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.
The validation server still uses substantially different target bond
lengths and angles, 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 CIF also targets one P-O as a
single and the other as formally a double bond, 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.
One approach that would be useful is to consider refinement on special
groups, like phosphate, with structural parameters, instead of actual
target bond lengths and angles, so R1 for the two PB-O1B and PB-O2B
distances, and R2 for the two PB-O3A and PB-O3B distances, and pairs of
angle restraints incorporating a complete delocalization model. See, for
example, Murray-Rust, Burgi, and Dunitz, J. Am. Chem. Soc., 97, 921
(1975), or Tamasi at al., The Open Crystallography Journal, 3, 1 (2010).
This could be used to directly address questions about delocalization and
hydrolytic capacity, rather than trying to determine then from bond
lengths.
Bernie
On Wed, August 27, 2014 2:05 pm, Boaz Shaanan wrote:
> Or use Grade:
> http://grade.globalphasing.org/cgi-bin/grade/server.cgi
> which gives the correct bond length.
> Boaz
>
> Boaz Shaanan, Ph.D.
> Dept. of Life Sciences
> Ben-Gurion University of the Negev
> Beer-Sheva 84105
> Israel
>
> E-mail: [log in to unmask]
> Phone: 972-8-647-2220 Skype: boaz.shaanan
> Fax: 972-8-647-2992 or 972-8-646-1710
>
> From: CCP4 bulletin board [[log in to unmask]] on behalf of
> Bernard D Santarsiero [[log in to unmask]]
> Sent: Wednesday, August 27, 2014 6:12 PM
> To: [log in to unmask]
> Subject: [ccp4bb] ATP library file in REFMAC
>
> I recently refined a structure in CCP4/REFMAC with ATP in the
> structure. Upon submission to Acta for publication, the wwPDB
> validation report was run. Several things were flagged, including the
> C4-C5 bond in the adenosine moiety as being too long. It generally
> refines to 1.46-1.47A. The "ideal" distance in the
> validation report is 1.38A, and the upon review of the ATP.cif file in
> the REFMAC library, the target distance is 1.49A (and listed as a
> double bond). Clearly 1.37-1.38A is a reasonable target value. HIC-Up
> gives the target bond length as 1.404A.
> Where can I grab a revised ATP.cif file? I guess I'll need to re-refine
> all of my structures and re-run the validation report. BTW, I also
> looked at the PDB_REDO structure report for my structure, and can't
> reproduce the Rcryst and Rfree values with the same model.
> Bernie --
|