So it would seem that the five-fold periodicity in the spot intensities
along the long axis is probably due to a short-range, 34 Ang pseudo-repeat
(the decamer) along the true 170 Ang cell axis (170 = 34 x 5).
I do not think that the streaks are helical layer lines, because the spacing
on the detector is too small, indicating that the "layers" are really ~170
Ang apart. If the decamer's helical repeats are really ~34 Ang each, this
wold not work out--the lines would be much further apart.
Rather, it could be that:
1. The long axis consists of five RNA decamers in a line (as Margriet
informs us), constituted of random orientations, which reunite strictly at
every fifth position, to form a more-ordered superlattice (170 Ang), which
is significant enough to make spots.
2. Alternatively, it might be that there are fibers with strict fivefold
(170 Ang) periodicity which are translated by n x 34 Ang with respect to
each other.
In both cases, the variety of distances in between the fibers due to the
variety of combinations of neighbors might be enough to make the streaks. I
think this combinatorial distance variety is what James was proposing before
to explain the streaks.
In terms of modelling the structure, I do not think it matters whether the
reality is 1 or 2, although both have unlikely features to them,
realistically.
Jacob
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Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: [email protected]
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