Contour the 2Fo-Fc map at lower sigma than 1.3, and see if the resulting
density looks like MES. As others have said, if there is no specific pocket or
interactions for the non-sulfonic acid head group, then I would expect that
density to be weaker or smeared out due to positional disorder.
Dia
2022 17:28
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] mysterious density
External Sender: Use caution.
A MES buffer molecule ?
> Le 13 mars 2022 à 18:08, doriano lamba a écrit :
>
> Glycerol-3-phosphate?
> My 2cents
> DL
> Il 2022-03-13 15:19 Amir Khan ha scritto:
A MES buffer molecule ?
> Le 13 mars 2022 à 18:08, doriano lamba a écrit :
>
> Glycerol-3-phosphate?
> My 2cents
> DL
> Il 2022-03-13 15:19 Amir Khan ha scritto:
>> Hi,
>> I wonder whether anyone can advise on the ‘tadpole’ like density.
>> The head is currently a phosphate
>> and I’ve placed a
On Fri, Sep 3, 2010 at 4:53 PM, Jin H. Park wrote:
> I have solved the structure. But, there seems oddly strong density above
> histidine residue.
> What could this density be?
> The protein was in Tris buffer, with NaCl and DTT, and crystallized in
> NaSCN with PEG.
> (electron density in the pic
Hi Jin,
The text book might suggest metal ions, or even phosphorylation.these do
require evidence in the form additional structure beyond the metal or
phosphorus though...
Bret
On 4/09/10 9:53 AM, "Jin H. Park" wrote:
>
>
> Dear CCP4 community,
>
>
>
> I have solved the structure.
Behalf Of Jin H. Park
[jinhp...@mail.med.upenn.edu]
Sent: 04 September 2010 09:53
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Mysterious density
Dear CCP4 community,
I have solved the structure. But, there seems oddly strong density above
histidine residue.
What could this density be?
The
Cyclized DTT can look similar to this blob. Of course the sulfur
atoms would make one end of the blob more dense than the other.
Dale Tronrud
On 07/09/10 05:12, Nick Quade wrote:
> Dear CCP4 community,
>
> I have solved the structure of a protein in complex with DNA. But,
> inside the protei
Another thing to consider is alternate ligand conformation. The water density
(elongated) and the pocket composition (aromatic) could result in two
alternative binding orientations (of the buffer? I need 3D). I would play
around with models to see if it fits the density.
Paula Lario
#778-828-
Blobology (a branch of macromolecular crystallography).
You could maybe place benzoate in there (the 6 membered ring on "top" in
the pictures), refine, compute a new map and see if you can make
something out of it. Why benzoate: because the ring would find its place
nicely in the "hydrophobic"
Dear CCP4 community,
I have solved the structure of a protein in complex with DNA. But,
inside the protein there seems to be a ligand binding pocket with some
strong density
(*http://picasaweb.google.de/113264696790316881054/Desktop#). *The
protein was in Tris buffer, with some NaCl, MgCl2 an
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