Re: [ccp4bb] Ligand occupancy refinement

[Steven Herron]

Dear Akanksha,

When you re-do the occupancy refinement, don't include a b-factor 
refinement along with the occupancy refinement.  Do them separately. Do 
one, then do the other, and then repeat until convergence.


If your B-factor values are either high or low, the computer will try to 
adjust using occupancy.  If your occupancy values are either high or 
low, then the computer will try to adjust using B-factors. In the end 
you want the best occupancy and b-factor estimates you can get by making 
sure the refinement programs don't get trapped.


Once you have a good estimate, I suggest that you try a few different 
initial occupancy values to make sure you are not trapped in a local 
minimum.  If you start off with a high occupancy, it should move back 
down during the refinement.  If you start off with a low occupancy, then 
it should back up during the refinement. B-Factors should do the same 
thing.


With a large ligand, I suspect that some of the waters will also have 
alternate orientations.  You also might look at the amino acids that 
bind to the ligand to see if there is any alternate conformations.



Best
Steven Herron



On 3/3/2022 8:51 AM, Akanksha Tomar wrote:

Thank you for the suggestions
I will try again by setting the occupancy of the entire ligand to the 
single average occupancy and re-do the refinement with Buster, Phenix 
refine and Remac5 with full positional and B-factor refinement and 
check the B-factor of the neighbouring residues.
The ligand is a 30 atom containing molecule binding at a shallow 
solvent-exposed site.




On Thu, 3 Mar 2022 at 20:38, Wim Burmeister  wrote:

Hello,
at 2.1 A resolution, atomic temperature factors and occupancy are
strongly correlated. So you have to be very careful with the results.
So the best is just to set the inhibitor to the average occupancy
and then to include it into a full positional and B-factor
refinement. You can check whether the result is coherent by
comparing the B-factors of the ligand and of the atoms, which are
in contact with it. If this is not the case, you may want to
adjust the occupancy manually. As ther are also solvent atoms at
the ligand positions, when it is not bound, there is another
source of inaccuracy and theoretically you would have to model the
site with the solvent and an occupancy 1-q and the ligand with an
occupancy q as alternate structures. But nobody does that and it
is not really required.
Best
Wim


*De: *"Akanksha Tomar" 
*À: *"CCP4BB" 
*Envoyé: *Jeudi 3 Mars 2022 15:15:07
*Objet: *[ccp4bb] Ligand occupancy refinement

Hi everyone,

I am trying to refine the occupancy of a bound ligand. After
fixing the protein model and water I fitted the ligand into it.
Currently, I am using Phenix Refine with occupancy refinement for
individual atoms switched on. After the refinement, the overall
occupancy of the ligand is 0.7 and the RSCC value is 0.86. The
resolution of the structure is 2.1 Å.

Now the problem is that the program has assigned different
occupancies to different atoms of the ligand. For some cases, it
has assigned 0 occupancies to atoms for which there is a clear
positive peak.

Why it has been done so and is it acceptable?

Any help would be greatly appreciated.

Thank you.

-- 
Best Regards,

Akanksha Tomar
Pre-Doctoral Fellow,
C\o Dr. Arockiasamy Arulandu,
Membrane Protein Biology Group,
International Center for Genetic Engineering and Biotechnology,
New Delhi, India



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-- 
*Wim Burmeister*

Professor
Institut de Biologie Structurale (IBS) CIBB
71 avenue des Martyrs

<https://www.google.com/maps/search/71+avenue+des+Martyrs?entry=gmail=g>
/ CS 20192
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Mobile:  +33 (0) 7 50 49 19 91
website

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Re: [ccp4bb] Co crystalization with less soluble ligand.

[Steven Herron]

Fatty acids are very soluble in glycerol or the PEGs.

Most proteins tolerate high concentrations (30-50%) glycerol and PEGs.� 
So, it is quite possible to make a solution that will allow the protein 
crsytal and the ligand to both be in the same solution.


