From: Gregory Bowman
Date: 16 September 2011 16:26
----------
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
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):
=====
/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
----------
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
No comments:
Post a Comment