Biological Small Angle Scattering Links

SAXS is a low-resolution structure determination method that does not require crystals and works with proteins that might be difficult to crystallize (e.g., containing disordered domains).
SAXS samples need to be free of aggregates and interparticle effects.
SAXS samples need to be very pure.
Required SAXS samples concentration is inversely proportional to the MW.
2-10 mg/ml in 100 to 200 uL volume is usually needed. In other words, milligram quantities of very pure material are required.
SAXS yields a molecular envelope that gives that global shape of the molecule at low resolution (12-20 Å). This low resolution shape is sufficient to answer many biological quesitons.
The maximum distance (Dmax), the maximum dimension of the molecule, has an experimental error of about 2% or about 2.7 Å. Changes in shape smaller than this error will be difficult to detect.
SAXS enables the study of biological macromolecules in a variety of solution conditions ranging from near physiological to highly denaturing.
Ab initio structure reconstruction methods enable the making a 3-D molecular envelopes from 1-D scattering data.
The modeling of protein:protein and protein:nucleic acid complexes is a valuable application of SAXS. High resolution structures of individual components can be placed inside the SAXS molecular envelope by rigid body fitting.
SANS facilitates the study of complexes with one or more deuterated components by contrast variation.
Mobile surface loops and domains that move too much to be seen in crystal structures can be visualized by SAXS.
Ensembles of partly or fully unfolded proteins or RNAs can be studied by SAXS.
The size range for biological SAXS to 5 KDa to 50 MDa.
The samples must be aggregate-free (check with dynamic light scattering). The samples should also be free of interparticle effects.
To test for interparticle interactions, scattering data are typically collected at three or four concentrations ranging from 1 to 10 mg/ml. The sample volume per measurement is 30 microliters. Data are collected from a matching buffer sample that should be obtained by dialysis. The interparticle interactions can be weakened by increasing the buffer concentration.
Avoid inorganic buffers like phosphate and cacodylate. Use MOPS, MES, or TRIS which scavenge free radicals generated by X-ray damage. 1-5 mM DTT, TCEP, and 2-mercaptoethanol also protect proteins from excessive radiation damage. So does glycerol but you must have a matching concentration in your buffer sample. 12. Take care with detergents. Some detergents scatter X-rays very strongly.
Methods of working membrane proteins using SAXS are summarized on pages 313-317 of the following review: Lipfert, J. and Doniach, S. (2007) Small-angle X-ray scattering from RNA, proteins, and protein complexes. Annu. Rev. Biophys. Biomol. Struct. 36, 307-27.
Membrance proteins embedded in nanodics can be studied by SAXS and SANS.
NMR and SAXS complement each other. NMR gives detailed structures while SAXS provides accurate information about the global shape.
Size Exclusion Chromatography (SEC)-SAXS is usaully preferred other statis SAXS. However, SEC-SAXS has its weaknesses. It is not a silver bullet.
Size Exclusion Chromatography (SEC)-SAXS does not work well with impure samples. Do not use SEC-SAXS as a polishing step for your protein purification protocol!

Advantages of Access to a Local SAXS Instrument

These arguments are useful for equipment grant applications.

Many samples are stable only for a one week or two after purification. Scheduled time at a beam line has to be arranged a minimum of two weeks in advance for a rapid access program and several months for regular programs.
Many samples are too fragile to transport without freezing. The jostling by FEDEX of unfrozen samples leads to protein denature.
Many samples lack freezing protocols.
Many samples need the solution conditions optimized to eliminate aggregation or interparticle effects. There is not much time during a trip to a beam line to optimize solution conditions. The required chemicals may not be available or there is not time to prepare them on sight. This leads to the need to make two or more trips.
While most beamlines allow access to a biotech lab to work on sample preparation, these labs vary widely in terms of the available supplies, equipment, access, and cleanliness. Your home lab will also be easier to use for sample preparation.
Interparticle effects are hard to detect by other methods.
Some samples are sensitive to radiation damage. The home source is 1000 times weaker so this is less of an issue. If it is still an issue, it is better to learn this locally than after the expense of travelling to a remote site to make this discovery.

