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

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CCP4bb <-- 2007 <-- May 2007 <-- 17 May 2007
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From: Jan Dohnalek dohnalek {- at -} IMC {- dot -} CAS {- dot -} CZ
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Subject: Re: Slightly off topic, ~H2O/residue vs resolution
From: Robbie Joosten rjoosten {- at -} CMBI {- dot -} RU {- dot -} NL
Date: 2007-05-17


Subject: Re: Slightly off topic, ~H2O/residue vs resolution
From: Martyn Winn m {- dot -} d {- dot -} winn {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-05-17
The CCP4 program rwcontents includes the data from
Carugo & Bordo, Acta Cryst D, 55, 479 (1999)

Headline figures are 1.0 waters per protein residue at 2.0A, and 1.6-1.7
waters per protein residue at 1.0A. They use mainly room temperature,
but also some cryo structures.

And, as Clemens said, you shouldn't use this as a target...

Martyn

On Thu, 2007-05-17 at 13:56 +0100, Clemens Vonrhein wrote:
> 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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>

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CCP4bb <-- 2007 <-- May 2007 <-- 17 May 2007
Previous message:
Subject: TeachSG Workshop on ligand searching and docking in Prague
From: Jan Dohnalek dohnalek {- at -} IMC {- dot -} CAS {- dot -} CZ
Date: 2007-05-17 		Next message:
Subject: Re: Slightly off topic, ~H2O/residue vs resolution
From: Robbie Joosten rjoosten {- at -} CMBI {- dot -} RU {- dot -} NL
Date: 2007-05-17


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