Dear all,
I apologize for the size of the images in my previous email. I didn't
notice that until I sent out the email. I am resending the compressed
ones. Please delete my previous email, and thanks Artem for pointing
it out.
Best,
Junyu
On Jul 19, 2009, at 7:11 PM, Artem Evdokimov wrote:
> What you're seeing is not necessarily pyrophosphate. The negative
> difference
> density appears to concentrate around oxygen atoms most distant from
> the
> protein (and perhaps around the putative phosphorous atom?). Some
> clues
> might be obtained from e.g. the B-factor profile of the refined
> atoms. From
> the side-view pictures you sent it's not clear whether the density in
> question suports two tetrahedral ions... instead it could be two
> planar ions
> e.g. a malonate or some other molecule with two flat groups and a
> linker.
> Take a closer look at your omit difference density maps for
> starters. Does
> the positive difference density indicate the presence of a heavier
> atom in
> the center of a putative tetrahedron of lighter ones? Is one of the
> sides
> tetrahedral and the other - planar?
>
> Incidentally, if you compress the images you sent it's possible to
> get the
> size down from 3 MB each (encoded for email it's actually 4MB each!)
> down to
> about 60-100 KB each without significant loss of quality. I am sorry
> for
> bringing up my pet peeve but not everyone on this list enjoys 8 MB
> mass
> emails, especially when the contents do not justify the size in any
> way :)
>
> Artem
>
> -----Original Message-----
> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf
> Of Junyu
> Xiao
> Sent: Sunday, July 19, 2009 7:30 PM
> To: [log in to unmask]
> Subject: [ccp4bb] Density for pyrophosphate?
>
> Dear all,
>
> I am at the late stage of refining a 1.97 A structure. There is
> something
> in the ligand binding pocket, and I am not sure what it is exactly.
> Since
> this protein can potentially generate pyrophosphate from ATP, and I
> have
> ATP in the protein solution, so I tried to fit in a pyrophosphate. The
> Rwork/Rfree after refinement are 0.198/0.243. Below is the refined
> map. The
> 2fofc map looks ok (contoured at 1 sigma), however, there is always
> some
> red density around the pyrophosphate in the fofc map (contoured at 3
> sigma). I have also tried to fit in the density as two free
> phosphates, and
> the results are worse. Can I get some advices on this? Any
> suggestion will
> be greatly appreciated.
>
> Best regards,
> Junyu
>
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