[ccp4bb] FW: Mild Denaturation to lose ligand

[Noam Adir]

Dear Andy,

We published a paper a while back showing that we could use up to 2M urea to 
prevent unwanted aggregation, and crystallize the sparingly soluble protein 
(Dines et al. J Struct. Biol. 2007) and then showed that we could solve the 
structure which was not affected by the presence of the urea (Dines et al. JBC 
2008). I am pretty sure that what you suggest will be fine, and even if there 
is residual urea, it will not affect the crystal structure.

Best wishes,

Noam

[cid:image001.jpg@01D351B7.F3896850]

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Andrew 
Lovering
Sent: Monday, October 30, 2017 5:29 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Mild Denaturation to lose ligand

Dear All,

I have a protein from which I’d like to lose the co-purifying ligand (Coenzyme 
A). The protein is his-tagged. The plan here is to bind it to a resin and then 
run over a mild denaturant solution to encourage ligand loss (it seems that 
extended dialysis does not achieve this).

Our starting protocol might aim at using roughly 1-1.5M Urea.

If anyone has trialled this (or a different protocol, say extremely high NaCl) 
for a similar or different protein:ligand combination then I’d be keen to hear 
your thoughts.

Thanks,
Andy

[ccp4bb] Mild Denaturation to lose ligand

[Andrew Lovering]

Dear All,

I have a protein from which I'd like to lose the co-purifying ligand (Coenzyme 
A). The protein is his-tagged. The plan here is to bind it to a resin and then 
run over a mild denaturant solution to encourage ligand loss (it seems that 
extended dialysis does not achieve this).

Our starting protocol might aim at using roughly 1-1.5M Urea.

If anyone has trialled this (or a different protocol, say extremely high NaCl) 
for a similar or different protein:ligand combination then I'd be keen to hear 
your thoughts.

Thanks,
Andy

Re: [ccp4bb] Vacuum pump in cold room

[William A. Neale]

You could always switch to a diaphragm vacuum pump - which is oil free -
and shouldn't be too fussed about working in a cold room. Quieter and
cleaner too.

Best wishes,

On 28 October 2017 at 18:17, Denis Rousseau 
wrote:

> Does anyone have experience with a vacuum pump in cold room? We have been
> told they may not start because of the viscosity of the oil?
>
> Thanks
>
> Denis Rousseau
> --
> *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Schulz,
> Eike-Christian [eike.sch...@mpsd.mpg.de]
> *Sent:* Friday, October 27, 2017 4:31 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] using CC1/2 to define resolution limit in Xscale
>
> Dear all,
>
>
>
> I would like to compare > 15 datasets and would like to use a common CC1/2
> value as an objective criterion to determine the resolution cut-off.
>
>
>
> All data were integrated in XDS.
>
>
>
> Is there a convenient way to apply this in XSCALE or in any of its
> alternatives?
>
>
>
> With best regards,
>
>
>
> Eike
>
>
>
>
>
>
>



-- 
William A. Neale
Postgraduate Research Student

Room 212, Huxley Building
Keele University, ST5 5BJ
w.a.ne...@keele.ac.uk
+44( 0)1782 (7)34441

[ccp4bb] Transcription levels

[Eugene Osipov]

Dear community,
sorry for a question non related to crystallography but I do not know where
to find relevant experts.
Please, look at the attached image:
In bacterial genome two operons, e.g. OPERON 1 and OPERON 2 lie close to
each other on different strands of DNA. Genes inside each operon have the
same expression level and both closely related. But
does neighborhood affect expression level of OPERON 1 and OPERON 2?  Is
there any published work about relationship between  expression levels of
closely arranged operons/genes?
Or may be someone knows about database where genes are mapped with their
expression level?

Thank you very much!

-- 
Eugene Osipov
Junior Research Scientist
Laboratory of Enzyme Engineering
A.N. Bach Institute of Biochemistry
Russian Academy of Sciences
Leninsky pr. 33, 119071 Moscow, Russia
e-mail: e.m.osi...@gmail.com

Re: [ccp4bb] Vacuum pump in cold room

[Jose Brandao-Neto]

Hi,

If for any usual random reason you got to stick to this pump, try it out first 
to see if it works, failing that talk to manufacturer and maybe change the oil, 
failing that get a heating blanket to start it up, failing that use a dry pump 
(checking if it likes operating at 4degC). 

