Re: [ccp4bb] Slightly off topic, ~H2O/residue vs resolution

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Subject: Re: Slightly off topic, ~H2O/residue vs resolution
From: Clemens Vonrhein vonrhein {- at -} GLOBALPHASING {- dot -} COM
Date: 2007-05-17

Hi Mark,

I attach a little plot based on a quick analysis of recent PDB entries
(between Jan 04 and Nov 06, only Xray). This shows the number of
waters (HOH residues) per ATOM record (i.e. mainly protein,
RNA/DNA). If you want the number of waters per amino-acid residue, you
could just multiply it by about 10?

Converted into a VERY ROUGH 'rule of thumb':

2.5 Angstroem = 0.5 water per residues
2.0 1.0
1.5 1.5
1.0 2.0

But note the large error bars (at higher resolution probably because I
ignored alternate conformations and partially occupied waters): so you
have to do your own decision also based on the data quality and maps
yourself, I guess. And: this is what deposited structures tell us -
it doesn't mean we have to follow this.

Hope that helps

Cheers

Clemens

On Thu, May 17, 2007 at 03:44:14AM -0400, mark michaels wrote:
> Hello everyone,
>
> I would like to ask for any information on reasonable, preferably
> quantitatively derived values for the approximate crystallographic
> H2O to residue ratio versus resolution for protein structures ?
>
> Any references or studies would be ideal, but rules of thumb
> would also help. If there are any studies with greater detail,
> such as per residue type, I'd appreciate learning of them also.
>
> I'd specifically like this for cryo conditions since that would
> influence the results and my analysis involves structures
> determined under cryo conditions.
>
> Thanks for any help.
>
> m
>
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Subject: TeachSG Workshop on ligand searching and docking in Prague
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