Serial femtosecond crystallography data processing at the global science data hub center at KISTI

Serial crystallography (SX) is an emerging technique for determining the room-temperature structures of macromolecules or small molecules, while minimizing radiation damage. SX combined with pump–probe or mix-and-inject experiments further enables the visualization of time-resolved molecular dynamics involved in reaction mechanisms. In SX experiments, hundreds of thousands to millions of diffraction images are typically collected to determine the three-dimensional structure, and high-performance computing resources are required to efficiently process such large datasets. In this study, we introduced the computing infrastructure of the Global Science Data hub Center (GSDC) at the Korea Institute of Science and Technology Information (KISTI) for Serial femtosecond crystallography (SFX) data processing generated using the Pohang Accelerator Laboratory X-ray Free Electron Laser (PAL-XFEL). We describe the hardware and software specifications of three dedicated servers for SX data processing at GSDC. Using this system, we processed SFX data for three different datasets, incorporating various inputs such as parallel processing with CPUs, indexing algorithms, and other indexing parameters, to understand the correlation between data processing speed and indexing efficiency. These results provide practical guidelines for SX data processing using the GSDC infrastructure and offer valuable insights for designing efficient data collection and analysis strategies.