Kilohertz serial crystallography with the JUNGFRAU detector at a fourth-generation synchrotron source

Status and perspective of protein crystallography at the first multi-bend achromat based synchrotron MAX IV

The first multi-bend achromat based synchrotron MAX IV operates two protein crystallography beamlines, BioMAX and MicroMAX. BioMAX is designed as a versatile, stable, high-throughput beamline catering for most protein crystallography experiments. MicroMAX is a more ambitious beamline dedicated to serial crystallography including time-resolved experiments. Both beamlines exploit the special characteristics of fourth-generation beamlines provided by the 3 GeV ring of MAX IV. In addition, the fragment-based drug discovery platform, FragMAX, is hosted and, at the FemtoMAX beamline, protein diffraction experiments exploring ultrafast time resolution can be performed. A technical and operational overview of the different beamlines and the platform is given as well as an outlook for protein crystallography embedded in the wider possibilities that MAX IV offers to users in the life sciences.

Real-time data processing for serial crystallography experiments

We report the use of streaming data interfaces to perform fully online data processing for serial crystallography experiments, without storing intermediate data on disk. The system produces Bragg reflection intensity measurements suitable for scaling and merging, with a latency of less than 1 s per frame. Our system uses the CrystFEL software in combination with the ASAP::O data framework. In a series of user experiments at PETRA III, frames from a 16 megapixel Dectris EIGER2 X detector were searched for peaks, indexed and integrated at the maximum full-frame readout speed of 133 frames per second. The computational resources required depend on various factors, most significantly the fraction of non-blank frames (`hits'). The average single-thread processing time per frame was 242 ms for blank frames and 455 ms for hits, meaning that a single 96-core computing node was sufficient to keep up with the data, with ample headroom for unexpected throughput reductions. Further significant improvements are expected, for example by binning pixel intensities together to reduce the pixel count. We discuss the implications of real-time data processing on the `data deluge' problem from recent and future photon-science experiments, in particular on calibration requirements, computing access patterns and the need for the preservation of raw data.

Photoswitch dissociation from a G protein-coupled receptor resolved by time-resolved serial crystallography

G protein-coupled receptors (GPCRs) are the largest family of cell surface receptors in humans. The binding and dissociation of ligands tunes the inherent conformational flexibility of these important drug targets towards distinct functional states. Here we show how to trigger and resolve protein-ligand interaction dynamics within the human adenosine A2A receptor. For this, we designed seven photochemical affinity switches derived from the anti-Parkinson's drug istradefylline. In a rational approach based on UV/Vis spectroscopy, time-resolved absorption spectroscopy, differential scanning fluorimetry and cryo-crystallography, we identified compounds suitable for time-resolved serial crystallography. Our analysis of millisecond-scale dynamics revealed how trans-to-cis isomerization shifts selected istradefylline derivatives within the binding pocket. Depending on the chemical nature of the ligand, interactions between extracellular loops 2 and 3, acting as a lid on the binding pocket, are disrupted and rearrangement of the orthosteric binding pocket is invoked upon ligand dissociation. This innovative approach provides insights into GPCR dynamics at the atomic level, offering potential for developing novel pharmaceuticals.

The evolution of raw data archiving and the growth of its importance in crystallography

The hardware for data archiving has expanded capacities for digital storage enormously in the past decade or more. The IUCr evaluated the costs and benefits of this within an official working group which advised that raw data archiving would allow ground truth reproducibility in published studies. Consultations of the IUCr's Commissions ensued via a newly constituted standing advisory committee, the Committee on Data. At all stages, the IUCr financed workshops to facilitate community discussions and possible methods of raw data archiving implementation. The recent launch of the IUCrData journal's Raw Data Letters is a milestone in the implementation of raw data archiving beyond the currently published studies: it includes diffraction patterns that have not been fully interpreted, if at all. The IUCr 75th Congress in Melbourne included a workshop on raw data reuse, discussing the successes and ongoing challenges of raw data reuse. This article charts the efforts of the IUCr to facilitate discussions and plans relating to raw data archiving and reuse within the various communities of crystallography, diffraction and scattering.

Structural biology in the age of X-ray free-electron lasers and exascale computing

Serial femtosecond X-ray crystallography has emerged as a powerful method for investigating biomolecular structure and dynamics. With the new generation of X-ray free-electron lasers, which generate ultrabright X-ray pulses at megahertz repetition rates, we can now rapidly probe ultrafast conformational changes and charge movement in biomolecules. Over the last year, another innovation has been the deployment of Frontier, the world's first exascale supercomputer. Synergizing extremely high repetition rate X-ray light sources and exascale computing has the potential to accelerate discovery in biomolecular sciences. Here we outline our perspective on each of these remarkable innovations individually, and the opportunities and challenges in yoking them within an integrated research infrastructure.

The time revolution in macromolecular crystallography

Macromolecular crystallography has historically provided the atomic structures of proteins fundamental to cellular functions. However, the advent of cryo-electron microscopy for structure determination of large and increasingly smaller and flexible proteins signaled a paradigm shift in structural biology. The extensive structural and sequence data from crystallography and advanced sequencing techniques have been pivotal for training computational models for accurate structure prediction, unveiling the general fold of most proteins. Here, we present a perspective on the rise of time-resolved crystallography as the new frontier of macromolecular structure determination. We trace the evolution from the pioneering time-resolved crystallography methods to modern serial crystallography, highlighting the synergy between rapid detection technologies and state-of-the-art x-ray sources. These innovations are redefining our exploration of protein dynamics, with high-resolution crystallography uniquely positioned to elucidate rapid dynamic processes at ambient temperatures, thus deepening our understanding of protein functionality. We propose that the integration of dynamic structural data with machine learning advancements will unlock predictive capabilities for protein kinetics, revolutionizing dynamics like macromolecular crystallography revolutionized structural biology.

X-Ray Crystallography of Viruses

Since the 1970s and for about 40 years, X-ray crystallography has been by far the most powerful approach for determining virus structures at close to atomic resolutions. Information provided by these studies has deeply and extensively enriched and shaped our vision of the virus world. In turn, the ever-increasing complexity and size of the virus structures being investigated have constituted a major driving force for methodological and conceptual developments in X-ray macromolecular crystallography (MX). Landmarks of the structure determination of viral particles, such as the ones from the first animal viruses or from the first membrane-containing viruses, have often been associated with methodological breakthroughs in X-ray crystallography.In recent years, the advent of new detectors with fast frame rate, high sensitivity, and low-noise background has changed the way MX data is collected, enabling new types of studies at X-ray free-electron laser and synchrotron facilities. In parallel, a very high degree of automation has been established at most MX synchrotron beamlines, allowing the screening of large number of crystals with very high throughputs. This has proved crucial for fragment-based drug design projects, of special relevance for the identification of new antiviral drugs.This change in the usage of X-ray crystallography is also mirrored in the recent advances in cryo-electron microscopy (cryo-EM), which can nowadays produce macromolecule structures at resolutions comparable to those obtained by MX. Since this technique is especially amenable for large protein assemblies, cryo-EM has progressively turned into the favored technique to study the structure of large viral particles at high resolution.In this chapter, we present the common ground of proteins and virus crystallography with an emphasis in the peculiarities of virus-related studies.