Re: [ccp4bb] tricoordinated ion?

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

Previous message:
Subject: Re: tricoordinated ion?
From: Klaus Piontek klaus {- dot -} piontek {- at -} OCBC {- dot -} UNI-FREIBURG {- dot -} DE
Date: 2008-11-04

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Subject: Re: Crystals grown from high ammonium sulphate
From: "Mark J {- dot -} van Raaij" mark {- dot -} vanraaij {- at -} USC {- dot -} ES
Date: 2008-11-04

Subject: Re: tricoordinated ion?
From: Roger Rowlett rrowlett {- at -} MAIL {- dot -} COLGATE {- dot -} EDU
Date: 2008-11-04

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Before jumping to any conclusions, you should definitely see what this
density looks like without the water molecules in this portion of the
model. I think it would be difficult to decide on what the actual "bond
lengths" are without removing model bias. If you model with waters, of
course the electron density will conform to some degree to what is
modeled there. You may find that without the waters, the electron
density shrinks up a bit, or can be adequately modeled with a trigonal
planar anion. On the other hand, maybe it is just a cluster of water
molecules, or an anion at less than 100% occupancy. From your water
model, however, it looks like you may have enough density for a full
occupancy anion. FYI, the surrounding ligands, Arg + Glu + another
H-bonding donor are certainly compatible with the few known bicarbonate
binding sites in proteins.

Roger Rowlett

Klaus Piontek wrote:

Hi Sebastiano,

I had similar experiences with various crystal structures. After a lot
of modeling (albeit at about 1 A resolution) I came to the conclusion
that these atoms correspond to disordered solvent molecules, e.g. water
and/or Zn. In other words the atoms have occupancies of < 1, but in the
sum it should be 1.

For CO2 or similar molecules the bond length are far too long (C-O is
about 1.4 A or so).

Good luck.

Klaus Piontek

Sebastiano Pasqualato wrote:

Hi all,
I wanted to ask you what would you model in the density in which I
have at the moment modelled 4 water molecules, which are however too
close to be waters, I guess (see attached image).
My crystallisation conditions contain NaCl, MgCl2, Peg400, TrisHCl, TCEP,
glycerol.
I can't think at a tricoordinated ion like that...
thanks in advance for the hints,
ciao
S



--
Dr. Klaus Piontek
Albert-Ludwigs-University Freiburg
Institute of Organic Chemistry and Biochemistry, Room 401 H
Albertstrasse 21
D-79104 Freiburg
Germany
Phone: ++49-761-203-6036
Fax: ++49-761-203-8714
Email: Klaus.Piontek@ocbc.uni-freiburg.de
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CCP4bb navigation

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

Previous message:
Subject: Re: tricoordinated ion?
From: Klaus Piontek klaus {- dot -} piontek {- at -} OCBC {- dot -} UNI-FREIBURG {- dot -} DE
Date: 2008-11-04

Next message:
Subject: Re: Crystals grown from high ammonium sulphate
From: "Mark J {- dot -} van Raaij" mark {- dot -} vanraaij {- at -} USC {- dot -} ES
Date: 2008-11-04