Dear Dale Tronrud,
Thanks for your advise. Initially, i focused on the shape of the density. As
you suggest, i checked all possible biological molecules and common additives
used in purification and crystallization. I found that the structure of
bis-tris-propane is similar to the target
and Regards
--
Sonali Dhindwal
“Live as if you were to die tomorrow. Learn as if you were to live
forever.”
-
From: sonali dhindwal
To: ccp4...@hotmail.com
Sent: Wednesday, 17 July 2013 9:44 AM
Subject: Re: [ccp4bb] Dose anyone see this ligand before?
hi Wei
Try here:
http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=8031loc=ec_rcs
download the sdf and use the sdf to pdb converter
Or I think phenix can read in sdf and convert them
Jürgen
On Jul 17, 2013, at 9:35 AM, Wei Feng wrote:
Dear all,
Thank you for your advices.
I had tried to use MPD
Do you have any reason to expect either of these molecules would be in
your crystal? The model you build has to fit the density, be consistent with
the surrounding environment (which you haven't shared with us) and you
have to have some story for how that molecule got in your crystal.
Wei
I heartily second Dale's comment. Since you do know what has been in contact
with your protein, you should be able to make a list of ALL POSSIBLE compounds
your protein has been exposed to. However, don't go off the deep end. You say
that We guess that the molecular formula should be
Special position ?
sulfate-size ?
Jürgen
On Jul 16, 2013, at 11:35 AM, Wei Feng wrote:
Dear all,
I found some redundant density in my structure beween two molecule. (see
picture 1 and 2)
But I am not sure which ligand will be.
Dose everyone see this ligand before? If so, can you tell the PDB
Of Bosch,
Juergen
Sent: Tuesday, July 16, 2013 11:53 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Dose anyone see this ligand before?
Special position ?
sulfate-size ?
Jürgen
On Jul 16, 2013, at 11:35 AM, Wei Feng wrote:
Dear all,
I found some redundant density in my structure beween two
/*/
*From:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf
Of *Bosch, Juergen
*Sent:* Tuesday, July 16, 2013 11:53 AM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Dose anyone see this ligand before?
Special position ?
sulfate-size ?
Jürgen
On Jul 16, 2013, at 11:35 AM, Wei
product of reaction.
Vaheh
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bosch,
Juergen
Sent: Tuesday, July 16, 2013 11:53 AM
To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Dose anyone see this ligand
[mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of
*Bosch,
Juergen
*Sent:* Tuesday, July 16, 2013 11:53 AM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Dose anyone see this ligand before?
Special position ?
sulfate-size ?
Jürgen
On Jul 16, 2013, at 11:35 AM, Wei Feng wrote:
Dear all,
I found
...@yahoo.co.in
To: ccp4...@hotmail.com ccp4...@hotmail.com
Sent: Wednesday, 17 July 2013 9:44 AM
Subject: Re: [ccp4bb] Dose anyone see this ligand before?
hi Wei,
This looks like MPD, 2-Methyl-2,4-pentanediol. May b u have added it as ur
cryo-protectant.
Thanks and Regards
--
Sonali
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