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

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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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

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Subject: LINK record in PDB file for REFMAC5?
From: Jie Liu jie {- at -} TRIMER {- dot -} MED {- dot -} CORNELL {- dot -} EDU
Date: 2007-05-17

Subject: Re: Slightly off topic, ~H2O/residue vs resolution
From: Robbie Joosten rjoosten {- at -} CMBI {- dot -} RU {- dot -} NL
Date: 2007-05-17

Hi Mark,

Getting reliable stats straight from the PDB is nearly impossible. Waters
are commonly used to fill the gaps in difference maps, just to lower the
R-factor. Just look at the density for almost any structure. You'll see
that there are quite a few waters that have no density at all, insanely
high B-factors, or are too far away from the other atoms to make hydrogen
bonds.
To get reasonable numebers you'll have to re-evaluate a numebr of PDB
entries.

Best wishes,
Robbie Joosten

Center for Molecular and Biomolecular Informatics
Nijmegen, The Netherlands

> 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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CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
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

Next message:
Subject: LINK record in PDB file for REFMAC5?
From: Jie Liu jie {- at -} TRIMER {- dot -} MED {- dot -} CORNELL {- dot -} EDU
Date: 2007-05-17