One of my former colleagues was in charge of dosing mice for drug 
testing.� He often had to get hydrophobic compounds into solution long 
enough to feed the compounds to the mice.


If the key compound is not soluble in the current system, change the 
system.


Some might complain that this is a lot of work (which it might be), but 
that might also be why no one else has done it yet.




On 6/23/2021 5:53 AM, Tim Gruene wrote:

Hi Frank,

heme becomes near completely insoluble when it dimerizes. Fatty acids
are also very insoluble. It is quite hard to get them into HSA, as far
as I remember.

Cheers,
Tim

On Wed, 23 Jun 2021 10:33:42 +0100 Frank von
Delft  wrote:


And then of course, you need to decide whether you at all care to
know anything about a compound that is so insoluble that it needs
that kind of treatment  :)

On 23/06/2021 09:52, hoh wrote:

Hi

As total insolubility does not exist, I regularly use another
method, which is to deposit a grain of the ligand directly into the
drop.

In this case, we no longer control the concentration. The goal is
to regularly freeze crystals (1 hour, 2 days, 1 week ..). Depending
on the results, it is possible to adjust the time. If after one
hour, the crystal no longer diffracts, redo the experience by
freezing at 10s, 30s, 2mn ..). If a blob appears, frozen after 1
week. This technique needs 2 things
, time and several exploitable crystals in the drop.


FH
  



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Re: [ccp4bb] Co crystalization with less soluble ligand.

[Steven Herron]

Dear Gourab,

Sorry for the delayed response, I missed your message earlier.

Can you grow the protein crystals easily (do you have lots of them)?

Is your ligand soluble in PEG, MPD, or Solutol?

Often, you can exchange the crystal solution without destroying the 
crystal.  But, you have to match the water activity of the original 
growth solution with the new solution.  This way you could get your 
ligand into one of these non-salt solutions and then move a crystal from 
your grow solution into the new solution with your ligand.  This would 
expose your crystal to the ligand.


Obviously, you will probably burn through several crystals to see what 
PEG, MPD, of Solutol concentration your crystals will tolerate.  To some 
degree, this is no different than hunting for the best cryo-condition.  
Thus, I would see which solution your ligand prefers first, so you can 
limit your crystal trials.


I worked on an enzyme that required calcium for activity, but we could 
only grow the crystals in ammonium sulfate.  I was able to exchange the 
crystal growth solution for a PEG solution.  The protein has some 
affinity for the sulfate ions, so the exchange needed to be done over a 
~4 hour period of time.  If I went faster, the sulfate would remain in 
the crystal channels and would precipitate when exposed to calcium.  It 
was tedious working this out, but it was essential for everything else 
that came later.


Steven Herron [sherron_...@yahoo.com]


On 4/23/2021 11:40 PM, Gourab Basu Choudhury wrote:
I tried sokaing ,high concentration of DMSO is effecting crystal, so I 
tried other contidtion where 10%DMSO is there. Got 1.9 A data with 
protein co crystalization with 10mM ligand. But ligand occupancy is 
not visble.
 I got the KD value from ITC, with reverse titration. With 10uM ligand 
in cell and 150uM protein in syringe. .


Can anybody suggest some views.please feel free to share your experiences.

On Sat, Apr 24, 2021, 10:49 AM Peat, Tom (Manufacturing, Parkville) 
 wrote:


Hello Gourab,

DMSO is not the only possible solvent- there are others to try.
I don't want to sound negative, but 40 micromolar is not a very
tight binding compound. It would also depend on how that binding
constant was measured- how did someone get enough in solution to
measure that?
Best of luck, tom

Tom Peat, PhD
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au


*From:* CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Gourab Basu Choudhury
mailto:goura...@csiriicb.res.in>>
*Sent:* Saturday, April 24, 2021 12:46 PM
*To:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
mailto:CCP4BB@JISCMAIL.AC.UK>>
*Subject:* [ccp4bb] Co crystalization with less soluble ligand.
Hello everyone,
I am finding it difficult for getting a ligand density inside the
protein as the ligand is very much insoluble. It's only soluble in
100% DMSO. I tried for co crystalization. Kd value of the ligand
is near 40um. Any suggestion what to do?