Historical Milestones in SAXS from Rambo and Tainer (2013)

Year	Event	Reference
1915	Debye equation	nnn
1939	Guinier approximation equation
1949	Scattering equation	Debye and Bueche
1951-1957	Porod, Debye, Kratky
1964	SAS model tRNA	Timashef 1961 ; Witz, 2003
1970	Contrast variations, Multipole expansion	Stuhrmann
1970s	Synchrotron SAXSn
1977	Indirect Fourier Transformation	Glatter
1980	Information Theory Applied to SAXS	Moore 2000
1987	30S SAS model
1992	GNOM, the application of the Tikhovnov regularization to the inverse problem	Svergun
1995	CRYSOL	Svergun et al.
1998-2000	ab initio methods: DaliGA DAMMIN SAXS3D GASBOR	Chacon et al. 1998; Chacon et al. 2000 Svergun -- Svergun et al. 2001
2007	Ensemble methods: EOM MES BSS-SAXS EROS	EOM, Bernado et al. 2007 MES, Pelikan et al. 2009 BSS-SAXS, Yang et al. 2010 EROS,Rozycki et al. 2011
after 2013	Residue-level Structure Determination with SAXS Data

Conditions that justify modeling SAXS data with an ensemble proposed by Rambo and Tainer (2013)

Lack of convergence of the Kratky plot
Invalidation of the Porod-Debye Law
Flory's inequality
Low particle density
Inability to model data with a single model

Miscellaneous Links

SAS Portal , THE home for Small Angle Scattering

SAXS Links Software for small angle scattering, maintained by Diamond Light Source, UK

Dmitri Svergun (EMBL), a leader of the biological SAXS field

Biological small-angle scattering wikipedia

SAXS wikipedia

List of synchrotron radiation facilities

EMBL, Practical Course: Solution Scattering from Biological Macromolecules

Biosync

Biosaxs links

SAXier, a forum about SAXS

SAXS data analysis

SAXS data processing

Dyksterhuis, introduction to SAXS

Kreichbaum

Concentric shell model, calculate scattering from cylinder

UTMB SAXS and SANS Group, access restricted to Gulf Coast Consortia, have many links

SANS beam lines

United States

ORNL, Oak Ridge National Lab,

LENS, Low Energy Neutron Source, Indiana U.

NIST, Center for Neutron Research

Lujan Neutron Scattering Center at LANSCE, Los Alamos National Laboratory, Low-Q Diffractometer, 0.003 to 0.5 Å^{-1}

EPSCOR Neutron Scattering Network

SAXS beam lines

United States Synchrotrons

Advanced Light Source, Berkeley, ALS 12.3.1. SAXS SIBYLS (described in a 2013 paper)

ALS SIBYLS proposal deadlines: 15th of the month for a two-month run cycle beginning one-and-half months after the preceding submission deadline

(e.g., apply before Dec. 15th and get time between Feb.1 and Mar. 30th).

ALS proposal link

Advanced Photon Source, Argonne National Lab, Chicago. biocat ID-18

APS, small-angle x-ray scattering

APS guide to writing a winning beam line proposal

The APS has a large number of SAXS beam lines with most of them dedicated to materials science. Attending the Beyond Rg Workshop at APS is a good way of becoming familiar with the capabilities of the beam lines as well as by talking to the beam line scientists which is strongly encouraged. Only Biocat beam line 18 is committed to doing bioSAXS and fiber diffraction (Tom Irving (irving@iit.edu) is the local expert on fiber diffraction). It is currently unique in having liquid chromatography SAXS (LC-SAXS) as an option. The beam line scientist Srinivas Chakravarthy is advocating this technique. The sample volume requirement is 300 microliters with 100 mls of dialysis buffer. The rising and falling shoulders of the peak coming off a 25 ml size exclusion column provide two dilution series and thus lots of data for determining Rg with extrapolation to infinite dilution. It takes an hour to run one sample, but only one sample is required per molecule or molecule* buffer combination. There is a talk of an even smaller SEC column that will enable the collection of data on six samples per hour if they have the sample buffer. The three stations at beam line 12 can be configured to do bioSAXS. 12-ID-C and -D can do time resolved and anomalous SAXS on biological samples. Xiaobing Zuo (zuox@anl.gov) is a beam line scientist at 12-ID-C and -D who has written software for calculating SAXS profiles that is unique in being able to allow the inclusion of heavier atoms in the calculated SAXS profile. This software is unpublished. It is available by writing to him. He also has published a number of papers on SAXS studies of RNA. Beam lines 12 and 18 have time-resolved capabilities with time resolution down to the 20 microsecond scale. One station at ID-5 can do bioSAXS with a flow cell. It requires 250-300 microliter samples per dilution, about 10x the sample requirement of a station with a liquid handling robot. ID-5 is the Dupont-Northwestern-Dow CAT. It has 25% general user access. Steven Weigand at this beam line has co-authored several bioSAXS papers.

