This deposition contains raw diffraction images collected at SACLA for the following paper. "Conformational alterations in unidirectional ion transport of a light-driven chloride pump revealed using X-ray free electron lasers" Toshiaki Hosaka, Takashi Nomura, Minoru Kubo, Takanori Nakane, Luo Fangjia, Shun-ichi Sekine, Takuhiro Ito, Kazutaka Murayama, Kentaro Ihara, Haruhiko Ehara, Kazuhiro Kashiwagi, Kazushige Katsura, Ryogo Akasaka, Tamao Hisano, Tomoyuki Tanaka, Rie Tanaka, Toshi Arima, Ayumi Yamashita, Michihiro Sugahara, Hisashi Naitow, Yoshinori Matsuura, Susumu Yoshizawa, Kensuke Tono, Shigeki Owada, Osamu Nureki, Tomomi Kimura-Someya, So Iwata, Eriko Nango, Mikako Shirouzu PNAS (2022), doi: 10.1073/pnas.2117433119 We encourage you to reprocess our datasets with new programs and ideas. We are happy to hear from you if you manage to solve the structures to higher resolution. * Datasets This deposition contains the following datasets mentioned in the paper. - Dark (i.e. no excitation) - With iodine - Dark (i.e. no excitation) - 16 nsec - 1 usec - 10 usec - 1 msec - With bromine - Dark (i.e. no excitation) - 1 msec In addition, we deposited an I-Minus dataset, which was collected with a negative delay (i.e. laser after X-ray exposure) as a control of light contamination. Datasets with excitation laser (including I-Minus) contain files suffixed with -dark1 and -dark2 (10 Hz excitation only). These are X-ray exposures (30 Hz) between excitation lasers (10 or 15 Hz). These images are not suitable for biological interpretation but we deposited them as they might be useful for e.g. data processing studies. Each dataset consists of images collected on two or three beam times, stored in different sub-directories. Each beam time needs different geometry files (see below). Checksums are provided in each directory. * Geometry MPCCD contains eight panels (512 x 1024 pixels each). In the HDF5 files the eight panels are stacked vertically to give a 512 x 8192 pixel image for a frame. The detector geometry is provided as CrystFEL geometry files. sacla-*-original.geom are the initial, non-optimized metrology based on facility provided values. Others are refined geometries used for final processing. * Processed stream file We also uploaded CrystFEL stream files in the Processed directory. As mentioned above, I-minus and *-d1, *-d2 datasets were not used for publication. Use -l (light) stream files for structure analysis. For Br-1msec, d1 and d2 were merged into one -d stream file. Also see below about indexing amgibuities. * Image processing Image files were written by Cheetah adapted for SACLA. Details of this pipeline were published in https://doi.org/10.1107/S1600576716005720. The images are ready for processing by CrystFEL. A dxtbx module necessary for processing with DIALS is also available. See https://github.com/biochem-fan/cheetah/wiki for detailed explanations and tutorials. Parameters we used are as follows. Best parameters for newer versions of CrystFEL are probably different. For P212121-Dark: 16Mar: -g sacla-16mar-500-opt-2ndday.geom --peaks=zaef --threshold=400 --min-gradient=200000 --min-snr=5 --indexing=dirax --int-radius=3,4,7 16May: -g sacla-16may-510-opt-predrefine.geom --peaks=zaef --threshold=400 --min-gradient=200000 --min-snr=3 --indexing=dirax --int-radius=3,4,7 For all others (C2): 17Apr: -g sacla-17apr-473-opt.geom --peaks=zaef --threshold=400 --min-snr=5 --min-gradient=200000 --indexing=dirax --int-radius=4,5,7 18Jul: -g sacla-18jul-hosaka-495-opt2.geom --peaks=peakfinder8 --threshold=0 --min-snr=4.5 --min-pix-count=2 --local-bg-radius=3 --indexing=dirax --int-radius=3,4,7 19Feb: -g sacla-19feb-hosaka-505-opt.geom --peaks=peakfinder8 --threshold=0 --min-snr=4.3 --min-pix-count=2 --local-bg-radius=3 --indexing=dirax --int-radius=3,4,7 19Jun: -g sacla-19jun-hosaka-515-opt.geom --peaks=zaef --threshold=100 --min-gradient=100000 --min-snr=4.0 --indexing=xgandalf --int-radius=3,4,7 (I-Dark) -g sacla-19jun-hosaka-515-opt.geom --peaks=zaef --threshold=100 --min-gradient=100000 --min-snr=4.0 --indexing=dirax --int-radius=3,4,7 (others) After integration of the C2 datasets, we executed ambigator with "--operator=h,-k,-h-l --highres=2.7 -y 2/m_uab" to resolve indexing ambiguity. Note that ambigator makes indexing consistent within each stream file but different stream files may have different indexing choices. This was resolved by re-indexing merged MTZ files when necessary. * Contact Questions about data processing should be sent to Takanori Nakane. Other questions should be sent to Toshiaki Hosaka. Mail addresses are shown in the CXIDB.