SAXS Package Reference Page
ALL SAXS RESULTS PROVIDE INFORMATION ON THE PROTEIN WITH A
HYDRATION LAYER
What
did I download with the SAXS data?
A folder containing 5 files.
1)
A file containing scalars extractable from SAXS Target_Scalars.txt
2)
A raw SAXS profile 3 columns (q, Intensity, Error) Target.dat
3)
A Fourier transform of the SAXS data 3 columns r, P(r), error Target.pofr
4)
A PDB file from SAXS data outlining the shape of the molecule
Target.pdb
5)
A SITUS file from SAXS data outlining the shape of the molecule Target.sit
6) A presentation in
".pdf" format summarizing all results
More
Information on SAXS data types from the .txt file
Experimentally
Extracted Scalar Data types |
Symbol |
Units |
Radius of Gyration from Gunier
+ Error |
Rg |
Angstroms (A) |
Degree of Flexibility |
PD |
Range (2 4) (Unfolded Globular) |
Experimental Mass |
MSAXS |
Daltons (Da) |
Maximum Dimension + Error |
DMax |
Angstroms (A) |
Radius of Cross-Section |
RXC |
Angstroms (A) |
Experimental Volume |
VSAXS |
Cubic Angstroms (A3) |
Radius of Gyration From P(r) Function |
Rg2 |
Angstroms (A) |
1-Dimensional
Data sets + Error (2x~500 matrix + error) |
Symbol |
File
Extension |
SAXS profile |
I(q) |
.dat |
Electron Pair Distribution Function |
P(r) |
.pofr |
Volumes
Formats SAXS shape cannot get correct hand |
File
Extension |
Protein Data Bank Files |
.pdb |
Situs Volume Maps |
.sit |
Relations
between Structure and Extracted Parameters listed above
Rg is second moment of inertia of a structure pymol has a calculator
http://pymolwiki.org/index.php/Radius_of_gyration
Degree of Flexibility The exponent of decay for a
SAXS curve depends on flexibility. q-2
for a flexible protein q-4 for a globular protein. A protein can
have a flexibility anywhere in between. The absolute value of the exponent is
listed.
Experimental Mass Mass can be determined from a
scattering profile as shown in
Rambo and Tainer Nature 496, 477-481 2013
Maximum Dimension Largest atom to atom distance
within a protein. Determined by defining where the P(r) function reaches zero
at large r.
Radius of Cross-Section Quantifies the second
moment of inertia for a cross-section of the protein and is valuable when the
cross-section is fairly constant ideally rod like.
Volume Calculated based on an integral of the
scattering curve.
Radius of Gyration from P(r) function Should be
similar to that described above however this is calculated using the P(r) which
in turn is calculated from the entire SAXS profile rather than a small region.
SAXS profile can be calculated from PDB
coordinates directly using FOXS calculator. Available as a script and web form
https://modbase.compbio.ucsf.edu/foxs/
Electron Pair Distribution Function P(r) A
histogram of electron pair distances which is equivalent to mass pair distance.
Relatively straightforward to calculate from a PDB, although water needs to be
taken into account.
ALL SAXS VOLUME DATA IS AMBIGUOUS TO HANDEDNESS
PDB based shape produced from the algorithm
GASBOR. Single shape representing the average shape in solution.
Situs Volume Map Should match the GASBOR PDB but
often easier to visualize over a target ribbon diagram as transparency can be
used.
Quality of SAXS data - For CASP13
SAXS results are scored (Gold, Silver and Bronze) for the quality of results
based on several quality judgement parameters and available controls. If
samples were available in limited quantity all controls may not have been
performed.
Challenges - When multimerization
is known to occur or flexible regions appear to be factors they are noted as
challenges.
What
should I be aware of when I use SAXS data?
SAXS measures the entire particle
in solution. SAXS data will include electron contribution from disordered
regions (90% of CASP12 targets) and will measure the particle as a multimer, if
occurring in solution (50% of CASP12 targets). CASP results are scored for
predicting specific portions of a target that may be only part of the protein
or complex measured in SAXS. Use of SAXS data for prediction requires proper
consideration of the contribution of the disordered regions or all parts of a
multimer.
It is possible to compare models
using SAXS single value metrics (e.g. Rg), curves, or volumes. If you use
the reciprocal space curve for comparison, please note that the curve is always
shown as a log plot because values can vary 103 over the range of q.
If you use a subtractive comparison (e.g. Chi Square), the comparison will be
weighted strongly towards the low q.
More discussion of CASP12 and potential pitfalls
were described in one of two April 2018 videoconferences (see link) and is
described in
1: Ogorzalek
TL, Hura GL, Belsom A,
Burnett KH, Kryshtafovych A, Tainer JA, Rappsilber J, Tsutakawa SE,
Fidelis K. Small angle X-ray scattering andcross-linking
for data assisted protein structure prediction in CASP 12 with prospects for
improved accuracy. Proteins. 2018 Mar;86 Suppl
1:202-214. doi: 10.1002/prot.25452.
Where
can I get more Information?
http://bl1231.als.lbl.gov/publications/PDFs/PutnamTainerSAXS_QRB.pdf
http://www.embl-hamburg.de/biosaxs/courses/
Authored by Greg Hura and Susan Tsutakawa (LBL), on
behalf of CASP