Investigating RNAs Involved in Translational Control by NMR and SAXS - Biophysical Approaches to Translational Control of Gene Expression - page 152

Fig. 8.9 The pair distance
distribution function (PDDF)
or p ( r ) reflects the shape of
the molecule. The PDDF can
be thought of as the
probability of finding two
atoms in the molecule a given
distance ( r ) apart. Adapted
from Koch et al. ( 2003 )

as the probability of finding two atoms a given distance ( r ) apart. R g and I (0) are
more accurately determined from the PDDF than from the Guinier transform
(Svergun 1992 ). Additionally, the PDDF provides an estimate of the maximum
dimension ( D max ) of the molecule; however, the value of D max cannot be determined
with the same level of accuracy as R g and is therefore not as widely employed.

8.1.3.3 Ab Initio Modeling of Molecular Shapes from SAXS Data

The information provided by the PDDF can be utilized to generate a low resolu-
tion envelope of an RNA using ab initio modeling techniques. Currently, DAMMIN
(Svergun 1999 ) and its more recent implementation, DAMMIF (Franke and
Svergun 2009 ), are the best software options for ab initio modeling of nucleic acid
molecules. Both of these programs employ a set of dummy atoms or beads to
simulate the general shape of the molecule. The predicted scattering amplitude of
the dummy atom model is calculated and compared to the experimental scattering
data. This process is repeated iteratively until a good fit is achieved. Typically,
only data in the range of q < 0.33 Å −1 are used with this method for the reasons
described in Sect. 8.1.3.2 .