| 1D scattering data to 3D low resolution density map. | ||
| The above movie shows the generation of a 3D model from scattering data using DAMMIN 5.11. The starting point is a cylinder of 40 Å diameter and 100 Å length filled with 5878 dummy atoms at a 2.5 packing radius. Each successful annealing step performed by DAMMIN was saved as a pdb file together with its back-calculated scattering profile (top right). The lower-right graph shows the residuals between the experimental (red) and the DAMMIN back-calculated (green) Kratky profiles. | ||
| The same bead reconstitution was repeated at least ten times. Below are the pictures of the other remaining reconstitutions. | |||
|
|
|
|
|
|
|
|
|
|
|
|
| The structural variability of individual DAMMIN reconstitutions can be resolved by aligning and averaging all ten structures into one. The superposition is achieved using SUPCOMB2 and the averaging with DAMAVER3. | |||
| The superposed model has a well-defined shape. Removal of the low occupancy atoms results in a more compact model. As the DAMAVER software calculates bead occupancy, it is possible to color the model based on this basis, where red and blue are high and low occupany respectively. | |||
 |
 |
 |
|
| All 10 models aligned and superposed | Filtered model | Filtered model colored by occupancy | |
| As the reconstitution from the SAXS profile generates a low-resolution overall shape, rather than a precice structure, the bead model was converted to a density map. The model was moved close to the origin in the positive quadrant, given a unit cell dimension and structure factors calculated using sfall from the CCP4 program suite4. The script used can be found here. PyMOL5 cannot handle structure factors in the xplor format, so it was converted to density map using a script in Xplor-NIH6. The xplor density map can the be viewed in PyMOL with : load output.xplor, map1 ; isosurface surf1, map1, 1; set transparency, 0.7, surf1. | |||
 |
|||
1 Svergun D.I. Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys J. 1999 Jun;76(6):2879-86. PMID: 10354416.
2 Kozin M.B. and Svergun D.I. Automated matching of high- and low- resolution structural models. J Appl Crystallogr. 2001 34:33-41. IUCr.
3 Volkov V.V. and Svergun D.I. Uniqueness of ab initio shape determination in small-angle scattering. J Appl Crystallogr. 2003 36:860-64. IUCr.
4 Collaborative Computational Project, Number 4 (CCP4). The CCP4 suite : Programs for protein crystallography. Acta Cryst. 1994 D50, 760-63. WWW.
5 Delano W.L. The Pymol Molecular Graphics System. 2002 Delano Scientific, Palo Alto, CA, USA. WWW.
6 Schwieters C.D., Kuszewski J.J., Tjandra N. and Clore G.M. The Xplor-NIH NMR Molecular Structure Determination Package. J. Magn. Res. 2003 160, 66-74. WWW.