[phenixbb] Unrealistic number of waters found by phenix?

Felix Frolow mbfrolow at post.tau.ac.il
Thu Feb 17 00:23:58 PST 2011

Dear Ina Lindemann
These are problems of the rich people...
Be happy and why not, after all your resolution is ~1.6 A
I would say that you have not enough water molecules. In such resolution and such molecular size
I would expect about 2 or even 3 water molecules per residue. So you are missing 198*2-334=62 water molecules.
As a frequent reviewer I would not let a paper describing such structure to pass!  ;-) ;-)

Dr Felix Frolow   
Professor of Structural Biology and Biotechnology
Department of Molecular Microbiology
and Biotechnology
Tel Aviv University 69978, Israel

Acta Crystallographica F, co-editor

e-mail: mbfrolow at post.tau.ac.il
Tel:  ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608

On Feb 17, 2011, at 09:52 , Ina Lindemann wrote:

> Hi,
> I am refining a crystal structure of a protein with 198 amino acids at 1.59 A resolution.
> I have used the function Update waters in phenix. After visual inspection of the found water molecules I deleted some of them, but there are still 334 water molecules left which show reasonable electron density. Many of them interacts just with other water molecules and not with the protein.
> I calculated the average B of water molecules = 26.3 and protein = 12.6.
> Now I am wondering if the number of water molecules and their average B value is to high with respect to the protein and would be very pleased about your answers.
> With best regards,
> Ina
> Ina Lindemann
> Philipps-Universität Marburg
> Pharmazeutische Chemie
> AG Klebe
> Marbacher Weg 6
> 35032 Marburg
> Tel.: 06421/2825908
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