Sofia
Jaho
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Lewis J.
Williams
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Gabriel
Karras
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Ann
Fitzpatrick
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Amy J.
Thompson
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Sinan
Battah
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Danny
Axford
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Sam
Horrell
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Marina
Lucic
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Kotone
Ishihara
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Machika
Kataoka
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Hiroaki
Matsuura
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Kanji
Shimba
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Kensuke
Tono
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Takehiko
Tosha
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Hiroshi
Sugimoto
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Shigeki
Owada
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Michael A.
Hough
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Jonathan A. R.
Worrall
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Robin L.
Owen
Diamond Proposal Number(s):
[18565, 28583, 27313]
Open Access
Abstract: Time-resolved X-ray crystallography is undergoing a renaissance due to the development of serial crystallography at synchrotron and XFEL beamlines. Crucial to such experiments are efficient and effective methods for uniformly initiating time-dependent processes within microcrystals, such as ligand binding, enzymatic reactions or signalling. A widely applicable approach is the use of photocaged substrates, where the photocage is soaked into the crystal in advance and then activated using a laser pulse to provide uniform initiation of the reaction throughout the crystal. This work characterizes photocage release of nitric oxide and binding of this ligand to two heme protein systems, cytochrome c′-β and dye-decolourizing peroxidase B using a fixed target sample delivery system. Laser parameters for photoactivation are systematically explored, and time-resolved structures over timescales ranging from 100 µs to 1.4 s using synchrotron and XFEL beamlines are described. The effective use of this photocage for time-resolved crystallography is demonstrated and appropriate illumination conditions for such experiments are determined.
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Sep 2025
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I15-1-X-ray Pair Distribution Function (XPDF)
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Adam F.
Sapnik
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Philip A.
Chater
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Dean S.
Keeble
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John S. O.
Evans
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Federica
Bertolotti
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Antonietta
Guagliardi
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Lise J.
Støckler
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Elodie A.
Harbourne
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Anders B.
Borup
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Rebecca S.
Silberg
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Adrien
Descamps
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Clemens
Prescher
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Benjamin D.
Klee
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Axel
Phelipeau
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Imran
Ullah
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Kárel G.
Medina
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Tobias A.
Bird
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Viktoria
Kaznelson
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William
Lynn
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Andrew L.
Goodwin
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Bo B.
Iversen
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Celine
Crepisson
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Emil S.
Bozin
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Kirsten M. Ø.
Jensen
,
Emma E.
Mcbride
,
Reinhard B.
Neder
,
Ian
Robinson
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Justin S.
Wark
,
Michał
Andrzejewski
,
Ulrike
Boesenberg
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Erik
Brambrink
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Carolina
Camarda
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Valerio
Cerantola
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Sebastian
Goede
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Hauke
Höppner
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Oliver S.
Humphries
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Zuzana
Konopkova
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Naresh
Kujala
,
Thomas
Michelat
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Motoaki
Nakatsutsumi
,
Alexander
Pelka
,
Thomas R.
Preston
,
Lisa
Randolph
,
Michael
Roeper
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Andreas
Schmidt
,
Cornelius
Strohm
,
Minxue
Tang
,
Peter
Talkovski
,
Ulf
Zastrau
,
Karen
Appel
,
David A.
Keen
Diamond Proposal Number(s):
[39017]
Open Access
Abstract: High-quality total scattering data, a key tool for understanding atomic-scale structure in disordered materials, require stable instrumentation and access to high momentum transfers. This is now routine at dedicated synchrotron instrumentation using high-energy X-ray beams, but it is very challenging to measure a total scattering dataset in less than a few microseconds. This limits their effectiveness for capturing structural changes that occur at the much faster timescales of atomic motion. Current X-ray free-electron lasers (XFELs) provide femtosecond-pulsed X-ray beams with maximum energies of ∼24 keV, giving the potential to measure total scattering and the attendant pair distribution functions (PDFs) on femtosecond timescales. We demonstrate that this potential has been realized using the HED scientific instrument at the European XFEL and present normalized total scattering data for 0.35 Å−1 < Q < 16.6 Å−1 and their PDFs from a broad spectrum of materials, including crystalline, nanocrystalline and amorphous solids, liquids and clusters in solution. We analyzed the data using a variety of methods, including Rietveld refinement, small-box PDF refinement, joint reciprocal–real-space refinement, cluster refinement and Debye scattering analysis. The resolution function of the setup is also characterized. We conclusively show that high-quality data can be obtained from a single ∼30 fs XFEL pulse for multiple different sample types. Our efforts not only significantly increase the existing maximum reported Q range for an S(Q) measured at an XFEL but also mean that XFELs are now a viable X-ray source for the broad community of people using reciprocal-space total scattering and PDF methods in their research.
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Sep 2025
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I20-Scanning-X-ray spectroscopy (XAS/XES)
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Jack
Stephens
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Ramesh
Rijal
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Daniel
Sier
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Nicholas T. T.
Tran
,
Jonathan W.
Dean
,
Paul
Di Pasquale
,
Tony
Kirk
,
Minh
Dao
,
Chanh Q.
Tran
,
Shusaku
Hayama
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Sofia
Diaz-Moreno
,
Christopher T.
