Re: [ccp4bb] SO4 or PO4

[Edwin Pozharski]

Consider removing sulfate from the mother liquor after crystals are
formed.  I recall having success replacing ammonium sulfate with sodium
malonate (it's a nice cryoprotectant as well).  This is assuming that
ammonium sulfate is your major precipitant.  If it's just an additive (say,
your conditions are some PEG + 0.2M ammonium sulfate), try transferring
crystal to whatever PEG/glycerol combo you need for cryoprotection minus
ammonium sulfate.

Strictly speaking, this is not answering your original question, as it
suggests to recollect data instead of advice on how to distinguish sulfate
from phosphate in your density.

On Sat, Feb 16, 2019 at 4:07 AM 张士军 <21620150150...@stu.xmu.edu.cn> 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:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] SO4 or PO4

[Keller, Jacob]

I see what you’re saying—you’re probably right.

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 
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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 
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From: Goldman, Adrian 
Sent: Sunday, February 17, 2019 10:48 PM
To: Keller, Jacob 
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] SO4 or PO4

The total number of electrons in the two systems is identical, so you are 
looking for that extra fraction located closer to S than to P due to the change 
in atomic number.
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 
mailto:kell...@janelia.hhmi.org>> 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

+
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: Eleanor Dodson 
mailto:eleanor.dod...@york.ac.uk>>
Sent: Sunday, February 17, 2019 6:12 PM
To: Keller, Jacob mailto:kell...@janelia.hhmi.org>>
Cc: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
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 
mailto:kell...@janelia.hhmi.org>> 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 mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Yu Qiu
Sent: Sunday, February 17, 2019 9:11 AM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of ???
Sent: Sunday, February 17, 2019 8:57 AM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
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 

Re: [ccp4bb] SO4 or PO4

[Goldman, Adrian]

The total number of electrons in the two systems is identical, so you are 
looking for that extra fraction located closer to S than to P due to the change 
in atomic number.
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 
mailto:kell...@janelia.hhmi.org>> 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

+
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: Eleanor Dodson 
mailto:eleanor.dod...@york.ac.uk>>
Sent: Sunday, February 17, 2019 6:12 PM
To: Keller, Jacob mailto:kell...@janelia.hhmi.org>>
Cc: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
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 
mailto:kell...@janelia.hhmi.org>> 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 mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Yu Qiu
Sent: Sunday, February 17, 2019 9:11 AM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of ???
Sent: Sunday, February 17, 2019 8:57 AM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
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" mailto:rrowl...@colgate.edu>>
Sent Time:2019-02-17 00:47:55 (Sunday)
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
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 
<21620150150...@stu.xmu.edu.cn<mailto

Re: [ccp4bb] SO4 or PO4

[Keller, Jacob]

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

+
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: Eleanor Dodson 
Sent: Sunday, February 17, 2019 6:12 PM
To: Keller, Jacob 
Cc: CCP4BB@JISCMAIL.AC.UK
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 
mailto:kell...@janelia.hhmi.org>> 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 mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Yu Qiu
Sent: Sunday, February 17, 2019 9:11 AM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of ???
Sent: Sunday, February 17, 2019 8:57 AM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
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" mailto:rrowl...@colgate.edu>>
Sent Time:2019-02-17 00:47:55 (Sunday)
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
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 
<21620150150...@stu.xmu.edu.cn<mailto:21620150150...@stu.xmu.edu.cn> 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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Re: [ccp4bb] : [ccp4bb] SO4 or PO4

[Jim Pflugrath]

Besides the anomalous difference peak which might be similar in height to
the anom diff peak from an intrinsic sulfur found in cysteine or
methionine, also consider hydrogen bonding.

In general, a sulfate will not be donating a hydrogen bond.  A phosphate
probably will.



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Re: [ccp4bb] SO4 or PO4

[Eleanor Dodson]

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 
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  *On Behalf Of *Yu Qiu
> *Sent:* Sunday, February 17, 2019 9:11 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *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:CCP4BB@JISCMAIL.AC.UK
> ] *On Behalf Of *???
> *Sent:* Sunday, February 17, 2019 8:57 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *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" 
> *Sent Time:*2019-02-17 00:47:55 (Sunday)
> *To:* CCP4BB@JISCMAIL.AC.UK
> *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 <21620150150...@stu.xmu.edu.cn 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:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwMGaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=J-_EnZntmgYSuwGfqAanOKOx4S6mpcVpSKdhaTM92OY=Kl40SjTwjL17lOBJyHjftyBGU5mhSWNptFzJ-gQMsQ4=Sk-9VtK7KIJXB1dvm2TarZMv6hpUype4vHKSOfMTqyA=>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwMGaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=J-_EnZntmgYSuwGfqAanOKOx4S6mpcVpSKdhaTM92OY=Kl40SjTwjL17lOBJyHjftyBGU5mhSWNptFzJ-gQMsQ4=Sk-9VtK7KIJXB1dvm2TarZMv6hpUype4vHKSOfMTqyA=>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmai

