> We have crystallized a cyanobacterial phycoerythrin which having two (alpha
> subunit) in an assymetric unit and held together by only three hydrogen bonds.
> When we compare the A and B molecule the RMSD is 1.32. because they same
> sequences then how it is possible to that two molecules are deviated at such
> extent. now the question is are both the molecules are crystallographic dimer?
> are two molecules are structural subunit as alpha 1 and alpha2?
> Is there any problem in refinement ? The structure was refined at 2.6 A with
> R 0.23/0.28
it sounds as if you have refined the structure without restraining the NCS. at
2.6A you would have to justify that (typically by showing that you get a
considerably lower Rfree without restraints than you do with restraints).
see these papers from the last millennium:
- G J Kleywegt & T A Jones, "Where freedom is given, liberties are taken",
Structure, 3, 535-540 (1995).
- G J Kleywegt, "Use of non-crystallographic symmetry in protein structure
refinement", Acta Crystallographica, D52, 842-857 (1996).
- G J Kleywegt & A T Brunger, "Checking your imagination: applications of the
free R value", Structure, 4, 897-904 (1996).
- G J Kleywegt & T A Jones, "Model-building and refinement practice", Methods
in Enzymology, 277, 208-230 (1997).
- G J Kleywegt, "Experimental assessment of differences between related
protein crystal structures", Acta Crystallographica, D55, 1878-1884 (1999).
- G J Kleywegt, "Validation of protein crystal structures" (Topical review),
Acta Crystallographica, D56, 249-265 (2000).
reprints available from http://xray.bmc.uu.se/gerard/citation.html
--dvd
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Gerard J. Kleywegt
[Research Fellow of the Royal Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology University of Uppsala
Biomedical Centre Box 596
SE-751 24 Uppsala SWEDEN
http://xray.bmc.uu.se/gerard/ mailto:[log in to unmask]
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