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Using the default radii stored by SHELXL the connectivity array should
automatically include Mn-O distaces less than 2.53 Angstroms as bonds,
and so would not apply antibumping restraints to these interactions.
Probably you are accidentally deleting these 'bonds' by the use of the
CONN 0 command. See page 7.18 of the SHELX manual. You can remedy the
situation either by specifying only atoms on the CONN instruction(s)
that are not involved in Mn-O bonds or - as you have done - by adding
BIND instructions. For waters bound to Mn, BIND may be safer, because it
will still work even if the distance exceeds 2.53A. I would recommend
retaining antibumping restraints for the rest of the structure even at
such high resolution, they will be useful for the disordered and less
well defined parts of the structure.
George
Marco Bellinzoni wrote:
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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
--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
