Re: [ccp4bb]: solvent content

[rajan sreekanth]

 
hi ethaya!!!
  the query has already come up in CCP4BB and i have pasted the reply by Gerard J.  Kleywegt which seems to a good one.

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




On Wed, 04 Jan 2006 Ethayathulla Abdulsamath wrote :
>   hi all
>can any tell me what is the highest solvent in protein !
>I want to know what is highest solvent in crystal structure
>
>Thanking you
>
>Ethayathulla
>
>
>
>###################################################
>A.S.Ethayathulla,Ph.D.
>Department of Biophysics
>All India Institute of Medical Sciences
>Ansari Nagar
>New Delhi-110029
>India.
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