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
>
> --
>
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[ccp4bb] 24th Annual Structural Biology Symposium, May 4th, Galveston TX - Registration is now OPEN

[Mark A. White]

You and your colleagues are cordially invited to join us for the 24th
Annual Structural Biology Symposium to be held at Levin Hall on the
University of Texas Medical Branch Campus on beautiful Galveston Island
on Saturday, May 4, 2019.  The meeting is organized by the Sealy Center
for Structural Biology & Molecular Biophysics and co-sponsored by the
Keck Center for Computational & Structural Biology.  This year’s
speakers include:

Thomas E. Cheatham, III, Ph.D.,
 Univ. of Utah 
 "Convergence, Reproducibility and Accuracy - 
There are Still Some Surprises in Modeling the Structure and Dynamics of
 Nucleic Acids"

Edward Egelman, Ph.D., 
  Univ. of Virginia School of Medicine
"Cryo-EM of Helical Polymers at Near Atomic Resolution"

  Matthieu G. Gagnon, Ph.D., 
 Univ. of Texas Medical Branch
  "How RRF and tRNA Disassemble the Ribosome During Recycling"

 Karen Maxwell, Ph.D., 
   Univ. of Toronto 
  "The Role of anti-CRISPRs in the Phage-Host Evolutionary Arms Race"

  Michael G. Rossman, Ph.D., 
   Purdue University
"The Structure of a 1900Å Diameter Chlorella Virus at Atomic Resolution"

  Liang Tong, Ph.D., 
  Columbia University
 "Structural Insights into RNA Processing and Quality Control"


   To register or for more information, visit
 http://scsb.utmb.edu/symposium

-- 
Yours sincerely, 

Mark A. White, Ph.D. 
Associate Professor of Biochemistry and Molecular Biology, 
Manager, Sealy Center for Structural Biology and Molecular Biophysics 
Macromolecular X-ray Laboratory, 
Basic Science Building, Room 6.658A 
University of Texas Medical Branch 
Galveston, TX 77555-0647 
mailto://mawh...@utmb.edu 
http://xray.utmb.edu 

QQ: "Some men would be wise if they did not already believe that they
were." 
- Baltasar Gracian (1658) 














































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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
+

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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 
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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
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
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.

[ccp4bb] MoRDa update

[Alexey Vagin]

Dear All

MoRDa is a pipeline for molecular replacement structure solution.

A new update to the package is now available. The structure solution program is 
improved and database is extended .

Both update and installation instructions are available from Morda homepage 
.

The update is also available for existing local Morda installations and can be 
installed from command line: change to installation directory (by default 
MoRDa_DB) and type ./update_morda.

Also Morda at ccp4online  has been updated. 

Best regards
Alexey




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