L On Aug 27, 2014 5:12 PM, "Santarsiero, Bernard D." <[email protected]> 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. > > 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 -- >