Cost these options and present to your boss :)

Jose'

Re: [ccp4bb] Dubious slide aggregator slideplayer.com

[Randy Read]

Dear Robbie,

Thanks for posting that!  When I share my slides, I generally try to do so only 
as PDF files to make it harder for anyone to reuse them without permission, but 
I hadn’t realised how much of an issue this is.  It seems that I’ve nonetheless 
let one PowerPoint into the wild (“Using molecular replacement to exploit 
multiple crystal forms”).  Searching for its title in Google, I’ve found copies 
on not only slideplayer.com but also on documents.tips (aka DocSlide), 
slideserve.com and studylib.net.  

Best wishes,

Randy

-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical ResearchTel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills RoadE-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   
www-structmed.cimr.cam.ac.uk

> On 30 Oct 2017, at 08:46, Robbie Joosten  wrote:
> 
> Dear CCP4BBers,
>  
> Yesterday I ran into one of my talks at Slideplayer.com, a slide aggregator 
> that makes money from advertising. You can watch presentations for free 
> (surrounded by ads), but to download them you have advertise for Slideplayer 
> by posting on social media.
> The presentations are seemingly uploaded by users, but as their names give no 
> real hits on Google, I assume these are proxies to abuse the protection that 
> the DMCA provides to aggregators where users can post stuff. This probably 
> why they are officially based in Virginia (but their communication is partly 
> in Russian). The presentations are just spidered from public websites.
> There are many talks from CCP4bb members on Slideplayer.com and I don’t like 
> it. There are already enough commercial enterprises that make money from our 
> scientific works, but at least we get credit for it. That is not the case 
> here.
> The good news is that if you send a copyright infringement notice they do 
> remove the presentations (while hiding behind the DMCA of course). Because of 
> US copyright laws, you have to actively protect your copyright. Below is a 
> template notice that worked for me.
>  
> All the best,
> Robbie
>  
>  
> Template:
> //
> Dear Slideplayer developers, 
>  
> This writing is to inform you that I reserve and own all rights to the 
> presentation titled "$TITLE". It has come to my attention that you have made 
> unauthorised use of this copyrighted work (http://slideplayer.com/slide/$ID) 
> by duplicating and sharing it on Slideplayer. 
> As you have not sought or requested authorisation to distribute this work, 
> you are hereby ordered to cease and desist any and all acts of unlawful 
> copyright infringement with respect to my work immediately. Failure to comply 
> with this notice will leave me no other option than to seek compensation for 
> your copyright infringement through legal action.
>  
> Sincerely, 
> $SIGNATURE

[ccp4bb] Dubious slide aggregator slideplayer.com

[Robbie Joosten]

Dear CCP4BBers,

Yesterday I ran into one of my talks at Slideplayer.com, a slide aggregator 
that makes money from advertising. You can watch presentations for free 
(surrounded by ads), but to download them you have advertise for Slideplayer by 
posting on social media.
The presentations are seemingly uploaded by users, but as their names give no 
real hits on Google, I assume these are proxies to abuse the protection that 
the DMCA provides to aggregators where users can post stuff. This probably why 
they are officially based in Virginia (but their communication is partly in 
Russian). The presentations are just spidered from public websites.
There are many talks from CCP4bb members on Slideplayer.com and I don’t like 
it. There are already enough commercial enterprises that make money from our 
scientific works, but at least we get credit for it. That is not the case here.
The good news is that if you send a copyright infringement notice they do 
remove the presentations (while hiding behind the DMCA of course). Because of 
US copyright laws, you have to actively protect your copyright. Below is a 
template notice that worked for me.

All the best,
Robbie


Template:
//
Dear Slideplayer developers,

This writing is to inform you that I reserve and own all rights to the 
presentation titled "$TITLE". It has come to my attention that you have made 
unauthorised use of this copyrighted work (http://slideplayer.com/slide/$ID) by 
duplicating and sharing it on Slideplayer.
As you have not sought or requested authorisation to distribute this work, you 
are hereby ordered to cease and desist any and all acts of unlawful copyright 
infringement with respect to my work immediately. Failure to comply with this 
notice will leave me no other option than to seek compensation for your 
copyright infringement through legal action.

Sincerely,
$SIGNATURE