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: [email protected] > Phone: 972-8-647-2220 Skype: boaz.shaanan > Fax: 972-8-647-2992 or 972-8-646-1710 > > From: CCP4 bulletin board [[email protected]] on behalf of > Bernard D Santarsiero [[email protected]] > Sent: Wednesday, August 27, 2014 6:12 PM > To: [email protected] > 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 --
