DNA cif files

From: Gregory Bowman
Date: 16 September 2011 16:26

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):

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/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

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/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

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From: Ian Tickle


Hi, it depends what you mean by 'different'.  The SUs of the new set are much lower than the old values (0.8 deg vs. 3.0) so one would assume that these are improved estimates based on new data.  The difference between the old and the new is (108.4 - 107.8) = 0.6 deg with a SU of the difference of sqrt(3^2 + 0.8^2) = 3.1 deg, so difference/SU = 0.6/3.1 = 0.2 sigma - hardly what one could call 'significantly different'.

Cheers

-- Ian