I haven’t checked but I doubt if this is easy even in ccdb, and I would be stunned if it is possible in the pdb. There might be a small chance by classifying h-bonding and implied lone pairs and angles, but I think even this can be difficult.

Sent from my iPhone

On 18 Feb 2019, at 03:39, Keller, Jacob <[log in to unmask]> wrote:

Let me clarify. I was thinking not of the anomalous but of the regular 2FO-FC density, which should be easy enough to quantify and compare to the relative heights in thousands of high-resolution PO4’s and S04’s in the PDB. One could even get a pretty good estimate of the likelihood the unknown’s being each. I would think this could really nail it.

JPK

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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: Eleanor Dodson <[log in to unmask]>
Sent: Sunday, February 17, 2019 6:12 PM
To: Keller, Jacob <[log in to unmask]>
Cc: [log in to unmask]
Subject: Re: [ccp4bb] SO4 or PO4

Well - I try to quantify the relative anom peak heights by checking those over MET or CYS S sites with similar B values v the disputed one.. The expected difference between P and S isnt very big, but it might give you a crystallographic clue.

Eleanor

On Sun, 17 Feb 2019 at 17:31, Keller, Jacob <[log in to unmask]> wrote:

Shouldn’t it be possible to look at the ratio of peak heights of O’s versus S or P to figure out which is more likely? The must be thousands of examples in the pdb with which to determine the ratio, even if one restricts the analysis to “high resolution” structures.

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

+++++++++++++++++++++++++++++++++++++++++++++++++

The content of this email is confidential and intended for the recipient specified in message only. It is strictly forbidden to share any part of this message with any third party, without a written consent of the sender. If you received this message by mistake, please reply to this message and follow with its deletion, so that we can ensure such a mistake does not occur in the future.

From: CCP4 bulletin board <[log in to unmask]> On Behalf Of Yu Qiu
Sent: Sunday, February 17, 2019 9:11 AM
To: [log in to unmask]
Subject: Re: [ccp4bb] SO4 or PO4

Hi Shijun,

I had a similar issue a while ago that a acetylated lysine binding site was occupied by acetate from buffer. In this case, I would suggest trying crystallize in a conditions without SO4, e.g. using NH4Cl instead, if it is reproducible.

Best,

Yu

From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of ???
Sent: Sunday, February 17, 2019 8:57 AM
To: [log in to unmask]
Subject: [EXTERNAL] Re: [ccp4bb] SO4 or PO4

Dear all

Thanks for all your suggestions. PO4 is from my Ligand PI3P, but I cannot see the electron density of the PI3P tail, and the binding site is exactly there. While my crystal buffer salt is 50mM (NH4)2SO4, so I am afraid the SO4 occupied the PO4 position.BTW, I can see the other SO4 electron density in the other places, but is small than this one, and the diffraction resolution is 1.6A.

Best Regards

Shijun

-----Original Messages-----
From:"Roger Rowlett" <[log in to unmask]>
Sent Time:2019-02-17 00:47:55 (Sunday)
To: [log in to unmask]
Cc:
Subject: Re: [ccp4bb] 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 <[log in to unmask] 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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