Data processing and ab initio analysis Al Kikhney EMBL Hamburg - PowerPoint PPT Presentation

DAMMIN IN Svergun, D.I. (1999) Biophys J 76 • Variable number of “dummy atoms” on a fixed grid • Scattering is computed using spherical harmonics • Monte-Carlo type search • Fixed search space (defined by D max ) • Provides volume/molecular weight estimate • Idea first published by P. Chacón et al. (1998) Biophys J 74

DAMMIF IF Franke, D. and Svergun, D.I. (2009) J Appl Cryst 42, 342 – 346 • Variable number of “dummy atoms” on a fixed grid • Scattering is computed using spherical harmonics • Monte-Carlo type search • Expandable search space • Provides volume/molecular weight estimate • 40 time faster than DAMMI N (D. I. Svergun (1999) Biophys J 76)

https://www.embl-hamburg.de/biosaxs/atsas-online/dammif.php

Ab initio shape reconstruction Single phase shape Fit one data set determination

Ab initio shape reconstruction: multi-phase dummy atom modelling Fit data from several subunits

https://www.embl-hamburg.de/biosaxs/atsas-online/monsa.php

Ab initio reconstruction: dummy residue modelling Number of dummy residues = number of residues on the protein 3.8 Å D max GASBOR Svergun, D.I., Petoukhov, M.V, Koch, M.H.J. (2001) Biophys J 80, 2946 – 2953.

Ab initio reconstruction: dummy residue modelling log 10 I(q) target curve calculated from the model q, nm -1

Ab initio reconstruction: dummy residue modelling log 10 I(q) target curve calculated from the model q, nm -1

Ab initio reconstruction: dummy residue modelling log 10 I(q) target curve calculated from the model q, nm -1

GASBOR Svergun, D.I., Petoukhov, M.V, Koch, M.H.J. (2001) Biophys J 80, 2946 – 2953 • Fixed number of “dummy residues” • Distances to neighbor “residues” like in proteins

GASBOR Svergun, D.I., Petoukhov, M.V, Koch, M.H.J. (2001) Biophys J 80, 2946 – 2953 • Fixed number of “dummy residues” • Distances to neighbor “residues” like in proteins • Fixed search space • Scattering is computed using Debye formula • Higher angles used (up to 12 nm -1 ) • Only for proteins smaller than 660 kDa