BioCAT, beam lines at sector 18, fiber diffraction and BioSAXS.

fibernet

CHESS, MacCHESS BioSAXS

NSLS SAXS X9 line

NSLS X21

SSRL BIOSAXS BL 4-2

proposal deadlines, SAXS under UV/X-ray

Foreign Synchrotrons

Australian Synchrotron SAXS 15ID

BioSAXS scattering cells

ESRF BM29

SAXS beam lines, mail in-services

ALS Mail In SAXS

Biosaxs.com, supervised by Dmitri Svergun

CHESS On-line Express-Mode Proposal Form

SAXS Databases

SASBDB: Small Angle Scattering Biological Database The most up to date database.
DARA, DAtabase for RApid search of structural neighbours for proteins based on their X - ray small - angle scattering patterns. DaRa is built from ~24,000 PDB structures with sequence homology of less than 90%. DaRa takes experimental data processed by Gnom as input. The molecular weight of the protein is used to filter the search pool. Sokolova et al. (2003) Prototype of a database for rapid protein classification based on solution scattering data. J. Appl. Cryst. 36, 865-868
<BIOISIS, Integrated Structures in Solution Databank the Protein Data Bank of SAXS; You can download SAXS data and use them as tutorials.

Cite BIOISIS as follows: Rambo, R. (2009). BIOISIS, http://www.bioisis.net/.

SAXS Equations

Note: use Chrome or Safari to copy LaTeX code for the equations (Chrome works better)

Right click on an equation. Select "Show Math As/TeX Commands". Select and copy the equation. Paste into *.tex file

Right click on an equation. Select "Show Math As/MathML Code". Select and copy the equation. Paste into MS Document.

Indices

Scattering Basics

SAXS and Molecular Weight Determination

SAXS profile calculation

SAXS ab initio structure calculation with spherical harmonics

Using SAXS to Study Protein Interactions

MathJax Links

mathjax.org

Latex commands in Mathjax

MathJax Syntax tutorial

TeX MathJax Documentation

List of mathematical symbols

Jump back to top

SAXS and Molecular Weight Determination:

Conditions for determination of MW of proteins in solution:

1. system must be monodisperse

2. the solution should be dilute enough to avoid interparticle effects

3. the solution should be statistically isotropic

4. the proteins should be homogeneous( e.g., all of their parts should have equivalent electron density so that the two electron density model can be applied.

5. the scattering curves need to be free of experimental smearing effects.

SAXS intensity from $ N $ proteins per unit volume:

$$ I(q)=NV(\triangle\rho)^{2}\intop_{0}^{D_{max}}4\pi r^{2}\gamma_{0}(r)\frac{sin\, qr}{qr}dr $$

where $ N $ is the number of proteins per unit volume, $ V $ is the protein volume, $ \triangle\rho $ is the contrast or the difference between the average electron density of the protein and that of the buffer, $ D_{max} $ is the maximum diameter of the protein, and $ \gamma_{0}(r) $ is the particle correlation function:

$$ \gamma_{0}(r)=\frac{\left\langle V(r)\right\rangle }{V} $$

where $ \left\langle V(r)\right\rangle $ is the orientational average of the intersection of the volume V of the protein and the same volume displaced by a vector $ r $. The particle correlation function has the following properties:

\begin{align} \\ & 1.\; \gamma_{0}(0)=1 \\ \\ & 2.\; \gamma_{0}(r)=0 \; for \; r > D_{max} \\ \\ & 3.\; \intop_{0}^{\infty}4\pi r^{2}\gamma_{0}(r)dr=V \\ \end{align}

Jump back to top

The Guinier Equation:

$$ I(q)\cong\rho_{o}^{2}V^{2}exp\left(-\frac{1}{3}q^{2}R_{g}^{2}\right) $$

The SAXS intensity extrapolated to $ q=0 $, $ I(0) $ is given by

$$ I(0)=N(\triangle\rho)^{2}V^{2} $$

Jump back to top

The integral of $ I(q)q^{2} $ from $ q=0 $ to $ q=\infty $ is termed the invariant, $ Q $.

$$ Q=\intop_{0}^{\infty}I(q)q^{2}dq=2\pi^{2}\left(\triangle\rho\right)^{2}V^{2} $$

The protein's volume is proportional to the ratio between $ I(0) $ and $ Q $ , so the volume can be determined directly from the data without the intensities being on an absolute scale.

$$ V=2\pi^{2}\frac{I(0)}{Q} $$

The method does not require knowledge of the protein concentration in the solution or the difference in the average electron density between the protein and the buffer.

Jump back to top

The molecular weight of the proteins obtained from the SAXS data is MW is calculated by multiplying the volume $ V $ in $ \unicode{xC5}^{3} $ by the average protein density $ \rho{}_{m} = 0.83 \; \times \; 10^{-3} kDa \; \unicode{xC5}^{-3} $ which is equivalent to the more commonly used value of $ \rho{}_{m} = 1.37\; g \; \times \; cm^{-3} $. This average was determined experimentally in solution by Squire and Himmel (1979) and Gekko & Noguchi (1979). This value is smaller than the theoretical value because it includes the effect of a shell of water.

