Hi there,
In crystallography there are so many places where you can have problems
(and need to solve these problems) that I cannot list them all.
"There is no twinning in the data" - you probably mean "the data does
not seem to indicate the presence of twinning but there might be
twinning"; what about the space group ? What about your crystal
appearing to have one space group for one component (example the
protein) but the space group for the other component (e.g. DNA, which
could be partially disordered, that happens) being different - and you
have processed the data in the apparent space group for the protein ?
The crystal could contain the protein:DNA complex plus one of the
components needed for the whole thing to pack (and form the crystals);
the model might be sufficiently different from "your" structure that all
the loops plus a good part of the core is improperly positioned - or you
have domain and subdomain "motions" etc etc.
There is one symptom: R-free seems to be stuck. What the reason is for
this is unknown. There are cases in the literature where molecular
replacement leads to this behaviour and where the crystallographers have
to use experimental phasing (and understand what the problem was with
molecular replacement afterwards, when the structure is solved).
Fred.
#HEW KAI LI KELLY# wrote:
Hi,
I am facing some problems in solving my structure now, so I am
wondering if anyone is able to give me any tips and tricks on this matter.
My protein-DNA complex structure diffracted to 1.5A. There are 4
missing residues, 2 on each terminal. There is no twinning in the
data. The angles, the bonds, the rotamers and the Ramachandran plot
are okay too. I am using molecular replacement for the phasing and the
sequence homology between my protein and my homologous model is 33%.
The electron density map for the protein looks very nice and there is
also nice density for the DNA. Rfree converged from the initial 39%.
However, Rfree refused to go down any further and it's still around
30-31%. Does anyone have any suggestions for me? Thank you in advance!
Warmest Regards,
Kelly Hew
*
*
*
*
*
*
