On 27/08/14 23:11, Santarsiero, Bernard D. wrote:
> I appreciate all of the comments and suggestions on how to locate a better
> CIF file for ATP. I adopted the suggestion of Boaz, and generated a new
> ATP.cif file, and refined one of my structures.
Grade is what I would have recommended, FWIW.
>
> The validation server still uses substantially different target bond
> lengths and angles,
to that in the dictionary from grade?
> so there is better agreement, but I still get flags.
> Both bond length and angles target values are more realistic than what was
> used in the REFMAC ATP.cif file, but I still find fault with the target
> values.
>
> For example, the bond lengths and angles around PB, the beta P atom, range
> from 104.4-108.7deg in the "grade" file, and are unrealistic since they
> are all less than the tetrahedral angle.
The angles of the terminal phosphate oxygens (O1G, O2G, O3G) to the
ester oxygen are less than ideal-tetrahedral because the internal angles
of the terminal phosphate oxygens are greater than ideal-tetrahedral.
I'd bet that the dictionary from grade reflects that.
> The CIF also targets one P-O as a
> single and the other as formally a double bond,
It is quite usual for different dictionary generators to specify the
bond orders (types) of delocalized groups differently. If the bond
*lengths* are based on the bond types then that's a more substantial
problem. Is that what you meant?
> but most crystallographic
> studies indicate at least some delocalization over both internal oxygen
> atoms, and a slight compression of that angle. The validation server has
> an "ideal" target value of 101.66deg which is surely contracted from a
> more reasonable value near 105deg.
Interesting - that is quite different to what I see (if we are talking
about the same thing (I am looking at the O1B-PB-O2B angle - is that
what you meant?)).
Paul.
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