Proteins have the 78% of the partial specific volume of RNA and RNA have 128% the partial specific volume of proteins.

$$ MW=V\rho_{m} $$ $$ MW=2\pi^{2}\frac{I(0)}{Q}\rho_{m} $$

The above equations allow the determination of the molecular weight from the SAXS data if the basic requirements above are met and if the $ Q $ is determined by integrating from $ q $ is equal to zero to very high $ q $. If high angle data are not included, there will be seriously truncation errors in the calculation of the invariant $ Q $.

Jump back to top

Experimentally, $ q $ is determined between $ q_{min} $ and $ q_{max} $. The intensity below $ q_{min} $ should extrapolated to $ I(0) $. The extrapolation can be done with the program GNOM.

The precise determination of $ I(q) $ at high $ q $ is generally not possible due to experimental limitations or the SAXS intensity is too weak at high $ q $ and thus difficult to record with acceptable precision within a reasonable counting time. Extrapolation of the SAXS intensity above $ q_{max} $ leads to results that are subject to large statistical errors and is generally avoided.

The calculation of $ Q $ as an integral up to $ q_{max} $ leads to $ Q' $ which is smaller than $ Q $:

$$ Q'=\intop_{0}^{q_{max}}I(q)q^{2}dq $$

This leads to the apparent volume, $ V' $:

$$ V'=2\pi^{2}\frac{I(0)}{Q'} $$

Jump back to top

The $ I(q) $ for a sphere of volume $ 10^{4} \unicode{xC5}^{3} $ and R = 13.4 $ \unicode{xC5} $ calculated from equation from Glatter and Kratky (1982):

$$ I(q)=(\triangle\rho^{2})V^{2}\left[3\frac{sin\, qR-qR\, cos\, qR}{(qR)^{3}}\right]^{2} $$

The plot of the above equation against $ q $ and of $ I(q)q^{2} $ show how $ Q $ (which is the integral of the Kratky plot) oscillates to high $ q $ and how truncation of the data lead to underestimation of $ Q $.

Jump back to top

A plot of the real volume of a sphere $ (V=\frac{4}{3}\pi R^{3}) $ versus the apparent volume $ V' $ calculated with different degrees of truncation (different $ q_{max} $ ). The approximation works for spheres with volumes larger than $ 3 \; \times \; 10^{4}\; \unicode{xC5}^{3} $ or protein complexes with a mass greater than 2.4 MDa.

The completeness factor of the invariant:

$$ \frac{Q'}{Q} $$

The SAXS curves $ I(q) $ were calculated by applying CRYSOL which using the following equation

$$ I(q)=\left\langle \left|A_{a}(q)-\rho_{s}A_{s}(q)+\delta\rho A_{b}\right|^{2}\right\rangle _{\Omega} $$

Jump back to top

Calculation of SAXS profile:

Calculation of the SAXS profile from atomic coordinates with Debye formula:

$$I(q)=\sum_{i=1}^{M}\sum_{j=1}^{M}F_{i}\left(q\right)F_{j}\left(q\right)\frac{sin(q\cdot r_{ij})}{q\cdot r_{ij}}$$ where $ F_{i} $ and $F_{j} $ are the (atomic) scattering factors of the individual particles (atoms) $ i $ and $ j $, and $ r_{ij} $ is the Euclidean distance between particles $ i $ and $ j $. The summations are overall all of the scattering (atoms) particles $ M $ . The particles could be as small as individual atoms or as large as whole amino acids or amino acids represented as two particles (see Svogaard et al. 2010 ).

Jump back to top

SAXS ab initio structure calculation with spherical harmonics

Stuhrman (1970) introduced the multipole expansion to represent the particle scattering density in spherical coordinates $ (r,\varpi)=(r,\theta,\varphi) $ as the following:

$$\rho\left(\mathbf{r}\right)=\rho_{L}\left(\mathbf{r}\right)=\sum_{l=0}^{L}\sum_{m=-1}^{1}\rho_{lm}\left(\mathbf{r}\right)Y_{lm}\left(\varpi\right)$$

where the spherical harmonics $ Y_{lm}\left(\varpi\right) $ are combinations of trigomometric functions of orders $ l $ and $ m $. The truncation value $ L $ determine the accuracy of the expansion as the low-order harmonics define the gross structural features of the particle and the higher harmonics describe the finer details.

