Re: [ccp4bb] "Finding Chlorine" =)

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

Previous message:
Subject: Re: "Finding Chlorine" =)
From: Tadeusz Skarzynski tadeusz {- dot -} j {- dot -} skarzynski {- at -} GSK {- dot -} COM
Date: 2007-11-29

Next message:
Subject: Re: "Finding Chlorine" =)
From: "Sabini, Elisabetta" sabini {- at -} UIC {- dot -} EDU
Date: 2007-11-29

Subject: Re: "Finding Chlorine" =)
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-11-29

But you can change it with the keyword

anomolous formfactor f' f''

Where f' and f'' correspond to values for a given wavelength.
See for details:
http://www.ysbl.york.ac.uk/refmac/data/refmac_news.html

Internally yes. It is CuKa.

Garib

On 29 Nov 2007, at 23:19, Tadeusz Skarzynski wrote:

>
> Dear Elisabetta,
> Which program did you use for refinement?
> If you used REFMAC, the atomic scattering factors are internally
> coded for copper radiation, and the resulting electron density map
> after refinement may be much lower for halide atoms than it should be!
> It is a known REFMAC issue.
> Tadeusz
>
>
>
> "Sabini, Elisabetta"
> Sent by: "CCP4 bulletin board"
> 29-Nov-2007 21:40
> Please respond to "Sabini, Elisabetta"
>
>
> To
> CCP4BB@JISCMAIL.AC.UK
> cc
> Subject
> [ccp4bb] "Finding Chlorine" =)
>
>
>
>
>
> Dear all,
>
> I am refining two structures which have in the active site a ligand
> containing a covalent bond between a carbon and a chlorine atom.
>
> I collected the data at APS, SERCAT ID-22.
>
> Because of radiation damage I tried different occupancy values for the
> chlorine atom and structure number #1 is best with occupancy 0.2 while
> structure #2 seems to be happy with occupancy 0 (occupancy for the
> rest of
> the ligand is 1).
>
> I checked by mass spec if my compound has the molecular weight
> expected
> with a chlorine atom and it does, so the original compound was
> correct.
>
> Can radiation damage make the chlorine completely disappear?
>
> Do the different occupancy values I get depend also on the resolution?
> In fact:
>
> Structure # 1 (OCC=0.2) refined to 1.8A (Rfact/Rfree=20/25%)
> Structure # 2 (OCC=0.0) refined to 2.5A (Rfact/Rfree=23/33%)
>
>
> When I make the figures for publication, do I draw the ligand with or
> without chlorine?
>
> Thanks,
>
> Eli =)
>
>
> --
> Elisabetta Sabini, Ph.D.
> Research Assistant Professor
> University of Illinois at Chicago
> Department of Biochemistry and Molecular Genetics
> Molecular Biology Research Building, Rm. 1108
> 900 South Ashland Avenue
> Chicago, IL 60607
> U.S.A.
>
> Tel: (312) 996-6299
> Fax: (312) 355-4535
> E-mail: sabini@uic.edu
>
>
>
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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: "Finding Chlorine" =)
From: Tadeusz Skarzynski tadeusz {- dot -} j {- dot -} skarzynski {- at -} GSK {- dot -} COM
Date: 2007-11-29

Next message:
Subject: Re: "Finding Chlorine" =)
From: "Sabini, Elisabetta" sabini {- at -} UIC {- dot -} EDU
Date: 2007-11-29