I have a question about the bond angle restraints in the DNA cif files. I recently submitted a protein-DNA complex to the PDB, and found out that many of the glycosidic bond angles (atoms O4'-C1'-N9/N1) were outside the accepted range. I switched from CCP4 6.1.13 to 6.2.0 (installed/updated with fink on Mac OSX 10.6.8), and this "fixed" the problem in that now there is a narrower distribution of bond angles, but the target/ideal values are different in these two CCP4 monomer libraries (108.4 versus 107.8):
===== /sw64/lib/ccp4-6.1.13/data/monomers file=a/AD.cif Ad A 'Adenosine ' DNA 32 21 . Ad N9 C1* O4* 108.400 3.000 file=c/CD.cif Cd C 'Cytidine ' DNA 30 19 . Cd N1 C1* O4* 108.400 3.000 file=g/GD.cif Gd G 'Guanosine ' DNA 33 22 . Gd N9 C1* O4* 108.400 3.000 file=t/TD.cif Td T 'Thymidine ' DNA 32 20 . Td N1 C1* O4* 108.400 3.000 ===== /sw64/lib/ccp4-6.2.0/data/monomers file=d/DA.cif DA DA '2'-DEOXYADENOSINE-5'-MONOPHOSPHATE ' DNA 34 22 . DA "O4'" "C1'" N9 107.800 0.800 file=d/DC.cif DC DC '2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE ' DNA 32 20 . DC "O4'" "C1'" N1 107.800 0.800 file=d/DG.cif DG DG '2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE ' DNA 35 23 . DG "O4'" "C1'" N9 107.800 0.800 file=d/DT.cif DT DT 'THYMIDINE-5'-MONOPHOSPHATE ' DNA 34 21 . DT "O4'" "C1'" N1 107.800 0.800 Why are these values different in the two libraries? Am I looking at the wrong files or the wrong bonds? Thanks! Greg
