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Dear all,
I am refining the structure of a metalloenzyme with shelxl, against very
good data at 0.85 A resolution. Since I have a dinuclear metal center
with Mn2+ ions, I would like to know which is the best way to prevent
shelxl from applying antibumping restraints between the Mn2+ ions and
their coordinating oxygens (from both protein carboxylic groups and
waters), while keeping active the option "BUMP" to avoid clashes between
solvent and protein. The target value applied by shelxl as antibumping
distance between Mn and O is 3.0 A, which is clearly not the case for a
Mn2+ cation in octahedral coordination (to my knowledge, typical values
are about 2.2 - 2.3 A).
Just to leave these values as unrestrained, I added each couple made of
the cation and a coordinating oxygen to the connectivity list with the
BIND command, as if they were connected by a covalent bond, and I did
not define any value as restraint for the corresponding distances. Would
an experienced shelxl user suggest me a better way than this turn
around? Or does this resolution justify refinement without antibumping
restraints at all? I wouldn't say it, at least in the initial steps...
Thank you very much for your help,
Marco
Marco Bellinzoni
Unité de Biochimie Structurale
Institut Pasteur
