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Dear all,
recently this item has been discussed here but I miss the summary.
Here my problem:
1. The CCP4 bond length/ bond angle library for DNA/RNA is taken from
Saenger-Book 1983.
2. The CNS library is taken from Parkinson et al. (1996) Acta Cryst.
One outcome from the last discussion was : It is not allowed to restrain
the sugar pucker
to C2' endo/exo...as it happens in XPLOR/CNS. That is also supported by
our own
finding: We got 5% better R-values (I know, the better structure is the
aim!) for a DNA
switching from CNS to REFMAC5.
But:
The only check of DNA/RNA stereochemical quality at the PDB is done by
WHATCHECK,
and WHATCHECK is based on the Parkinson data. In our case such a quality
check
results in 5-6 sigma deviations for bond angles in the DNA-backbone
which was
refined with REFMAC5.
What library can be recommended? Or, what can be done to improve the
1.6A structure?
Changing from WT=0.3 to higher values will not work, because the
complete DNA molecule has
an alternate conformation.
Thank you in advance,
Juergen
