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[ccp4bb]: refinement with higher resolution data
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This is a refinement problem with higher resolutiuon data.
Once the 2.4 A structure was solved, and now I have collected 1.4 A data for
the same crystal form. The cell constants differ very little. The sequence is
not known, but some homologous sequences exist. Two molecules in the A.U., but
I have not found the NCS aixs.
I use the 2.4A structure (water deleted, B factor reset 15.00) as initial model
to do MR with the new 1.4 A data. The data is very good (Rmerge is 4.0% for the
whole data set and 20% for last shell. I am using CNS to refine it.(just did rigid.inp
and anneal.inp, and the R and Rf were only lowered a little, R~35%, Rf~36%).
The question is:
1. Most residues can be found in the map, only one loop including 9 a.a. in both
molecules (each 64 a.a.) have very poor density in the sa-omit.map.
Someone suggests that I delete these residues from the PDB file, and add waters
in the these places in the map first, then maybe I can find some good density there.
Is this method ok? or other choice?
How should I do in this case?
2. At this high resolution (I directly use the 1.4 A data to refine), how about
the NCS restraints? Since I have not found the NCS axis for the 2 molecules, can
I use NCS restrints? (esp. at this resolution)
3. in CNS inputs files, there are choices on B factors and bulk-slovent. When shall
I use the "anisotropic" for B factors and "true" for bulk_solvent? In the example
files of CNS tutorial, I found them were choosed in the early stages.
4. can anyone give some advices on my refinement work? or what strategy should I
use when refine a low resolution structure with higher resolution data?
Thanks in advance.