Help

SASBDB is a curated repository that makes small angle scattering (SAS) data underlying scientific publications discoverable and citable. You can browse the SAS data, search by various keywords including macromolecule name, buffer composition, experiment setup and author/affiliation details.

SASBDB contents

Experimental SAS data logarithmic plot

Experimental SAS data

SAS data from solutions of biological macromolecules are presented as log10I(s) vs. s where I(s) is the intensity (in arbitrary units) and s is the modulus of the scattering vector (in inverse nanometres, s = 4πsin(θ)/λ, where 2θ is the scattering angle, λ is the wavelength). Due to experimental errors a small number of intensities may be negative, these data points are shown in red.
Experimental SAS data Guinier plot

Guinier plot

Low angle data plotted as ln I(s) vs. s2 is called the Guinier plot. From it one can estimate the radius of gyration (Rg) by making a linear fit at sufficiently small scattering vectors (in the range up to sRg < 1.0–1.3; s = 1/Rg is marked with a vertical grey line). The linearity of the Guinier plot is a sensitive indicator of the quality of the experimental SAS data; deviations from linearity usually point to strong interference effects, polydispersity of the samples or improper background subtraction.

Rg: radius of gyration

From the slope of the Guinier plot fit one can estimate the radius of gyration of the particle – average of square center-of-mass distances in the particle weighted by the scattering length density. Rg is a measure for the overall size of a macromolecule; e.g. a protein with a smaller Rg is more compact than a protein with a larger Rg, provided both have the same molecular weight (MW). A more precise Rg estimate can be obtained from integrating the p(r) function (see below).

I(0): forward scattering intensity

The intercept of the Guinier plot fit gives the forward scattering (or zero angle scattering) intensity I(0) which is proportional to the solution concentration and to the number of atoms in the particle.

MWI(0): molecular weight estimated from forward scattering

I(0) usually comes in arbitrary units, however if a standard was measured (e.g. water or a reference protein like BSA with known MW) then I(0) can be used to obtain a rough estimate of the molecular weight of the sample.

MWexpected: expected molecular weight

Estimated MW is compared to the expected molecular weight (e.g. calculated from the sequence). This gives an idea of the oligomeric state of the sample.
Experimental SAS data dimensionless Kratky plot

Experimental SAS data dimensionless Kratky plot

Degree of compactness of a protein is most conveniently represented as s2I(s) vs. s: a bell-shaped peak indicates a globular particle, a plateau is typical for extended/unfolded proteins.
If the intensities are divided by I(0) and s is multiplied by Rg then the plot is called normalized (or dimensionless) Kratky plot. In case of a globular particle the peak position would at √3, maximum at 1.104 (marked with grey lines).

VPorod: Porod volume

For globular particles of uniform density the excluded volume of the hydrated particle is inversely related to the area below the Kratky plot. For globular proteins the hydrated volume in nm3 should be about 1.6 times the MW in kDa.
SAS distance distribution function p(r)

Pair distance distribution function

p(r) represents the distribution of distances between all pairs of atoms within the particle weighted by the respective electron densities. p(r) is the Fourier transform of I(s) (and vice versa). Rg and I(0) can be estimated from integrating the p(r) function. Acceptable formats are: ATSAS GNOM, GIFT, BioXTAS RAW and Scâ„«tter.

Dmax: maximum intra-particle distance

The point where p(r) is decaying to zero is called Dmax and represents the maximum size of the particle.

Modelling

Fit to experimental SAS data

Fit to the experimental data

The experimental scattering curve (in blue) can be compared with the theoretical curve calculated from a model (in red).
ab initio dummy atom model

Ab initio model

Reconstruction of the low resolution shape based on experimental scattering data only is called an ab initio model. Typically the particle shape is represented by densely packed spheres that are assembled such that their computed scattering fits the experimental data. On a page with data details please click the ab initio model image to load the 3D view.
hybrid SAS model

Hybrid model

It is possible to compute a theoretical solution scattering curve from the given atomic coordinates. A number of programs can assemble models that fit given experimental SAS data using structures obtained from X-ray crystallography, NMR and other techniques. On a page with data details please click the hybrid model image to load the 3D view.
Download SAS data and models

Download

It is possible to download:
  • SAS data curves (text format, 1st column: s, 2nd column: I(s), 3rd column: associated errors);
  • p(r) functions;
  • fits to the experimental data (text format, typically 1st column: s, 2nd column: I(s), 3rd column (optional): associated errors, 4th column: intensities calculated from the model);
  • ab initio models (in pseudo-PDB format where the beads are represented by CA atoms);
  • hybrid models (in pseudo-PDB format);
  • the whole data set as a single packaged file (in zip format);
  • sasCIF file.

REST API

SASBDB provides a programmatic way to obtain information in JSON and XML formats: REST calls based on SASBDB entry data

 

Contact us

SASBDB is powered by the Biological Small Angle Scattering Group, European Molecular Biology Laboratory, Hamburg Outstation.
For questions and feedback please contact: .