Cant you edit the ATP.cif on your computer to have the correct expected
bond length?
Best, Matthias
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Dr. Matthias Zebisch
Division of Structural Biology,
Wellcome Trust Centre for Human Genetics,
University of Oxford,
Roosevelt Drive,
Oxford OX3 7BN, UK
Phone (+44) 1865 287549;
Fax (+44) 1865 287547
Email [email protected]
Website http://www.strubi.ox.ac.uk
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On 8/27/2014 4:12 PM, Bernard D Santarsiero wrote:
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
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