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Re: [ccp4bb] in crystallo enzymatic activity

[Steven Herron]

Yes, the pH optimum of a reaction can be changed with a mutation of one 
of the catalytic residue or with a neighboring non-catalytic residue.  A 
classic example is the K166R mutation of mandelate racemase.

 see: Biochemistry. 1995 Mar 7;34(9):2788-97
 https://www.ncbi.nlm.nih.gov/pubmed/7893690
 http://pubs.acs.org/doi/pdf/10.1021/bi9a007

When lysine-166 is changed to arginine, one side of the reaction pH 
profile shifts to the basic.  If I remember correctly, the mutation 
causes a 2 pH unit shift of the basic side of the pH reaction profile.


Steven Herron
sherron_...@yahoo.com


On 4/14/2017 1:35 PM, Petri Kursula wrote:

Hi,

apart from the possibilities of conformational flexibility affected by 
crystal packing, just wondering if this mutation is supposed to 
actually cause an increase or decrease in the corresponding activity 
(outside the context of a crystal)? k(cat) and K(M) measured in 
solution would help here. Is the pH in the crystal far from the 
optimum of the wild-type protein? Can optimal pH change with the mutation?


Petri

Petri Kursula
--
Professor
Department of Biomedicine
University of Bergen, Norway
http://www.uib.no/en/rg/petrikursula 
<http://www.uib.no/en/persons/Petri.Kursula>

petri.kurs...@uib.no <mailto:petri.kurs...@biomed.uib.no>
--
Group Leader, Adjunct Professor
Faculty of Biochemistry and Molecular Medicine
University of Oulu, Finland
--



On 13 Apr 2017, at 17:27, Pierre Nioche 
<pierre.nio...@parisdescartes.fr 
<mailto:pierre.nio...@parisdescartes.fr>> wrote:


Dear CCP4bb,

We work on an enzyme that we crystallized with two substrates bound 
in the active site (the reaction transform two substrates into two 
products). We have also the structure with the two products. We are 
able to see densities for the substrates when we collect data at 
different time point post-crystallization (days or weeks later). 
There is no change over time and no in crystallo enzymatic reaction 
despite the fact that in solution using the same crystallization 
solution, the reaction occurs readily.
This is not surprising and there are already many examples in the 
literature.
However, when we crystallize a single amino acid variant (mutant 
within the active site) with the same two substrates, we initially 
see the substrates but we then observe in crystallo enzymatic 
activity and formation of the final products over time. This 
structure is identical to the one determined with the two products 
co-crystallized with the enzyme. The crystal packing does not seem to 
be at play here.
I understand that in crystallo activities are well documented in the 
literature and can be induced by addition of ligands, X-rays, change 
in oxidative environment, etc?
Here, the substrates are present from the beginning of the 
crystallization experiments with the same concentration. Nothing is 
added to the crystals later on. Only the time differentiate the two 
type of crystals: after a couple of weeks, one has the substrates in 
the active site (wt) while the other has the products (variant).


Is anyone aware of similar examples where a variant induce in 
crystallo enzymatic activity without perturbation of the crystal?


Thanks,

Pierre
Dept of Pharmacology, Toxicology and cellular signaling
Paris Descartes University

Re: [ccp4bb] Recommendations for Robotic Crystal Screening Services

[Steven Herron]

Does the Hauptman-Woodward Medical Research Institute have any sample 
data-sets, so we can see what the results look like?




On 4/14/2017 8:58 AM, Edward Snell wrote:


Dear Elizabeth,


The High-Throughput Crystallization Screening Center and the 
Hauptman-Woodward Medical Research Institute has been operating for 
over a decade with considerable success. There are comprehensive 
details at http://getacrystal.org but basically your samples are 
screened against a large range of commercially available conditions 
plus some more unique ones. Video microscope images are provided over 
a period of six weeks or longer by request and the imaging also 
includes SONICC (detecting very tiny crystals or crystals in 
precipitate) and UV-TPEF to ensure the sample is protein. There are a 
large range of analysis tools that can be used on the data. Much of 
the information is provided on the link above. Success rates are 
pretty high and many entries in the PDB have had their initial crystal 
hits there.



