Re: [ccp4bb] tricoordinated ion?

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

Previous message:
Subject: Re: Crystals grown from high ammonium sulphate
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2008-11-04

Next message:
Subject: Re: Crystals grown from high ammonium sulphate
From: shiliang shiliang {- at -} MOON {- dot -} IBP {- dot -} AC {- dot -} CN
Date: 2008-11-04

Subject: Re: tricoordinated ion?
From: "Borhani, David" David {- dot -} Borhani {- at -} DESHAWRESEARCH {- dot -} COM
Date: 2008-11-04

Sebastiano, it might be a trigonal planar anion, as Roger and others
suggest, but the density doesn't look very symmetrical to me; also, the
bond lengths look too long (e.g., bicarbonate should be ~1.4 Angs., I
believe).

Try taking the waters out (zero occ.), and see what the maps tell you at
that point after a bit of refinement (you also seem to have a fair
amount of +ve & -ve diff. density peaks around that region already).

It could be a planar ion (maybe the bond lengths appear too long, due to
water/water van der Waals repulsions of your refinement program), or
several mutually-exclusive waters (will need alt. conf. flags), or maybe
(hard to tell from a 2D picture) a hydrated Mg2+ ion (bond lengths look
correct; you would expect hexacoordination, pretty close to octahedral
geometry.

Hope this helps,
Dave
David Borhani, Ph.D.
D. E. Shaw Research, LLC
120 West Forty-Fifth Street, 39th Floor
New York, NY 10036
David.Borhani@DEShawResearch.com
212-478-0698
http://www.deshawresearch.com

________________________________

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On
Behalf Of Roger Rowlett
Sent: Tuesday, November 04, 2008 12:45 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] tricoordinated ion?

Sebastiano,

The density is possibly consistent with a trigonal planar anion
such as bicarbonate or nitrate. Bicarbonate can enter the solution from
CO2 in the atmosphere.

Cheers,

--

________________________________

Roger S. Rowlett
Professor
Colgate University Presidential Scholar
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowlett@mail.colgate.edu

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

--
Sebastiano Pasqualato, PhD
IFOM-IEO Campus
Dipartimento di Oncologia Sperimentale
Istituto Europeo di Oncologia
via Adamello, 16
20139 - Milano
Italy

tel +39 02 9437 5094
fax +39 02 574 303 310

________________________________

CCP4bb navigation

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

Previous message:
Subject: Re: Crystals grown from high ammonium sulphate
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2008-11-04

Next message:
Subject: Re: Crystals grown from high ammonium sulphate
From: shiliang shiliang {- at -} MOON {- dot -} IBP {- dot -} AC {- dot -} CN
Date: 2008-11-04