8RPM

Lysozyme structure based on automated real-time serial crystallography data processing using CrystFEL

Summary for 8RPM

• Entry DOI: 10.2210/pdb8rpm/pdb
• Descriptor: Lysozyme C, CHLORIDE ION, SODIUM ION, ... (4 entities in total)
• Functional Keywords: jinxed, real-time data processing, hydrolase
• Biological source: Gallus
• Total number of polymer chains: 1
• Total formula weight: 14425.06

Authors

White, T.A.,Oberthuer, D.,Henkel, A. (deposition date: 2024-01-16, release date: 2024-02-21, Last modification date: 2025-01-22)

Primary citation

White, T.,Schoof, T.,Yakubov, S.,Tolstikova, A.,Middendorf, P.,Karnevskiy, M.,Mariani, V.,Henkel, A.,Klopprogge, B.,Hannappel, J.,Oberthuer, D.,De Gennaro Aquino, I.,Egorov, D.,Munke, A.,Sprenger, J.,Pompidor, G.,Taberman, H.,Gruzinov, A.,Meyer, J.,Hakanpaa, J.,Gasthuber, M.
Real-time data processing for serial crystallography experiments.
Iucrj, 12:97-108, 2025

PubMed Abstract: 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.

PubMed: 39714221
DOI: 10.1107/S2052252524011837

Experimental method

X-RAY DIFFRACTION (1.8 Å)