I hope this helps, the center does not advertise much but works with a 
lot of laboratories.



Cheers,


Eddie.


Edward Snell Ph.D.

President and CEO Hauptman-Woodward Medical Research Institute

Assistant Prof. Department of Structural Biology, University at Buffalo

700 Ellicott Street, Buffalo, NY 14203-1102

hwi.buffalo.edu 

Phone: (716) 898 8631 Fax: (716) 898 8660

Skype: eddie.snell Email: esn...@hwi.buffalo.edu 



Heisenberg was probably here!




*From:* CCP4 bulletin board  on behalf of 
Elizabeth Diaz 

*Sent:* Friday, April 14, 2017 9:06 AM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] Recommendations for Robotic Crystal Screening 
Services

All,

I am currently attempting to crystallize a peptide/protein complex and 
am wanting to know about robotic screening services that you would 
recommend. We have done some in house conditions with little luck, and 
want to broaden our search, but that would require going externally 
for screening. Do you have any recommendations for robotic crystal 
screening services, preferably in the United States?


Thank you so much,

Elizabeth Diaz
University of Delaware

Re: [ccp4bb] Refining Metal Ion Occupancy

[Steven Herron]

Refining the occupancy will help your R-factor and flatten your density, 
but you need to be careful to also refine the B-factor of the metal 
ion.  Don't refine both the occupancy and the B-factor during the same 
run (the two are correlated at this resolution), refine the occupancy of 
just the metal ion and then refine the B-factor of just the metal ion 
(repeat as needed).  I used X-plor/CNS to do my refinements, so it was 
easy to refine the occupancy (or B-factor) of just the metal ion.  After 
a few rounds of refinement both parameters will stop changing and you 
will have your answer.  The final B-factor of the metal ion should be 
similar to the amino acid residues that are coordinated to it.


Soaking in several different ion concentrations and collecting 
additional datasets is also a good idea (if you have the time).  I did 
this type of experiment once before  (see: JBC 278(14):12271-7. [ Apr 4, 
2003]) (or: http://www.ncbi.nlm.nih.gov/pubmed/12540845).  I soaked in 
several different Ca2+ ion concentrations and was able to determine the 
binding affinity for that calcium ion using crystallography.


To make sure I was not stuck in a local minima, I would modify either 
the occupancy of the B-factor of the metal while keeping the other fixed 
and do a refinement.  I even tried both large and small changes (both 
increases and decreases in value).  It always came back to the earlier 
answer.


Different Ca2+ ion concentrations can give some additional insight into 
the metal binding site.  Between the no-Ca2+ structure and the high-Ca2+ 
structure there was a conserved Asp-residue that changed conformation.  
So, I soaked in the appropriate amount of Ca2+ to see the residue in 
both positions.  There was a high correlation between the asp residue 
orientation and the Ca2+ ion occupancy.


Steven Herron
sherron_...@yahoo.com




On 5/6/2014 11:02 AM, Chris Fage wrote:

Hi Everyone,

In my 2.5-angstrom structure, there is negative Fo-Fc density
surrounding a metal ion after refining in Phenix. From anomalous
diffraction I am certain of the metal's identity and position in each
monomer. Also, the ion is appropriately coordinated by nearby side
chains. Should I be refining the occupancy of the ion in attempt to
flatten the negative density? I am considering soaking the metal ion
into crystals or cocrystallizing and collecting additional datasets.

Thanks for your help!

Regards,
Chris

Re: [ccp4bb] Of topic, trying to identify a reference for multiple crystal data collection

[Steven Herron]

Can you scan the page and submit the image to the bb?