SANS Examples (to be finished later)

Instrument scientist at NIST

SAXS Examples (to be finished later)

SAXS Examples by Experiment Type

Ab initio shape determination

anomalous scattering

Complexes

Domain Motion

Determine Protein-Protein Interaction Potentials in Solution

Kim et al. 2008

Phasing Diffraction Data with Envelope from SAXS

Hao 2006

Homology Model Selection

NMR and SAXS

Mobile surface loops

Time-resolved SAXS

Unfolding studies

SAXS Examples by Disease

Cancer

Diabetes

Heart

Infectious Disease--Bacteria

Infectious Disease--Eucaryote

Infectious Disease--Viral

Prion Diseases

Vision

SAXS Examples by Macromolecule Type

Complexes of proteins

Complexes of proteins and DNA

Complexes of proteins and RNA

Complexes of Protein and Peptides

Complexes of Protein and small molecular ligands

DNA

Disordered proteins

Glycoproteins

Glycans

Integral membrane proteins

Metalloproteins

RNA

WAXS Examples

Combining WAXS and crystallography to locate heavy atoms

Hong and Hao 2009

SAXS fee for service

BioSAXS.com

SAXS Instruments

Anton Par

Bruker

Hecus MicroCALIX, bought by Bruker

Rigaku wiki

Rigaku bioSAXS1000

BioSAXS-1000

Dec 2012: 5 BioSAXS systems sold and 3 of those are installed:

UTMB (installed), IGBMC (France - installed), Brown Univ (installed),

McMaster Univ (Canada - installation by Feb), Masaryk Univ (Czech Rep - installation by Feb)

Peer reviewed papers with data collected with the BioSAXS-1000:

Polizzi et al. (2013) Biochemistry 52, 3888 - 3898.

Xenocs SAXS and WAXS systems

SAXS Meetings

SAS2015, International Small-Angle Scattering Conference , 12-18 September 2015, Berlin, Germany

SAS2018, International Small-Angle Scattering Conference, sponsored by APS ,October 2018, Traverse City, Michigan

Link to SAXS meetings

SAXS and Molecular Graphics

Calculate SAXS curves from pdb file (uses FoxS): /Tools/Higher-Order Structure/Small-Angle X-ray Profile

SAXS and Molecular Graphics

SAXS envelopes:

set solvent_radius, 5

set mesh_solvent, 1

If importing a PDB structure, use the [A] drag coordinates command to move the model

(Use the SHIFT-mouse to move or rotate the model)

SAXS and Molecular Graphics: SITUS:

unfinished

SITUS: SAXS tutorial

SAXS and Molecular Graphics: VMD:

unfinished

SAXS Software (alphabetical order):

Allosmod-FoXS v, uses sampling algorithms to generate structures that are then put into FoXS to calculate scattering profile

AquaSAXS , calculate SAXS from pdb file.

ATSAS on-line

ATSAS download version 2.4 Data Analysis Software for Mac 10.6; 2.5 for Mac 10.7; windows and linux versions too.

To get started with the ATSAS software on the Mac, type "primus" in a X11 or terminal window. It is usually installed /usr/bin. You may have to start it by typing "/usr/bin/primus"

AXES : Analysis of X-ray Scattering in Explicit Solvent

Bilbomd: a webapp that enables conformational sampling by molecular dynamics simulation with the SAXS data as a restraint

BioXTAS RAW: is a comprehensive package that is comparable to ATSAS and Scatter. It can do Singular Value Decompostion and Evolutionary Factor Analysis of SEC-SAXS data. It is wrapped in Python and is the only one of the three packages that is open-source. It has on-line documentation.

BioCAT's X-ray Tools: on-line Q range calculator.

CRYSOL: Svergun Group at EMBL-Hamburg, method of theoretical scattering profile calculation using multipole expansion

Dalai_GA: uses genetic algorithm to fit SAXS data with bead models

Fast-SAXS-pro: , Yang Lab at Case Western, upload a PDB file and compute its theoretical SAXS profile. The PDB file can be of protein, DNA, RNA, or their complex. Coordinates can be at an atomic or a coarse-grained (e.g., Ca atoms of a protein)

FastSAXS: , predecessor of FAST-SAXS-pro, Ad Bax Group

FlexFitSAXS is a SAXS-based modeling tool that flexibly fits an initial protein structure with a given solution X-ray scattering profile based on a modified elastic network model. Click here for access to a 2011 article about this program. This tool is available as a linux-based pre-compiled executables. Please contact Wenjun Zheng (wjzheng@buffalo.edu) for further information.

FoXS: : a web server for rapid computation and fitting of SAXS profiles using the Debye Formula. Andre Sali group at UCSF, built into IMP, the Integrative Modeling Platform

FoXSDock: : Macromolecular Docking with SAXS Profile

HyPred: server at U of Chicago: reads in a pdb and emails the user with predicted hydration shell densities and crystallographic water sites

HyPred: related software

hydropro predicts Rg and other hydrodynamic parameters from 3D models

IMP, Integrative Modeling Platform: , binary and source available

Irena: package for analysis of small-angle scattering data

SANS and USANS: Analysis with IGOR Pro

Igor 6.2: , required for Irena

Martini: Coarse Grain Force Field for Biomolecular Simulations. Well-integrated with GROMACS and used in NAMD.