Chantler
Diamond Proposal Number(s):
[39257]
Open Access
Abstract: The discovery of the novel n = 2 satellite transition in the Kβ emission spectrum of manganese and its evolution with incident photon energy are presented. Using the XR-HERFD (extended-range high-energy-resolution fluorescence detection) technique, we conclusively demonstrate the existence of this phenomenon with a statistical significance corresponding to 652 σse across the measured spectrum, far above the discovery threshold of 3–6 σse. We apply principal component analysis (PCA) to the XR-HERFD data to extract advanced structural insights. The evolution of this novel spectral feature and physical process are quantified by incorporating regression, revealing the increase in intensity over a wide range of incident photon energies. We validate these findings through independent test data. These results directly challenge the conventional treatment of the many-body reduction factor S02 as a constant independent of incident photon energy in the standard XAFS (X-ray absorption fine structure) equation. Thereby, these results present compelling evidence that S02 should be modelled as a varying function of incident photon energy, marking the first observation of this behaviour in Kβ spectra. This facilitates a greater quantitative understanding of HERFD spectra and a comprehensive representation of many-body effects in condensed matter systems.
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Sep 2025
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Open Access
Abstract: Advancements in macromolecular crystallography, driven by improved sources and cryocooling techniques, have enabled the use of increasingly smaller crystals for structure determination, with microfocus beamlines now widely accessible. Initially developed for challenging samples, these techniques have culminated in advanced beamlines such as VMXm. Here, an in vacuo sample environment improves the signal-to-noise ratio in X-ray diffraction experiments, and thus enables the use of submicrometre crystals. The advancement of techniques such as microcrystal electron diffraction (MicroED) for atomic-level insights into charged states and hydrogen positions, along with room-temperature crystallography to observe physiological states via serial crystallography, has driven a resurgence in the use of microcrystals. Reproducibly preparing small crystals, especially from samples that typically yield larger crystals, requires considerable effort, as no one singular approach guarantees optimal crystals for every technique. This review discusses methods for generating such small crystals, including mechanical crushing and batch crystallization with seeding, and evaluates their compatibility with microcrystal data-collection modalities. Additionally, we examine sample-delivery methods, which are crucial for selecting appropriate crystallization strategies. Establishing reliable protocols for sample preparation and delivery opens new avenues for macromolecular crystallography, particularly in the rapidly progressing field of time-resolved crystallography.
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May 2025
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Lewis J.
Williams
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Amy J.
Thompson
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Philipp
Dijkstal
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Martin
Appleby
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Greta
Assmann
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Florian S. N.
Dworkowski
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Nicole
Hiller
,
Chia-Ying
Huang
,
Tom
Mason
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Samuel
Perrett
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Eduard
Prat
,
Didier
Voulot
,
Bill
Pedrini
,
John H.
Beale
,
Michael A.
Hough
,
Jonathan A. R.
Worrall
,
Robin L.
Owen
Open Access
Abstract: Serial femtosecond crystallography (SFX) exploits extremely brief X-ray free-electron laser pulses to obtain diffraction data before destruction of the crystal. However, during the pulse X-ray-induced site-specific radiation damage can occur, leading to electronic state and/or structural changes. Here, we present a systematic exploration of the effect of single-pulse duration and energy (and consequently different dose rates) on site-specific radiation damage under typical SFX room-temperature experimental conditions. For the first time in SFX we directly measured the photon pulse duration, varying from less than 10 fs to more than 50 fs, and used three pulse energies to probe in-pulse damage in two radiation-sensitive proteins: the iron-heme peroxidase DtpAa and the disulfide-rich thaumatin. While difference-map features arising from radiation damage are observed, they do not lead to significant change in refined atomic coordinates or key bond lengths. Our work thus provides experimental verification that average atomic coordinates are not significantly perturbed by radiation damage in typical SFX experiments.
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May 2025
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Open Access
Abstract: Conformational heterogeneity of biological macromolecules is a challenge in single-particle averaging (SPA). Current standard practice is to employ classification and filtering methods that may allow a discrete number of conformational states to be reconstructed. However, the conformation space accessible to these molecules is continuous and, therefore, explored incompletely by a small number of discrete classes. Recently developed heterogeneous reconstruction algorithms (HRAs) to analyse continuous heterogeneity rely on machine-learning methods that employ low-dimensional latent space representations. The non-linear nature of many of these methods poses a challenge to their validation and interpretation and to identifying functionally relevant conformational trajectories. These methods would benefit from in-depth benchmarking using high-quality synthetic data and concomitant ground truth information. We present a framework for the simulation and subsequent analysis with respect to the ground truth of cryo-EM micrographs containing particles whose conformational heterogeneity is sourced from molecular dynamics simulations. These synthetic data can be processed as if they were experimental data, allowing aspects of standard SPA workflows as well as heterogeneous reconstruction methods to be compared with known ground truth using available utilities. The simulation and analysis of several such datasets are demonstrated and an initial investigation into HRAs is presented.
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Nov 2024
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Open Access
Abstract: The accuracy of the information in the Protein Data Bank (PDB) is of great importance for the myriad downstream applications that make use of protein structural information. Despite best efforts, the occasional introduction of errors is inevitable, especially where the experimental data are of limited resolution. A novel protein structure validation approach based on spotting inconsistencies between the residue contacts and distances observed in a structural model and those computationally predicted by methods such as AlphaFold2 has previously been established. It is particularly well suited to the detection of register errors. Importantly, this new approach is orthogonal to traditional methods based on stereochemistry or map–model agreement, and is resolution independent. Here, thousands of likely register errors are identified by scanning 3–5 Å resolution structures in the PDB. Unlike most methods, the application of this approach yields suggested corrections to the register of affected regions, which it is shown, even by limited implementation, lead to improved refinement statistics in the vast majority of cases. A few limitations and confounding factors such as fold-switching proteins are characterized, but this approach is expected to have broad application in spotting potential issues in current accessions and, through its implementation and distribution in CCP4, helping to ensure the accuracy of future depositions.
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Nov 2024
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