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CCP4BB Home

CCP4BB  January 2008

CCP4BB January 2008

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Subject:

Re: Web site GOOD, Attachment BAD (was: salt sensitive complex)

From:

Martyn Winn <[log in to unmask]>

Reply-To:

[log in to unmask]

Date:

Thu, 31 Jan 2008 10:18:23 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (160 lines)

Yes, we do discourage attachments. Links are better.
This is a strong recommendation rather than a hanging offence (we are
easy-going people).
I've added a sentence to that effect at http://www.ccp4.ac.uk/ccp4bb.php

Regards
Martyn

On Thu, 2008-01-31 at 08:58 +0000, Frank von Delft wrote:
> Actually, it's not book keeping, it's simple courtesy -- and not only on 
> a BB:  an attachment is lazy, and a large attachment is downright rude. 
> 
> I am routinely stuck with a slow connection (travelling), and others are 
> *permanently* stuck with one.  So please be nice... ;)
> 
> phx.
> 
> 
> 
> Anastassis Perrakis wrote:
> > Dear all -
> >
> > Sorry to intervene on a 'book keeping' issue, but indeed over the last 
> > few months an increasing number of people (Jerry is not the first, so 
> > Jerry please do not take it personally) attach pictures etc. I think 
> > in a bb standard practice dictates to only use text - if illustrations 
> > are needed to explain the problem, you can put them in eg a web site.
> >
> > Some text like that was in the 'code of conduct' off ccp4bb in the 
> > past, but I could no longer find it.
> >
> > Thus apologies if I am wrong and policies have changed, but maybe the 
> > ccp4 crowd could tell us what is the suggested policy.
> >
> > And, if you really want to send an image please do bother to make it 
> > small. The initial posting had a 630k image, which it took me 1 min to 
> > make 20k and it still makes the point (attached so I can also violate 
> > the rules i am suggesting - I love inconsistency).
> >
> > Thanks, Tassos
> >
> >
> >
> >
> > On Jan 30, 2008, at 20:11, Jerry McCully wrote:
> >
> >>
> >> Dear All:
> >>
> >>       Thanks a lot for the prompt reply on this topic of salt 
> >> sensitive complex.
> >>
> >>       Attached please find one ITC final figure done under 25mM 
> >> Tris(pH8.0), 60mM NaCl.
> >>
> >>       As mentioned before, the ionization of Tris will interfere with 
> >> the ITC experiments.
> >>
> >>      Therefore I am sure of my binding results.
> >>
> >>       Can anyone give me some comments on this ITC experiment? 
> >> Basically do these two proteins bind to each other? If so, how should 
> >> I improve the ITC experiments to get a similar affinity shown by 
> >> BIAcore(about 0.5uM)?
> >>
> >>     Thanks again.
> >>
> >> Jerry
> >>
> >>     ------------------------------------------------------------------------
> >>
> >>     Hi Jerry,
> >>      
> >>     Tris can cause problems, you are better off using something like
> >>     HEPES, and HEPES should be ok at pH 8. (Buffers with an
> >>     ethane-sulphonic acid group tend to be the best - those ending in
> >>     'ES', so MES, TES and HEPES)
> >>      
> >>     FYI, the error on your K is bigger than the actual measurement -
> >>     1.49x10^5 ± 1.5x10^5.
> >>     Signal to noise to is probably your enemy, which is making the curve
> >>     fitting difficult. Changing buffer may help this - there may be some
> >>     non-specific component to what you're seeing  - increasing salt a bit
> >>     or dropping in something like 5% glycerol may help with this.
> >>      
> >>     Would you be able to post a jpeg/pdf of the curve?
> >>      
> >>     Regards,
> >>      
> >>     David
> >>      
> >>      
> >>     On 25/01/2008, Jerry McCully  wrote:
> >>     >
> >>     >  Dear All:
> >>     >
> >>     >        Firstly  I would like to thank many folks here for giving me great
> >>     > ideas several days ago.
> >>     >
> >>     >       The following are some updates for this question.
> >>     >
> >>     >      I did ITC experiments again using 25mMTris(pH8), 60mM NaCl(low salt
> >>     > condition).
> >>     >
> >>     >     But things still turn out to be a little weird.
> >>     >
> >>     >     I increased the concentration of both proteins(60uM in the cell and
> >>     > 1200uM in the syringe). At the end of the ITC, I saw a little of
> >>     > precipitation of both the proteins.
> >>     >
> >>     >     Fortunately I can roughly fit the curve this time. However, the heat was
> >>     > still low, around 1Kcal/mole of per injectant.  I am not sure about the
> >>     > fitting statistics.
> >>     >
> >>     >
> >>     >
> >>     > N         1.10     ±0.17
> >>     >
> >>     > K         1.49E5 ±1.5E5
> >>     >
> >>     > DH       -893.5  ±213
> >>     >
> >>     > DS       20.7
> >>     >
> >>     > Was the enthalpy was offset by the ionization of Tris buffer?
> >>     >
> >>     > Can I use Hepes buffer around pH8 to do ITC?
> >>     >
> >>     >
> >>     >   Welcome any comments about the statistics and suggestions on how to
> >>     > improve the ITC experiments.have a nice weekend.
> >>     >
> >>     > Jerry
> >>     >
> >>
> >>
> >>
> >>     ------------------------------------------------------------------------
> >>     Helping your favorite cause is as easy as instant messaging. You
> >>     IM, we give. Learn more.
> >>     <http://im.live.com/Messenger/IM/Home/?source=text_hotmail_join> 
> >>
> >>
> >> ------------------------------------------------------------------------
> >> Shed those extra pounds with MSN and The Biggest Loser! Learn more. 
> >> <http://biggestloser.msn.com/>
> >> <test-ITC-012608.JPG>
> >
> 
-- 
***********************************************************************
*                                                                     *
*               Dr. Martyn Winn                                       *
*                                                                     *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455    E-mail: [log in to unmask]                 *
*   Fax: +44 1925 603825    Skype name: martyn.winn                   * 
*             URL: http://www.ccp4.ac.uk/martyn/                      *
***********************************************************************

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