EMBO' 2012 course materials - Biological small angle scattering

ATSAS online | Forum | User information | EMBL Hamburg

Solution Scattering from Biological Macromolecules

October 17-24, 2012
EMBL Hamburg, Germany
Organisers: Dmitri Svergun, Al Kikhney, Maxim Petoukhov, Manfred Roessle

The course aims at young biochemists/biophysicists and researchers active in related structural methods with little or no experience in solution scattering. The course will cover basics of SAXS/SANS, instrumentation, data collection, modelling techniques and complementary use with other methods. The students are encouraged to bring their own samples to perform synchrotron solution scattering experiments on-site and the results will be used for practical tutorials and discussed on the last day of the course.

There will be an additional possibility for a combination of SAXS with sample optimization and crystallization experiments, supported by the EU program P-Cube. The selected participants will be offered the opportunity to send their samples in advance to the EMBL Hamburg high-throughput crystallization platform. Depending on the crystallization results, P-Cube may sponsor optimization of the sample conditions, use of the EMBL Sample Preparation and Characterization facility and more extensive SAXS experiments during the course. Please contact Rob Meijers for more information.
The course is supported by BIOSAXS.

SAXS group at Facebook

Abstracts of the talks and slides in PDF

Abstract	X-ray scattering – the basics (3MB) – Manfred Roessle
Abstract	Neutron scattering – the basics (8MB) – Jill Trewhella
Abstract	Validation of biomacromolecular structures (17MB) – Gerard Kleywegt
Abstract	Sample preparation and characterisation (3MB) – Rob Meijers
Abstract	Data reduction and processing (7MB) – Al Kikhney
	Data reduction and processing tutorial (3MB) – Petr Konarev
Abstract	Ab initio methods: how they work (10MB) – Dmitri Svergun
	Ab initio modelling: DAMMIN and DAMMIF (1MB) – Daniel Franke
	Ab initio modelling: GASBOR and MONSA (1MB) – Maxim Petoukhov
Abstract	Rigid body refinement (basics) (6MB) – Dmitri Svergun
Abstract	Form and structure factors, interactions, modelling (4MB) – Jan Skov Pedersen
	EOM tutorial (4MB) – Giancarlo Tria
Abstract	Joint use of SAXS and NMR (10MB) – Annalisa Pastore
Abstract	Joint use of SAS and AUC (7MB) – Olwyn Byron
Abstract	Maximum occurrence of conformations from average data (28MB) – Claudio Luchinat
Abstract	Ubiquitin conjugation and deconjugation in DNA regulation (6MB) – Titia Sixma
Abstract	Structural studies of lipid systems (3MB) – Regine Willumeit
Abstract	High brilliance synchrotrons for SAXS and WAXS (9MB) – Robert Fischetti
Abstract	Combining microfluidics and synchrotron SAXS (5MB) – Lise Arleth

Recommended reading

Single copies of the articles below can be downloaded and printed only for the reader's personal research and study.

Book	Feigin, L.A. & Svergun, D.I. (1987) Structure Analysis by Small-Angle X-Ray and Neutron Scattering © Plenum Press / Springer
Reviews	Mertens H.D.T. & Svergun D.I. (2010) Structural characterization of proteins and complexes using small-angle X-ray solution scattering. J. Struct. Biol. 172(1), 128-41
	Svergun, D.I. (2007) Small-angle scattering studies of macromolecular solutions. J. Appl. Cryst. 40, s10-s17
	Svergun, D.I. & Koch, M.H.J. (2003) Small-angle scattering studies of biological macromolecules in solution. Rep. Prog. Phys. 66, 1735-1782
ATSAS	Petoukhov, M.V., Franke, D., Shkumatov, A.V., Tria, G., Kikhney, A.G., Gajda, M., Gorba, C., Mertens, H.D.T., Konarev, P.V. and Svergun, D.I. (2012) New developments in the ATSAS program package for small-angle scattering data analysis. J. Appl. Cryst. 45, 342-350
	Petoukhov, M.V., Konarev, P.V., Kikhney A.G. & Svergun, D.I. (2007) ATSAS 2.1 - towards automated and web-supported small-angle scattering data analysis. J. Appl. Cryst. 40, s223-s228
	Konarev, P.V., Petoukhov, M.V., Volkov, V.V., & Svergun, D.I. (2006) ATSAS 2.1, a program package for small-angle scattering data analysis. J. Appl. Cryst. 39, 277-286
PRIMUS	Konarev, P.V., Volkov, V.V., Sokolova, A.V., Koch M.H.J. & Svergun, D.I. (2003) PRIMUS: a Windows PC-based system for small-angle scattering data analysis. J. Appl. Cryst. 36, 1277-1282
GNOM	Svergun D.I. (1992) Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J. Appl. Crystallogr. 25, 495-503
DAMMIN	Svergun, D. I. (1999) Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys. J. 76, 2879-2886
DAMMIF	Franke, D. and Svergun, D.I. (2009) DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering. J. Appl. Cryst., 42, 342-346
GASBOR	Svergun, D.I., Petoukhov, M.V. & Koch, M.H.J. (2001) Determination of domain structure of proteins from X-ray solution scattering. Biophys. J. 80, 2946-2953
CRYSOL	Svergun D.I., Barberato C., & Koch M.H.J. (1995) CRYSOL - a program to evalate X-ray solution scattering of biological macromolecules from atomic coordinates. J. Appl. Crystallogr. 28, 768-773
SASREF, BUNCH	Petoukhov, M.V. & Svergun, D.I. (2005) Global rigid body modelling of macromolecular complexes against small-angle scattering data. Biophys. J. 89, 1237-1250
MASSHA	Konarev, P.V., Petoukhov, M.V. & Svergun, D.I. (2001) MASSHA - a graphic system for rigid body modelling of macromolecular complexes against solution scattering data. J. Appl. Crystallogr. 34, 527-532
EOM	Bernado, P., Mylonas, E., Petoukhov, M.V., Blackledge, M., Svergun, D.I. (2007) Structural Characterization of Flexible Proteins Using Small-Angle X-ray Scattering. J. Am. Chem. Soc. 129(17), 5656-5664

Last modified: October 25, 2012