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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

On Fri, Sep 16, 2011 at 4:26 PM, Gregory Bowman <[log in to unmask]> wrote:

> 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
>
>
>
>