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.
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 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
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
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
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 protein
