Re: [ccp4bb] Identifying an unknown ligand

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

Previous message:
Subject: Identifying an unknown ligand
From: Abhinav Kumar abhinavk {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2009-04-02

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Subject: cryoprotectant for 1,6 hexanediol
From: HanJie_Heng Chiat Tai chemtai2001 {- at -} HOTMAIL {- dot -} COM
Date: 2009-04-02

Subject: Re: Identifying an unknown ligand
From: Roger Rowlett rrowlett {- at -} MAIL {- dot -} COLGATE {- dot -} EDU
Date: 2009-04-02

Some context would be helpful (essential?). What's
in the crystallization solution? What, if anything, is known about the
protein of interest? What is the ligand interacting with (metal ions,
hydrogen bonding donors/acceptors, charged residues, etc?), and what
are the interaction distances? Do any of the atoms appear to be "heavy"
or show anomalous scattering, if applicable, at the wavelength used?
etc. etc.

--

Roger S. Rowlett

Professor

Colgate University Presidential Scholar

Department of Chemistry

Colgate University

13 Oak Drive

Hamilton, NY 13346

tel: (315)-228-7245

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fax: (315)-228-7935

email: rrowlett@mail.colgate.edu

Abhinav Kumar wrote:

Hi,

I am refining a structure and have a region of unmodeled density into 
which I am trying to fit a ligand. The identity of the ligand is not 
obvious, so I modeled a bunch of dummy atoms into the density.
Could you please have a look at the map and pdb files and help me 
identify this ligand?

Please see http://smb.slac.stanford.edu/~abhinavk/UNL/unl.html

Thanks 
Abhinav 

Stanford Synchrotron Radiation Laboratory 
Joint Center for Structural Genomics 
Mail Stop 99 
Phone: (650) 926-2992 
Fax: (650) 926-3292

CCP4bb navigation

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

Previous message:
Subject: Identifying an unknown ligand
From: Abhinav Kumar abhinavk {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2009-04-02

Next message:
Subject: cryoprotectant for 1,6 hexanediol
From: HanJie_Heng Chiat Tai chemtai2001 {- at -} HOTMAIL {- dot -} COM
Date: 2009-04-02