Re: [ccp4bb] ATP library file in REFMAC

[Boaz Shaanan]

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: bshaa...@bgu.ac.il Phone: 972-8-647-2220  Skype: boaz.shaanan                  Fax:   972-8-647-2992 or 972-8-646-1710                          From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Bernard D Santarsiero [b...@uic.edu] Sent: Wednesday, August 27, 2014 6:12 PM To: CCP4BB@JISCMAIL.AC.UK 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 --  Bernard D. Santarsiero Research Professor Center for Pharmaceutical Biotechnology and the  Department of Medicinal Chemistry and Pharmacognosy Center for Structural Biology Center for Clinical and Translational Science University of Illinois at Chicago MC870  3070MBRB  900 South Ashland Avenue Chicago, IL 60607-7173  USA (312) 413-0339 (office) (312) 413-9303 (FAX) http://www.uic.edu/labs/bds  http://scholar.google.com/citations?user=fGauLBMAAAAJ