From: samer halabi
Sent: 21 July 2020 11:08
To: ccp4bb@jiscmail.ac.uk ; David Briggs
Subject: Re: [ccp4bb] electron density close Histidine side chain
Hello,
Thank you for your kind reply.
If the distances are still less than 2.2Å, would coot and Refmac still consider
Hello,Thank you for your kind reply.In this case that could be either Zinc or
Nickel. Sorry, I should've mentioned how I purified the protein complex.
The protein is secreted in HighFive cells, to purify it by its 6xHis tag, I
used Ni sepharose excel beads, eluted with Imidazole and then furthe
Sent: Monday, July 20, 2020 5:27:37 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] electron density close Histidine side chain Dear Samer,
What king of cryo-protectant did you use ?
Such a bent density, with that size, looks like an ethylene-diol.
Best regards,
Nils Marech
Hello,Thank you for your kind reply.We used glycerol to fish out the
crystals.Sorry for not including more info before, I thinkI should have
mentioned how I purified the protein complex.
The protein is secreted in HighFive cells, to purify it by its 6xHis tag, I
used Ni sepharose excel beads,
Hello,Thank you for your kind reply.Do I need to link them together in the
structure? Is there a method for that?
>From the other replies I thought I should mention how I purified the protein
>complex.The protein is secreted in HighFive cells, to purify it by its 6xHis
>tag, I used Ni sepharos
Hello, do you have any negative difference density for the current position of
the His side chain? If so, it may be in two confirmations. Just a thought.
Best wishes, Jon Cooper, E-mail: jon.b.coo...@protonmail.com
Original Message
On 20 Jul 2020, 17:16, samer halabi wrote:
>
Almost certainly a metal ion, possibly Ni(2+) if a Ni-NTA column was used
for purification. Ni-N bond lengths are typically around 2.0 A. Additional
density is probably coordinated water molecules, which should have similar
Ni-O bond distances around 1.9 A. It is fairly common to find adventitious
on behalf of Nils Marechal
<4954a024d277-dmarc-requ...@jiscmail.ac.uk>
Sent: Monday, July 20, 2020 5:27:37 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] electron density close Histidine side chain
Dear Samer,
What king of cryo-protectant did you use ?
Such a bent density, with
Dear
Samer,
What king of cryo-protectant did you use ?
Such a bent density, with that size, looks like an ethylene-diol.
Best regards,
Nils Marechal
De : "samer
halabi" <30c2162795b2-dmarc-requ...@jiscmail.ac.uk>
A : CCP4BB@JISCMAIL.AC.UK
Envoyé: lundi 20 Juillet 2020 18:17
Objet : [c
If there is a covalent link, maybe sending a sample off to mass spec
would be a good idea. That would remove some of the guesswork.
Dale Tronrud
On 7/20/2020 9:16 AM, samer halabi wrote:
> Hello all,
> I have few blobs in an MHC II structure I am working on, especially
> opposite to Histidine
Hello,
what immediately comes into mind is phosphohistidine, especially since the
density looks rather large, but the geometry seems a bit off for that but I
cannot judge only from one angle. You could of course try to fit it in and
see how it looks.
Cheers,
Arne
On Mon, Jul 20, 2020 at 6:17 PM
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