MES Minimal Ensemble Search

MES tutorial

Nika: , 2-D to 1-D data reduction prior to analysis by Irena above, need Igor Pro

RMsd_calc: (calculate RMSD for subset of atoms with current operator)

SASfit: for fitting small-angle scattering curves

SASSIE: suite of program for generating molecular structures.

SASTBX:

SAXProf , on-line for predicting scattering profiles, Kratky plots, Guinier plots (the last three have the Shannon Limit included on the Plot; noise in the Guinier; the P(r) function. You can also download the calculated scattering with noise.

SAXS 2011: , Colorado State University Software Package

SAXS software at ESRF, linux and windows binaries and source code

saxs3d; xlattice; pdb2xyz_saxs

SAXSgui: A Graphical User Interface for Visualizing, Transforming and Reducing SAXS Images (as well as Limited Fitting)

SaxsMDView, SAXSANA, TraceBeads, SaxsAnalysis, SVD and reconstruction, UnfoldingFit, CalibCCD at Tokyo University

SAXSview: , process 2-D data and 1-D data, source forge download

MoW: , run from website, requires GNOM output with data in (angstrom)-1, calculates MW and oligimerization.

SAXS similarity matrix , on-line service.

SAXSpipe, python wrapper of several programs by Dr. Lester Carter at SSRL BL 4-2

SAXSTER: uses SAXS profile to select homology model template.

ScÅtter software for the analysis of biological SAXS datasets, computes the new statistics described in the 2013 Nature paper by Rambo and Tainer

SCULPTOR: interactive multi-resolution docking and visualization program for low-resolution density maps and atomic structures.

SITUS: package for the modeling of atomic resolution structures into low-resolution density maps e.g. from electron microscopy, tomography, or small angle X-ray scattering.

Singlebody: calculates p(r) and I(q) functions of models defined by sets of IF conditions using a Monte-Carlo approach. Cross section and thickness functions of cylinders and lamellae can be calculated as well. The program is freeware. Executable for Windows.

WAXS profile calculator from , on-line, U of Chicago.

Collections of SAXS Software

Links to sites involved in predicting SAXS profiles.

CCP13 SAXS software

Manfred Kriechbaum collection of java scripts for calculating SAXS profiles from geometric shapes

SAXS Software Wiki

SAXS software at ESRF

ESRF software

Sastbx: The Small Angle Scattering ToolBox

Sastbx Online Services

SAXS Software Developer Groups

ado State, Data Analysis for Small Angle X-ray Scattering

EMBL-Hamburg, Biological Small Angle Scattering Group

ESRF, Grenoble, France; SAXS Platform for Structural Biology

SAXNS, UTMB SAXS and SANS Group, has some unique software and many links

SAXS Related Software: Molecular Motion Simulation

ProDy--Python package for protein structural dynamics analysis.

DDPT--A Comprehensive Toolbox for the Analysis of Protein Motion

SAXS Reviews

2001

Doniach, S. (2001) Changes in biomolecular conformation seen by small angle X-ray scattering. Chem Rev 101, 1763-1778.

2003

Koch et al. (2003) Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution. Q Rev Biophys 36, 147-227. (Comment: a very rigorous review.)

Vachette et al. (2003) Looking behind the beamstop: X-ray solution scattering studies of structure and conformational changes of biological macromolecules. Methods Enzymol 374, 584-615.

2006

Das, R. and Doniach, S. (2006). Structural studies of proteins and nucleic acids in solution using small angle x-ray scattering (SAXS)," in Soft Matter: Scattering, Imaging and Manipulation, eds. Pecora, R. and Borsali, R., Kluwer Press.

2007

Lipfert, J. and Doniach, S. (2007) Small-angle X-ray scattering from RNA, proteins, and protein complexes. Annu. Rev. Biophys. Biomol. Struct. 36, 307-27.

Putnam et al. (2007) X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution. Q Rev Biophys 40, 191-285. (Deep and complete review).

Stuhrmann, H. B. (2007) Small-angle scattering and its interplay with crystallography, contrast variation in SAXS and SANS. Acta Crystallographica. Section A, Foundations of Crystallography 64, 181-91.

Svergun, DI (2007) Small-angle scattering studies of macromolecular solutions. J. Appl. Crystallogr. 40, s10-s17.

2009

Doniach, S. and Lipfert, J. (2009) Use of small angle X-ray scattering (SAXS) to characterize conformational states of functional RNAs. Methods Enzymol 469, 237-251.

Hura et al. (2009) Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS). Nat Methods 6, 606-612.