Besides increasing the chance of identifying the source, I am sure I am 
not the only one who is curious to see the mystery page.


Steven Herron


On 7/18/2013 9:29 PM, Edward Snell wrote:

Dear All,

On a beamline visit I came across a photocopy of a table comprising point groups, 
number of random images and the percentage completeness that resulted. The Table is 
labeled 17.1 and the table legend starts with the text Data from randomly 
oriented images. The figures shown are the percentage completeness to 3A resolution. 
These were calculated by predicting reflections from 90 images with randomly 
generated mis-setting angles, arbitrary cell, wavelength of 0.9A and oscillation 
range of 0.4 degree. Only reflections more than 50% recorded were accepted  The 
figures are essentially independent of resolution.

I would very much like to reference this but I don't have any idea where it 
came from other than the number 17.1 suggesting it is a rather large book - 
there were no details on the copy. If you recognize this table and could 
provide the reference I'd be very grateful. If I should have read your book 
where it appeared I apologize! I doubt the board would be interested in this so 
please send me a reply offline.

Thanks.

Eddie

Edward Snell Ph.D.
Assistant Prof. Department of Structural Biology, SUNY Buffalo,
Senior Scientist, Hauptman-Woodward Medical Research Institute
700 Ellicott Street, Buffalo, NY 14203-1102
Phone: (716) 898 8631 Fax: (716) 898 8660
Skype:  eddie.snell Email: esn...@hwi.buffalo.edu
Telepathy: 42.2 GHz

Heisenberg was probably here!

Re: [ccp4bb] atomic coloring for the color blind

[Steven Herron]

David,

Do you know of a program to make accurate braille representations of an 
electron density map :)

That would be cool.

Maybe in the future [See: 
http://www.wired.com/wiredscience/2012/08/smart-fingertips-virtual-senses/ 
http://www.ethlife.ethz.ch/archive_articles/100816_virtuelle_realitaet_cho/index_EN 
  and 
http://www.technologyreview.com/news/428736/disney-researchers-add-virtual-touch-to-the-real-world/] 



For the really hard core scientist (this is a little creepy): 
http://io9.com/5846275/biotech-breakthrough-monkeys-can-feel-virtual-objects-using-a-brain-implant


Food for thought,
Steve
sherron_...@yahoo.com




On 6/1/2013 12:16 PM, David Schuller wrote:

How about Braille for those who are blind to all colours?

Re: [ccp4bb] Freezing crystal (Liquid Propane Crystal Prep)

[Steven Herron]

Jürgen Quote: Propane for whatever reason has gone extinct in certain 
areas of the world :-) .



I went to SSRL (Stanford) with a colleague who wanted to use liquid 
propane.  We had to go through a mound of paper work to get permission 
bring propane on site and set up the experiments.  I don't blame SSRL 
for their safety policy, but I can clearly understand why liquid propane 
is not commonly used.


If you don't think it is much of a danger, you might enjoy: 
http://www.stupidvideos.com/video/stunts/propane_tank/#2974
You might also enjoy:  
http://www.stupidvideos.com/video/stunts/C4_Propane_Explosion/#175408

 Note:  We did not bring any C-4 to SSRL:)

Steve



On 2/7/2012 10:50 AM, Bosch, Juergen wrote:

Hi Dirk,

I remember a neat paper don't recall who wrote it. I think it was in 
Acta D where the authors made a tiny probe the size of an elongated 
crystal glued to a [/Advertisement on] Hampton loop [/Advertisement 
off]. The probe was a temperature sensor and they recorded the cooling 
rate under different methods. The winner as far as I recall was 
freezing in liquid propane for the lack of the missing gas layer, but 
the second best method was LN2. Propane for whatever reason has gone 
extinct in certain areas of the world :-) . I'll try to find that 
reference but perhaps somebody else on this highly educated board 
knows which paper I'm referring to. I want to say it was published 
around 2004-2006.


