This deposition contains raw diffraction images collected at SACLA for the
following paper.

"Heavy Atom Detergent/Lipid Combined X-ray Crystallography for Elucidating
the Structure-Function Relationships of Membrane Proteins"

Shinya Hanashima, Takanori Nakane and Eiichi Mizohata

Membranes (2021), doi: 10.3390/membranes11110823

We encourage you to reprocess this dataset 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 two datasets mentioned in the paper, HAD16 and HAD16H.
Checksums are provided in respective folders.

* 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-15nov-500-opt.geom was used for final data processing.
sacla-15nov-500-original.geom is the initial, non-optimized metrology based on facility provided values.

* Processed stream file

We also uploaded CrystFEL stream files in the Processed directory.

* 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. For example:

    indexamajig -i HAD16.lst -o HAD16.stream -j 12 -g sacla-15nov-500-opt.geom -p ../cell-sfx.cell \
        --indexing=dirax --peaks=zaef --threshold=400 --min-gradient=1000000 --min-snr=3 --int-radius=3,4,7

    indexamajig -i HAD16H.lst -o HAD16H.stream -j 12 -g sacla-15nov-500-opt.geom -p ../cell-sfx.cell \
        --indexing=dirax --peaks=zaef --threshold=400 --min-gradient=2000000 --min-snr=3 --int-radius=3,4,7

These are parameters we used with CrystFEL 0.6.1. Best parameters for newer versions of CrystFEL are probably different.

A dxtbx module necessary for processing with DIALS is also available.

See https://github.com/biochem-fan/cheetah/wiki for detailed explanations and tutorials.

* Contact

Questions about data processing should be sent to Takanori Nakane.
Other questions should be sent to Eiichi Mizohata.
Mail addresses are shown in the CXIDB.