Re: [ccp4bb] disulfide bonds, SE sample, and Xray absorption edges

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

Previous message:
Subject: Re: Deglycosylation
From: "A {- dot -} Radu Aricescu" radu {- at -} STRUBI {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-09-26

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Subject: Re: Quick-soak
From: Matt Vetting vetting {- at -} MEDUSA {- dot -} BIOC {- dot -} AECOM {- dot -} YU {- dot -} EDU
Date: 2008-09-26

Subject: Re: disulfide bonds, SE sample, and Xray absorption edges
From: "konstantin v {- dot -} korotkov" kk27 {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2008-09-26

Your case might be different, but it could also be a true Se signal from
Se-Cys incorporated into your protein during Se-Met expression. Depending
on the protocol you used, Se may get incorporated into Cys, especially if
only source of "sulfur" is Se-Met. We have seen such signals from Cys-
containing proteins produced in E.coli. Nice thing is that you get extra
sites to use in phasing!

Konstantin

K.Korotkov,
University of Washington
Department of Biochemistry
Box 357742
Seattle, WA 98195

On Thu, 25 Sep 2008, George M. Sheldrick wrote:

>
> Unexpected peaks in a S-SAD experiment sometimes turn out to be chloride,
> sulfate or a metal ion. I would suggest that you run shelxd with and
> without the disulfide option (or with different numbers of disulfides)
> to see which is best, and also run SHELXE with the -b flag set. This will
> produce an analysis of the anomalous density at the sites that you
> inputted and a list of peaks in the anomalous map. I also suggest that
> you look at the anomalous density by feeding the .pha file from SHELXE
> (generated if -b is set) into e.g. Coot.
>
> George
>
> Prof. George M. Sheldrick FRS
> Dept. Structural Chemistry,
> University of Goettingen,
> Tammannstr. 4,
> D37077 Goettingen, Germany
> Tel. +49-551-39-3021 or -3068
> Fax. +49-551-39-22582
>
>
> On Thu, 25 Sep 2008, Michael Jackson wrote:
>
>> Hello,
>> Â I had recently collected and solved the phases for a protein molecule using CCP4 and the ShelXCDE SAD method in it.Â What I was wondering was that the peaks for the three SE incorporated methionines are there as expected, but there is one peak scored roughly as the second largest where the disulfide is based on ShelXD's HA search algorithm. This data was collected at 0.97960 Angstroms which is close to the peak Xray absorption edge for Se but does anyone know if a disulfide has any absorption edge overlapping here?
>>
>>
>>
>>

CCP4bb navigation

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

Previous message:
Subject: Re: Deglycosylation
From: "A {- dot -} Radu Aricescu" radu {- at -} STRUBI {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-09-26

Next message:
Subject: Re: Quick-soak
From: Matt Vetting vetting {- at -} MEDUSA {- dot -} BIOC {- dot -} AECOM {- dot -} YU {- dot -} EDU
Date: 2008-09-26