SAXS dataset for data analysis tutorial

Tutorial here.

Composition of the dataset

This dataset includes processed (radially averaged and mask-corrected) SAXS data from a sample of hen egg white lysozyme. The concentrations used were:

• 8 mg/ml (02700_F2-T1_lys_8*.dat)
• 4 mg/ml (02702_F2-T1_lys_8*.dat)
• 2 mg/ml (02704_F2-T1_lys_8*.dat)
• 1 mg/ml (02706_F2-T1_lys_8*.dat)
• buffer (02698_F1-T1_buff_lys*.dat)

Data can be found in the scattering_data/processed folder.

The rest of the data (averaged, subtracted, output of various analysis softwares) is saved in the described structure below.

├── README.md           <- The top-level README for developers using this project.
│
├── processed_data
|   ├── CRYSOL          <- Output of CRYSOL.
│   ├── DAMMIF          <- Output of DAMMIF.
|   ├── DENSS           <- Output of DENSS.
|   ├── GASBOR          <- Output of GASBOR
|   ├── GNOM            <- Output of GNOM.
|   └── SUPCOMB         <- Output of SUPCOMB.
|
├── references          <- Data dictionaries, manuals, and all other explanatory materials.
|   └── pdb_models      <- High resolution structural models.
|   └── sasbdb_models   <- SAXS data from the SASBDB
|
├── reports             <- Generated analysis files.
|   └── figures         <- Generated graphics and figures to be used in reporting.
│
├── scattering_data
|   ├── averaged        <- Averaged data.
|   ├── processed       <- Integrated SAXS data acquired.
|   ├── subtracted      <- The final, buffer-subtracted averaged scattering data for modeling.
|   └── uv              <- UV data acquired.
|
├── scripts             <- Various scripts to run programs and generate figures.
|
└── workspaces          <- RAW workspaces.

Experimental conditions

Ten frames were acquired during 120 seconds at 20 °C in the MAXS configuration (detector distance from sample of 600 mm).

The data was acquired on 2019-12-17 by Normand Cyr at the Structural Biology Platform of the Université de Montréal.

• Instrument: Xenocs BioXolver L
• X-rays generator: Excillum MetalJet D2+ 70 kV (λ = 1.34 Å)
• Detector: Dectris PILATUS3 R 300K

Additional sample information

The buffer used was 20 mM Tris pH 7.5, 150 mM NaCl.

The full sequence of lysozyme is:

>sp|P00698|LYSC_CHICK Lysozyme C OS=Gallus gallus OX=9031 GN=LYZ PE=1 SV=1
MRSLLILVLCFLPLAALGKVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQA
TNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDG
NGMNAWVAWRNRCKGTDVQAWIRGCRL

See UNIPROT entry P00698 for more details.

The sample used for the SAXS experiments comprises amino acids 19 to 147 of the protein. Many X-ray crystal structures exist in the PDB. A good example is entry 1LYS. The PDB file can be found in references/pdb_models.

Another example dataset for lysozyme is present in references /sasbdb_models. It corresponds to the SASDA96 entry of the SASBDB.