*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
Hi folks:
I have a question regarding a Br mad data set on RNA.
We have a crystal of an RNA in the lab in which the molecule has been
transcribed and incorporates 11 Br-U residues at known positions in
the sequence, and we have a MAD data set on this to about 3 A
resolution (as well as a native data set).
mmtbx.xtriage reports that we may have up to 3 molecules in the
asymmetric unit (of P21), meaning 11, 22 and 33 Br sites are possible:
----------------------------------------------------------------
| Copies | Solvent content | Matthews Coef. | P(solvent cont.) |
|--------|-----------------|----------------|------------------|
| 1 | 0.828 | 7.146 | 0.012 |
| 2 | 0.656 | 3.573 | 0.238 |
| 3 | 0.484 | 2.382 | 0.652 |
| 4 | 0.312 | 1.786 | 0.091 |
| 5 | 0.140 | 1.429 | 0.007 |
----------------------------------------------------------------
| Best guess : 3 copies in the asu |
----------------------------------------------------------------
I've been using ShelxD to find Br sites, and the maps, though quite
promising, still need significant improvement. I also haven't
convinced myself that there is a clear NCS 2-fold or 3-fold, and so
have been trying with 1,2, and 3 molecules.
Since there are regions of this molecule that (presumably) have
canonical A-form RNA helices, and these have Br-U in them at known
positions, I'd like to make use of the distance constraints these put
on the Br sites, as well as the Br absorption in the mad peak data.
Is it possible to do molecular replacement using the Br anomalous
signal and model helices to help pin down the locations of the Br atoms?
Thanks in advance.
Bill Scott
