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.