Re: [ccp4bb] SO4 or PO4

[Keller, Jacob]

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  On Behalf Of Yu Qiu
Sent: Sunday, February 17, 2019 9:11 AM
To: CCP4BB@JISCMAIL.AC.UK
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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of ???
Sent: Sunday, February 17, 2019 8:57 AM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
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" mailto:rrowl...@colgate.edu>>
Sent Time:2019-02-17 00:47:55 (Sunday)
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
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 
<21620150150...@stu.xmu.edu.cn<mailto:21620150150...@stu.xmu.edu.cn> 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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Re: [ccp4bb] SO4 or PO4

[Yu Qiu]

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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of ???
Sent: Sunday, February 17, 2019 8:57 AM
To: CCP4BB@JISCMAIL.AC.UK
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" 
Sent Time:2019-02-17 00:47:55 (Sunday)
To: CCP4BB@JISCMAIL.AC.UK
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 
<21620150150...@stu.xmu.edu.cn<mailto:21620150150...@stu.xmu.edu.cn> 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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Re: [ccp4bb] SO4 or PO4

[张士军]

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" 
Sent Time:2019-02-17 00:47:55 (Sunday)
To: CCP4BB@JISCMAIL.AC.UK
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 <21620150150...@stu.xmu.edu.cn 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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Re: [ccp4bb] Fwd: [ccp4bb] SO4 or PO4

[Jan Stransky]

This can be done at Diamond I23 beamline.

https://doi.org/10.1016/j.nimb.2016.12.005

Best regards,

Jan

Dne 16.02.2019 v 18:49 Patrick Loll napsal(a):
> 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 > <mailto:jlliu20022...@gmail.com>>
>> *Subject: **Re: [ccp4bb] SO4 or PO4*
>> *Date: *February 16, 2019 at 11:14:07 AM EST
>> *To: *CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
>> *Reply-To: *jlliu20022002 liu > <mailto:jlliu20022...@gmail.com>>
>>
>> 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 <21620150150...@stu.xmu.edu.cn
>> <mailto:21620150150...@stu.xmu.edu.cn>> 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:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>
> ---
>
> Patrick J. Loll, Ph. D.  
>
> Professor of Biochemistry & Molecular Biology
>
> Drexel University College of Medicine
>
> Room 10-102 New College Building
>
> 245 N. 15th St., Mailstop 497
>
> Philadelphia, PA  19102-1192  USA
>
>
> (215) 762-7706
>
> pjl...@gmail.com <mailto:pjl...@gmail.com>
>
> pj...@drexel.edu <mailto:pj...@drexel.edu>
>
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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>



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Re: [ccp4bb] SO4 or PO4

[mesters]

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 <21620150150...@stu.xmu.edu.cn 
> 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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--
*Dr.math. et dis. nat.Jeroen R. Mesters*
Deputy, Lecturer, Program Coordinator /Infection Biology
/ 
Visiting 
Professorship (South Bohemian University) in Biophysics

Logo Uni Lübeck
*University of Lübeck*
Center for Structural and Cell Biology in Medicine
*Institute of Biochemistry*

Tel +49 451 3101 3105 (secretariate 3101)
Fax +49 451 3101 3104
jeroen.mest...@uni-luebeck.de 
www.biochem.uni-luebeck.de 

*Ratzeburger Allee 160
23538 Lübeck, Schleswig-Holstein
Germany*




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[ccp4bb] Fwd: [ccp4bb] SO4 or PO4

[Patrick Loll]

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 
> Subject: Re: [ccp4bb] SO4 or PO4
> Date: February 16, 2019 at 11:14:07 AM EST
> To: CCP4BB@JISCMAIL.AC.UK
> Reply-To: jlliu20022002 liu 
> 
> 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 <21620150150...@stu.xmu.edu.cn 
> <mailto:21620150150...@stu.xmu.edu.cn>> 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:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 
> <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1>
> To unsubscribe from the CCP4BB list, click the following link:
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> <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1>
---
Patrick J. Loll, Ph. D.  
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA  19102-1192  USA

(215) 762-7706
pjl...@gmail.com
pj...@drexel.edu




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Re: [ccp4bb] SO4 or PO4

[Roger Rowlett]

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 <21620150150...@stu.xmu.edu.cn 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:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] SO4 or PO4

[jlliu20022002 liu]

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 <21620150150...@stu.xmu.edu.cn> 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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[ccp4bb] SO4 or PO4

[张士军]

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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