on 13/10/14 6:33 PM, Pedro Matias <[log in to unmask]> wrote:
> In relation to this topic, I'd like to mention that SF4 has replaced FS4
> as the Fe4S4 monomer in the CCP4 monomer library.
>
> However, the dictionary values for bond lengths and angles are not
> correct, and this is especially noticeable when the dictionary is used
> in a high-resolution refinement (e.g., 1.05 A). In particular, the
> Fe-S-Fe angles are all set to 90 degrees, when in fact some are smaller
> and others are larger.
>
> This introduces a bias in the final rms angle deviation values. Fe4S4 is
> a distorted cubane, not a perfect cube.
>
Pedro,
Yes you are 100% correct
The dictionaries I sent have values that are obtained from an analysis of
small
molecule crystal structures in the CSD (by "hand" with conquest). For
instance
the Fe-Scluster-Fe angle has a mean of 73.4 degree with a standard
deviation
of 0.7 degrees. The restraints are compatible with Engh and Huber restraints
you
will be using for your protein and for that matter the Parkinson et al
restraints used
for any nucleic acid (because they come from a similar data mining
procedure).
So if Stephen used this dictionary he would not " introduce a bias in the
final rms
angle deviation value" because the restraint values would be sensible.
If you to check the restraint values are sensible then you check them
against atomic
resolution structures for instance
http://www.rcsb.org/pdb/explore/explore.do?structureId=1B0Y
at 0.93 Å resolution structure determined by George Sheldrick. This has SF4
with
Fe-Scluster-Fe angles around 73.3 degrees.
I would strongly advise anyone against using a restraint dictionary for
Fe4S4 that uses
90 degree as the ideal angle because you are restraining towards values that
make no sense. If the dictionary contains chiral volume terms then I would
ask the
question why? But this is just my personal take.
If CCP4 would like to redistribute/work the dictionaries sent then we would
be happy
(please email off-list).
Dr Oliver Smart
Director SmartSci Limited http://www.smartsci.uk/
& Consultant Global Phasing Ltd http://www.globalphasing.com/
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