2010

Rambo, R.P. and Tainer, J.A. (2010) Bridging the solution divide: comprehensive structural analyses of dynamic RNA, DNA, and protein assemblies by small-angle X-ray scattering. Curr Opin Struct Biol 20, 128-37. (Short Overview)

Yang, S., Parisien, M., Major, F. and Roux, B. (2010) RNA structure determination using SAXS data. J. Phys. Chem. B, 114, 10039-48.

2011

Kathuria SV, Guo L, Graceffa R, Barrea R, Nobrega RP, Matthews CR, Irving TC, Bilsel O. (2011) Minireview: Structural insights into early folding events using continuous-flow time-resolved small-angle X-ray scattering. Biopolymers 95, 550-558.

Rambo, R.P. and Tainer, J.A. (2011) Characterizing flexible and intrinsically unstructured biological macromolecules by SAS using the Porod-Debye law. Biopolymers 95, 559-571.

2012

Bernado, P. and Svergun, D.I. (2012) Structural analysis of intrinsically disordered proteins by small-angle X-ray scattering. Mol. Biosyst. 8, 151-67.

Czjzek, M., Fierobe, H.P., and Receveur-Brechot, V. (2012) Small-angle X-ray scattering and crystallography: a winning combination for exploring the multimodular organization of cellulolytic macromolecular complexes. Methods Enzymol 510, 183-210.

Doniach, S. and Lipfert, J. (2012) "Small and Wide Angle X-ray Scattering from Biological Macromolecules and their Complexes in Solution." In: Edward H. Egelman, editor: Comprehensive Biophysics, Vol 1, Biophysical Techniques for Structural Characterization of Macromolecules, H. Jane Dyson. Oxford: Academic Press, 2012. pp. 376-397.

Hammel, M. (2012). Validation of macromolecular flexibility in solution by small-angle X-ray scattering (SAXS). Eur Biophys J 41, 789-99.

Petoukhov, M. V., Franke, D., Shkumatov, A. V., Tria, G., Kikhney, A. G., Gajda, M., Gorba, C., Mertens, H. D. T., Konarev, P. V., Svergun, D. I. (2012). New developments in the ATSAS program package for small-angle scattering data analysis. J Appl Crystallogr, 45(2), 342-350.

Schneidman-Duhovny, D., Kim, S.J., and Sali, A. (2012) Integrative structural modeling with small angle X-ray scattering profiles. BMC Structural Biology 12:17. COMMENT: A comprehensive review of the computational methods for incorporating SAS scattering profiles into structural modeling.

2013

Meisburger, S.P., Warkentin, M., Chen, H., Hopkins, J.B., Gillilan, R.E., Pollack, L., and Thorne, R.E. (2013) Breaking the radiation damage limit with Cryo-SAXS. Biophys J. 2013 104, 227-336. COMMENT: this method could reduce sample size requirements and radiation damage. It could revolutionize biological SAXS.

Perry, J.J. and Tainer, J.A. (2013) Developing advanced X-ray scattering methods combined with crystallography and computation. Methods 59, 363-371.

Petoukhov, M.V. and Svergun, D.I. (2013) Applications of small-angle X-ray scattering to biomacromolecular solutions. The International Journal of Biochemistry & Cell Biology 45, 429-437. COMMENT: Timely review that includes rigid body modeling, several examples of cutting edge applications of biological SAXS, and the status of high throughput SAXS.

Rambo, R.R. and Tainer, J.A. (2013) Super-Resolution in Solution X-Ray Scattering and Its Applications to Structural Systems Biology. Annual Review of Biophysics 42, 415-441. COMMENT: Makes the case for modern SAXS. Provides concise comparison of current ab initio model building programs.

Rambo, R.P. and Tainer, J.A. (2013) Accurate assessment of mass, models and resolution by small-angle scattering. Nature 496, 477-481. COMMENT: Presents four new SAS parameters. First, a new SAS invariant, V_c, the volume of correlation that defines a Q_R ratio that in turn determines the molecular mass independent of the concentration. This paper also presents χ²_free, a cross validated measure of the agreement between the model and the data that is analogous to R_free in crystallography. Finally, R_SAS is presented for the quantitative evaluation of resolution.

Trewhella, J., Hendrickson, WA., Kleywegt, G.J., Sali, A., Sato, M., Schwede, T., Svergun, D.I., Tainer, J.A., Westbrook, J., and Berman, H.M. (2013) Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB. Structure 21, 875-881. COMMENT: Presents the conclusions and recommendations of the 12-13 July 2012 meeting of the Small-Angle Scattering Task Force of the worldwide Protein Data Bank at Rutgers Univ. in New Brunswick, New Jersey with regards to the archiving of SAXS data and the models derived from SAXS data.