Jürgen

On Feb 7, 2012, at 11:12 AM, Dirk Kostrewa wrote:


Dear Jürgen,

Am 07.02.12 16:58, schrieb Bosch, Juergen:
snip

Then one last remark, LN2 versus cryo-stream freeze. Dipping in LN2
leads to a quicker freeze of your material.

/snip

Are you sure? There was a publication by Warkentin et al. [1] about a
cold gas layer above liquid nitrogen that reduces the expected cooling
rate a lot!
My very personal experience is, that cryo-cooling in the N2-stream
worked better for me than in LN2 in a variety of projects - but the
reason could just be me ;-)

Best regards,

Dirk.

[1] Matthew Warkentin, Viatcheslav Berejnov, Naji S Husseini, and Robert
E Thorne: Hyperquenching for protein cryocrystallography, J. Appl.
Crystallogr., 39, 805-811 (2006)

--

***
Dirk Kostrewa
Gene Center Munich
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail:kostr...@genzentrum.lmu.de mailto:kostr...@genzentrum.lmu.de
WWW:www.genzentrum.lmu.de
***


..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry  Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-2926
http://web.mac.com/bosch_lab/




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Re: [ccp4bb] X-Ray films

[Steven Herron]

The Race for the Double Helix (2004)
http://www.amazon.com/Race-Double-Helix-VHS-Pigott-Smith/dp/6303247911/ref=sr_1_1?ie=UTF8s=dvdqid=1271365899sr=1-1
When crystallography was on FILMS not CCD's:) 





Eva Kirchner wrote:


favourite movies involving real science

The Dark Crystal (1982)!

(Crystallography is voodoo, voodoo is magic, magic is fantasy, therefore 
fantasy is science, and this movie involves science. Ha!)

It tells you what awful consequences arise if you break a crystal.

;-)


Am 15.04.2010 um 22:07 schrieb Brock Schuman:

 


Wrath
of
Khan

On Thu, Apr 15, 2010 at 11:42 AM, Chayne Piscitelli pisci...@ohsu.edu wrote:
   


The documentary Naturally Obsessed: The Making of a Scientist
is definitely a must-see film.  It captures the story of life and
science in a crystallography lab, that of Dr. Larry Shapiro at Columbia
University, and follows the graduate students journey of fortune
and misfortune that crystallographers know so well.  Not to sound too sappy
about it, but it is almost like a coming of age story for graduate
students

Check it out:
http://naturallyobsessed.com/

-Chayne Piscitelli


From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of Brad Bennett
[bradbennet...@gmail.com]
Sent: Thursday, April 15, 2010 9:43 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] X-Ray films

Hi Harry-
X-ray crystallography played an integral part in discoveries made in Michael
Crichton's Andromeda Strain. Mainly it was used to determine the elemental
composition and arrangement of the capsid or shell that the foreign
organism was found within.

Best-
Brad

On Thu, Apr 15, 2010 at 12:16 PM, harry powell ha...@mrc-lmb.cam.ac.uk
wrote:
 


Hi

Not a question about films for recording X-rays on, but a question about
films about X-rays, Crystallography and related subjects!

I was wondering what ccp4bbers favourite movies involving real science,
especially crystallography might be? If they're from Hollywood, though, I'd
guess it should be favorite...

I'm a little tired, but the only one I can think of at the moment is
actually based on results from fibre diffraction - Life Story, with Jeff
Goldblum. There must be others, though.

Harry
--
Dr Harry Powell,
MRC Laboratory of Molecular Biology,
Hills Road,
Cambridge,
CB2 0QH
   

 



--
---
---
Brock Schuman, Graduate Student
Department of Biochemistry  Microbiology
University of Victoria
PO Box 3055 STN CSC
Victoria, BC, V8W 3P6
CANADA

tel:   250-721-8945
FAX:250-721-8855
   



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Dr. Eva Kirchner
Unité de Virologie Structurale
Département de Virologie
Institut Pasteur
25, rue du Dr Roux
75015 Paris
France
Phone: +33 (0)1 45 68 82 87
Email: eva.kirch...@pasteur.fr