Hi!
As suggested below sulfur/phosphorous anomalous difference Fourier density
would be nice, but you might be able to figure out what's going without
collecting more data. Have you investigated the direct interaction partners of
your mystery oxyanion? Unless you are at extreme pH values, phosphate will
have at least one proton that is looking for a hydrogen bond acceptor. In
contrast, sulfate/sulphate will generally not have a proton to donate (SO4--).
You might want to inspect the binding sites of sulfate and phosphate binding
protein, respectively.
My two Kronas, Hudel
Date: Sat, 16 Feb 2019 17:05:17 +0800
From: 张士军 <[email protected]>
Subject: SO4 or PO4
Dear all
I have got a crystal grown at the condition both have ion of SO4 and PO4,
and the diffraction resolution is very well, but the problem is coming: how to
tell which is which just from electron density? I think they are exactly same.
Thanks a lot !!!
Beat Regards
Shijun
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------------------------------
Date: Sat, 16 Feb 2019 11:14:07 -0500
From: jlliu20022002 liu <[email protected]>
Subject: Re: SO4 or PO4
How about collect data at sulfur peak. You might see anomalous peak for
sulfur.
Jinyu
On Sat, Feb 16, 2019 at 4:07 AM 张士军 <[email protected]> wrote:
> Dear all
>
> I have got a crystal grown at the condition both have ion of SO4 and PO4,
> and the diffraction resolution is very well, but the problem is coming:
how
> to tell which is which just from electron density? I think they are
exactly
> same. Thanks a lot !!!
>
> Beat Regards
>
> Shijun
>
> ------------------------------
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------------------------------
Date: Sat, 16 Feb 2019 11:47:55 -0500
From: Roger Rowlett <[email protected]>
Subject: Re: SO4 or PO4
Two things to look at that could provide a clue:
Examine the anomalous map for some density over the central atom. Sulfur
will often, but not always have significant anomalous density depending on
the wavelength and quality of data set.
Phosphate is normally HPO4= or H2PO4-. Look for phosphate donor to acceptor
hydrogen bonding contacts. Sulfate rarely has donor to acceptor hydrogen
bonding contacts, as it is SO4= at any reasonable pH.
Roger Rowlett
On Sat, Feb 16, 2019, 4:06 AM 张士军 <[email protected] wrote:
> Dear all
>
> I have got a crystal grown at the condition both have ion of SO4 and PO4,
> and the diffraction resolution is very well, but the problem is coming:
how
> to tell which is which just from electron density? I think they are
exactly
> same. Thanks a lot !!!
>
> Beat Regards
>
> Shijun
>
> ------------------------------
>
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>
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------------------------------
Date: Sat, 16 Feb 2019 16:54:37 +0000
From: "david lawson (JIC)" <[email protected]>
Subject: Warning - ccp4 update 7.0.069 breaks ccp4i2 on MacBook running
Mojave (v 10.14.2)
Hi All,
I installed the latest ccp4 update on my MacBook through the CCP4i2 update
manager. After doing so, refmac appeared to be broken. I tried to restart the
I2 GUI but it refused to even after a reboot.
Eventually I got running again by uninstalling this update through the
CCP4i update manager (i.e. the old GUI). After cloning my failed refmac job in
CCP4i2, it ran without a hitch.
Dave
-------------------------------
Dr. David M. Lawson
Department of Biological Chemistry,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Fax: +44-(0)1603-450018
Email: [email protected]<mailto:[email protected]>
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------------------------------
Date: Sat, 16 Feb 2019 12:49:45 -0500
From: Patrick Loll <[email protected]>
Subject: Fwd: [ccp4bb] SO4 or PO4
S has about 0.56 anomalous electrons at 8 keV, whereas P has about 0.44.
This is a small difference between two weak signals—unlikely to give a clear
result. If you could get to the sulfur & phosphorus edges, then you could (in
principle) answer this, but that’s a very hard experiment to accomplish.
> Begin forwarded message:
>
> From: jlliu20022002 liu <[email protected]>
> Subject: Re: [ccp4bb] SO4 or PO4
> Date: February 16, 2019 at 11:14:07 AM EST
> To: [email protected]
> Reply-To: jlliu20022002 liu <[email protected]>
>
> How about collect data at sulfur peak. You might see anomalous peak for
sulfur.
>
> Jinyu
>
> On Sat, Feb 16, 2019 at 4:07 AM 张士军 <[email protected]
<mailto:[email protected]>> wrote:
> Dear all
>
> I have got a crystal grown at the condition both have ion of SO4 and PO4,
and the diffraction resolution is very well, but the problem is coming: how to
tell which is which just from electron density? I think they are exactly same.
Thanks a lot !!!
>
> Beat Regards
>
> Shijun
>
>
> To unsubscribe from the CCP4BB list, click the following link:
>
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Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
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------------------------------
Date: Sat, 16 Feb 2019 18:55:49 +0100
From: mesters <[email protected]>
Subject: Re: SO4 or PO4
Anomalous is the way to go but it helps to think about the final
concentrations used..... With 50 mM PO4 (buffer) and 2 M SO4 (ammonium
sulfate) most "bindin sites in quesiton" will be occupied by SO4...
My 2 cents
Jeroen
> On Sat, Feb 16, 2019 at 4:07 AM 张士军 <[email protected]
> <mailto:[email protected]>> wrote:
>
> Dear all
>
> I have got a crystal grown at the condition both have ion of SO4
> and PO4, and the diffraction resolution is very well, but the
> problem is coming: how to tell which is which just from electron
> density? I think they are exactly same. Thanks a lot !!!
>
> Beat Regards
>
> Shijun
>
>
>
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