Re: [ccp4bb] "Finding Chlorine" =)

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

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

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

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

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"
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29-Nov-2007 21:40
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[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: "Sabini, Elisabetta" sabini {- at -} UIC {- dot -} EDU
Date: 2007-11-29

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