Re: [ccp4bb] Electron density

[Keller, Jacob]

I know you mentioned trying buffer components, but it does look a lot like TRIS 
to me, maybe a different conformation than you’re modelling?

JPK

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
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From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Daniel 
Garcia
Sent: Sunday, May 13, 2018 8:40 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Electron density

Dear all,

I am currently refining a structure and found a intriguing electron density at 
the protein surface (pictures attached, the Fo-Fc map is contoured at >3.5 
sigma). My first candidates were molecules from my protein prep or 
crystallisation buffer, but none of them seem to fit well. I can observe that 
the ligand is nearby the side chains of a tyrosine, a lysine, a threonine and a 
glutamate residue, and it is close to the carbonyl oxygens of the protein 
backbone of a nearby loop. The shape of this density is not pyramidal, but it 
is not planar either.

Do you have any suggestions to solve this density based on your own experience? 
My crystallisation buffer contains tartrate, ammonium sulphate, and CHES, and 
my protein is in Tris buffer containing DTT and sodium chloride.

Best regards,

--
Mario

Re: [ccp4bb] Electron density

[Daniel Garcia]

Thanks for your quick responses. I used ethylene glycol as cryoprotectant.
Indeed I had 1% DMSO as part of the crystallisation condition (I forgot to
include that), but DMSO is too small to fit this density and DMSO has a
trigonal pyramidal structure, which differs a bit to what I have in my
structure.

On Mon, May 14, 2018 at 11:12 AM, Ethan Merritt 
wrote:

> On Monday, 14 May 2018 10:39:32 Daniel Garcia wrote:
> > Dear all,
> >
> > I am currently refining a structure and found a intriguing electron
> density
> > at the protein surface (pictures attached, the Fo-Fc map is contoured at
> > >3.5 sigma). My first candidates were molecules from my protein prep or
> > crystallisation buffer, but none of them seem to fit well. I can observe
> > that the ligand is nearby the side chains of a tyrosine, a lysine, a
> > threonine and a glutamate residue, and it is close to the carbonyl
> oxygens
> > of the protein backbone of a nearby loop. The shape of this density is
> not
> > pyramidal, but it is not planar either.
> >
> > Do you have any suggestions to solve this density based on your own
> > experience? My crystallisation buffer contains tartrate, ammonium
> sulphate,
> > and CHES, and my protein is in Tris buffer containing DTT and sodium
> > chloride.
>
> DMSO?
>
>
> >
> > Best regards,
> >
> >
>
> --
> Ethan A Merritt, Dept of Biochemistry
> Biomolecular Structure Center,  K-428 Health Sciences Bldg
> MS 357742,   University of Washington, Seattle 98195-7742
>



-- 
Mario Daniel García

Re: [ccp4bb] Electron density

[Ethan Merritt]

On Monday, 14 May 2018 10:39:32 Daniel Garcia wrote:
> Dear all,
> 
> I am currently refining a structure and found a intriguing electron density
> at the protein surface (pictures attached, the Fo-Fc map is contoured at
> >3.5 sigma). My first candidates were molecules from my protein prep or
> crystallisation buffer, but none of them seem to fit well. I can observe
> that the ligand is nearby the side chains of a tyrosine, a lysine, a
> threonine and a glutamate residue, and it is close to the carbonyl oxygens
> of the protein backbone of a nearby loop. The shape of this density is not
> pyramidal, but it is not planar either.
> 
> Do you have any suggestions to solve this density based on your own
> experience? My crystallisation buffer contains tartrate, ammonium sulphate,
> and CHES, and my protein is in Tris buffer containing DTT and sodium
> chloride.

DMSO?


> 
> Best regards,
> 
> 

-- 
Ethan A Merritt, Dept of Biochemistry
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] Electron density

[Joel Tyndall]

Did you happen to use glycerol as a cryoprotectant?

From: CCP4 bulletin board  On Behalf Of Daniel Garcia
Sent: Monday, 14 May 2018 12:40 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Electron density

Dear all,

I am currently refining a structure and found a intriguing electron density at 
the protein surface (pictures attached, the Fo-Fc map is contoured at >3.5 
sigma). My first candidates were molecules from my protein prep or 
crystallisation buffer, but none of them seem to fit well. I can observe that 
the ligand is nearby the side chains of a tyrosine, a lysine, a threonine and a 
glutamate residue, and it is close to the carbonyl oxygens of the protein 
backbone of a nearby loop. The shape of this density is not pyramidal, but it 
is not planar either.

Do you have any suggestions to solve this density based on your own experience? 
My crystallisation buffer contains tartrate, ammonium sulphate, and CHES, and 
my protein is in Tris buffer containing DTT and sodium chloride.

Best regards,

--
Mario

[ccp4bb] Postdoctoral scientist position in Structural Biology / Biophysics: Dundee, UK

[Dr Alessio Ciulli]

Dear all

We are currently looking for a highly motivated structural biologist to join a 
multi-disciplinary team of drug discovery scientists. This team is engaged in 
an exciting drug discovery collaboration between my laboratory and Boehringer 
Ingelheim. Our mission is to discover and develop a class of small-molecule 
drugs for targeted protein degradation as a novel therapeutic paradigm to treat 
cancer and other human diseases with serious unmet medical needs. 

Following a successful start to the collaboration we are now significantly 
expanding our team (6 open positions) in order to accelerate the translation of 
research in this field into therapeutic reality. Link below:

https://www.nature.com/naturejobs/science/jobs/642693-structural-biology-biophysics-scientist
 


Best wishes,

Alessio

-
Prof. Alessio Ciulli, FRSC
Professor of Chemical & Structural Biology
School of Life Sciences, University of Dundee
Division of Biological Chemistry and Drug Discovery
James Black Centre, Dow Street, Dundee DD1 5EH
United Kingdom

Phone: +44 (0)1382 386230Fax: +44 (0)1382 386373
http://www.lifesci.dundee.ac.uk/groups/alessio-ciulli