Kofinger, J., and Hummer, G. (2013) Atomic-resolution structural information from scattering experiments on macromolecules in solution. Physical review. E, Statistical, nonlinear, and soft matter physics 87, 052712. COMMENT: Theoretical analysis suggests that PDDF may reveal atomic resolution detail when used with scattering data collection in X-ray laser experiments.

Petoukhov MV, Billas IM, Takacs M, Graewert MA, Moras D, Svergun DI. (2013) Reconstruction of Quaternary Structure from X-ray Scattering by EquilibriumMixtures of Biological Macromolecules. Biochemistry. 52, 6844-55. COMMENT: Presents the application of GASBORMX and SASREFMX to simultaneous structure determination and oligomer analysis to certain types of polydisperse systems. This is a landmark paper. The approach is limited to monomers with as little as 15% volume fraction, so the approach it limited to systems with lower molecular symmetry (up to six-fold symmetry).

2014

SAXS Seminars, Local

John Tanner (U of Missouri) May 20, 2013, OU-Norman

Ed Snell, (Hauptman-Woodward Institute), June 19, 2013, 4 PM, BRC 109 OUHSC-OKC

SAXS Textbooks

Hamley (2021) Small-Angle Scattering: Theory, Instrumentation, Data, and Applications. Wiley
Lattman, Grant, and Snell (2018). Biological Small Angle Scattering: Theory and Practice. IUCr Book Series/Oxford Science Publications. This is a complete and compact guide for beginners. There is an authoratative review by Professor Jill Trewhella

Chaudhuri, Munoz, Qian, and Urban (2017). Biological Small Angle Scattering: Techniques, Strategies and Tips, Springer
Svergun, D. I., Koch, M. H. J., Timmins, P.A., and May, R. P. (Nov. 1, 2013). Small Angle X-Ray and Neutron Scattering from Solutions of Biological Macromolecules (International Union of Crystallography Texts on Crystallography). Oxford University Press. Parts can be viewed on-line at Amazon.con
Feigin, L.A. and Svergun, D.I. (1987). Structure Analysis by Small-Angle X-Ray and Neutron Scattering. New York: Plenum Press. p. 40. ISBN 0-306-42629-3. Download here
Glatter, Otto and Kratky, Otto (eds.) (1982).: Small Angle X-ray Scattering. London: Academic Press. Out of print but can download by clicking on authors's names.
Guinier, A. and Fournet, G. (1955): Small-angle scattering of x-rays. New York: John Wiley and Sons.

Lipfert and Donaich (coming some year) Small-Angle X-Ray Scattering: Applications to Structural Molecular Biology.

SAXS Tutorials:

From sample prep to data deposition in 8 steps at BioISIS

ACA 2013 meeting BioSAS Training Workshop: tutorials including data

SAXS Working Groups:

Small Angles Net:

canSAS

smallangle.org, portal to SAS related information including lists of software

SANS Workshops in USA:

5th Workshop on Neutron Scattering Applications in Structural Biology, Oak Ridge, Tennessee; June 16 - June 20, 2014; April 18th deadline

people from EPSCOR state can get travel fellowships

SAXS Webinars:

SIBYLS webinars

Advanced Light Source

SAXS Workshops in USA, upcoming:

SAXS Workshops in USA, recent past:

4th annual SIBYLS bioSAXS workshop ; Advance Light Source (ALS) at Lawrence Berkeley National Laboratory , Berkeley, CA. Registration: To attend the workshop you need register for the 2013 Advanced Light Source User Meeting. ALS user meeting will be held at Berkeley Lab October 7-9. Workshop will begin October 8th and continue through October 9th. When you registering, you must indicate ``Small Angle X-Ray Scattering Studies In Structural Biology'' as your workshop. Enrollment is limited to 30 participants. Inquires: Jane Tanamachi jtanamachi@lbl.gov.

APS, beyond Rg, SAXS Short-course Advanced Photon Source, Argonne National Laboratory, October 26 - 31, 2013. No registration fee. Registration closed at end of June.

ACA 2013 meeting BioSAS Training Workshop: slides.

This was a dual track workshop: Beginner's Track for those getting started with SAXS and Advanced Methods Track for experienced users ready to master advanced methods.

APS: Irena and Nika, Argonne National Lab, Chicago; SAXS Software Packages Irena and Nika Spring 2013 Course;

Thurs.- Fri., May 9-10, 2013 ; free ; limit of 20.

BNL-NSLS, Brookhaven National Lab-National Synchrotron Light Source; X9 SAXS Workbench;

April 18-21, 2013; free; deadline April 1

CHESS, Cornell:

two full days; March 21-23, 2013; $250 registration fee.

SSRL, Stanford Synchrotron Radiation Lightsource, Menlo Park;

three full days; March 18 - 20, 2013; $100 registration fee.