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Re: [ccp4bb]: unusually high solvent content (trying again)
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a quick way to see all pdb entries with high or very high Vm values is to go
the PDBREPORT index of error messages:
http://www.cmbi.kun.nl/gv/pdbreport/pdbreport/revindex.html
there you'll find:
279 entries with a very high Vm:
http://www.cmbi.kun.nl/gv/pdbreport/pdbreport/revindex18.html
and 1061 entries with a high Vm:
http://www.cmbi.kun.nl/gv/pdbreport/pdbreport/revindex19.html
(and, for the curious, also 487 entries with surprisingly low Vm:
http://www.cmbi.kun.nl/gv/pdbreport/pdbreport/revindex20.html)
i suspect the record must be a Vm of 2794.815 A3/Da for 1DZS [*] ... (from
uppsala, of course ;-). this immediately shows one problem with the lists,
namely that NCS molecules that are not explicitly represented in a PDB file
can give rise to flummoxingly whopping Vm values. other problems may arise
from incorrect Z-values on the CRYST1 card (also for 1DZS), errors in the
spacegroup name, cell constants, etc. however, despite these caveats the lists
ought to help you locate other examples with genuinely high Vm values
[*] yes, i know that 1KGH has a Vm of 43906.746 A3/Da according to pdbreport,
but that's not a crystal structure so it doesn't count
--dvd
******************************************************************
Gerard J. Kleywegt
[Research Fellow of the Royal Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology University of Uppsala
Biomedical Centre Box 596
SE-751 24 Uppsala SWEDEN
http://xray.bmc.uu.se/gerard/ mailto:gerard@xray.bmc.uu.se
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