Publishing SAXS data
Acknowledging the Beamline in your Publications and Outputs
The beamline team are always happy to support users through to the publication of their work. Please consider the form you would like this acknowledgement to take given the contribution of your beamline scientist. Please note:
Beamline staff are Scientists. When they make an intellectual and/or experimental contribution to a publication they deserve to be recognised and acknowledged, just as any other co-author would be.
National facilities are not just instruments provided in a room; they are populated by highly-skilled and experienced individuals who make complex experiments possible, and provide essential support in very specialised technologies, often with an intellectual contribution to the project. Proper acknowledgment of facilities enables them to obtain financial support.
Beamline staff should have the opportunity to participate in drafting the pertinent part of the paper, and give final approval to the wording and conclusions drawn before publication, as any other contributing Scientist would. This will also ensure the data is interpreted correctly, avoids data misinterpretation, and more information on your samples through advanced analysis may be obtained.
We risk widening the gap between academic and beamline staff if prior practices and non-acknowledgement are allowed to continue.
The research community as a whole, academic and technical alike, should work towards the mutual goal of research excellence across the sector.
To acknowledge the beamline without an authorship please use the words:
Part (or all), of this work was carried out on the BioSAXS beamline at the Australian Synchrotron, ANSTO.
Thanks to Natasha Stephen, University of Plymouth, for developing original policy documentation
Publication guidelines for Biomolecular Small-Angle Scattering
There are guidelines for publishing structural biology studies using SAXS (and SANS) to ensure the quality of data and validity of models is presented clearly to readers. These guidelines are published in the following articles:
https://journals.iucr.org/paper?jc5010
https://journals.iucr.org/d/issues/2023/02/00/cb5145/
When you publish data collected on BioSAXS you should include details following these guidelines. If you have complementary SANS data, there is SANS specific details that you should also include (refer to the above guidelines as these are not covered here).
A summary of these guidelines and the template tables are presented below but we encourage you to read through the original articles as well.
The 2023 article provides a template table in the supplementary Table S3 which you can download as a word document. This template is copied below (including footnotes copied from publication) with a guide to BioSAXS specific information in red text or highlighted yellow:
Table S3 SAS sample details, data collection, analysis, and 3D modelling details for biomolecules in solution.
(a) Sample details | |||
Organism |
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Source (Catalogue No. or reference) |
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| Sample 1 | Sample 2 | Sample 3 etc |
Scattering particle composition |
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Protein(s)a |
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DNA/RNA(s)b |
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Carbohydrates/glycansc |
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Stoichiometry of components |
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Sample environment/configuration |
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Solvent compositiond |
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Sample temperature (°C) |
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In beam sample celle | E.g. 1 mm quartz capillary, coflow |
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Batch measurements | If batch mode was not used, delete these rows |
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Sample concentration(s), mg/ml or g/cm3 |
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Size Exclusion Chromatography SEC-SAS | If SEC-SAXS was not used, delete these rows |
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Sample injection concentration, mg/ml or g/cm3 |
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Sample injection volume, mL |
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SEC column type |
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SEC flowrate, mL/min |
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(b) SAS data collection | |||
Data acquisition/reduction software | BioSAXS Data Reduction algorithm using pyFAI | ||
Source/instrument description or reference | BioSAXS beamline Australian Synchrotron, ANSTO | ||
Measured q-range (qmin – qmax; Å-1, nm-1) | This can be determined from your reduced scattering profiles - open in a text editor and these values are given in the header. See snapshot below table. BioSAXS uses Angstroms | ||
Method for scaling intensitiesf | Absolute scaling (cm-1) referenced to water** **If using coflow, the effective sample path length is <1 cm, so the intensity is not automatically absolutely scaled. You will need to calculate the actual sample pathlength using a sample to sheath fluid ratio of 0.4 (Kirby et al., 2016) Or, report the intensity as arbitrary units (a.u.) | ||
Exposure time(s), number of exposures. For SEC-SAS, final number of sample frames used for averaging. | The exposure time is recorded in the HDF file for each sample. BioSAXS typically uses an exposure time of 1 s. SEC-SAXS number of sample frames will be recorded in the .dat file you generated from the LC series analysis using CHROMIXS or RAW LC Analysis. | ||
Additional relevant detailsg |
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(c) SAS-derived structural parameters | |||
Methods/Software |
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Guinier Analysis | Sample 1 | Sample 2 | Sample 3 |
I(0) ± s (cm-1; a.u) |
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Rg ± s (Å, nm) |
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min < qRg < max limit (or data point range) |
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Linear fit assessment (definition)h |
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PDDF/P(r) analysis | Sample 1 | Sample 2 | Sample 3 |
I(0) ± s (cm-1; a.u.) |
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Rg ± s (Å, nm) |
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dmax (Å, nm) |
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q-range (Å-1, nm-1) |
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P(r) fit assessment (definition)i |
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(d) Scattering particle size | |||
Methods/Software |
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| Sample 1 | Sample 2 | Sample 3 |
Volume estimates |
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Porod volume, Vp (Å3, nm3) |
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Molecular weight (M) estimates (kDa) |
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From chemical composition |
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From SAS, concentration independent methodj |
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From I(0)/concentrationk |
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Partial specific volume, n (cm3/g) |
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Contrast, Δρ (cm-2) |
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From SAS-independent measurel (method) |
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(e) Modelling (a complete sub-panel for each method) | |||
Shape modelling method(s) (if used) |
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| Sample 1 | Sample 2 | Sample 3 |
Software |
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q-range for fit (qmin – qmax; Å-1, nm-1) |
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Symmetry/anisotropy assumptions |
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Number of individual model reconstructions |
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c2, CorMap P-values for fit |
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For multiple phase models: Rg values (Å, nm) and relative phase volumes (Å3, nm3) |
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Atomistic modelling methods (if used) |
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| Sample 1 | Sample 2 | Sample 3. |
Software |
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q-range for fit (qmin – qmax; Å-1, nm-1) |
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Symmetry/anisotropy assumptions |
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Number of individual model reconstructions |
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c2, CorMap P-values for fit |
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(f) Data and model deposition |
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