Re: [ccp4bb] Another paper & structure retracted

[Ibrahim Moustafa]

But, the mistakes in the retracted work could have been avoided easily if
the person did the structure spent some efforts to understand/know what
he/she is doing! or if the authors asked for some help from professionals.

  Ibrahim
-- 

Ibrahim M. Moustafa, Ph.D.
Biochemistry and Molecular Biology Dept.
201 Althouse Lab., University Park,
Pennsylvania State University
PA 16802

Tel. (814) 863-8703
Fax (814) 865-7927



On 8/11/11 4:33 PM, "Maia Cherney"  wrote:

> As the macromolecular crystallography becomes more automated and
> user-friendly many biologists learn to solve structures and they can
> make mistakes. Besides, new data become available that can give new
> ideas etc. I don't think that's so horrible to make an honest mistake
> and retract papers. Even great scientists sometimes published papers
> with wrong analysis.
> 
> Maia
> 
> On 11/08/2011 1:05 PM, Judith Murray-Rust wrote:
>> Just another point -  the macromolecular community are not the only ones with
>> a problem - I've just been shown
>> http://retractionwatch.wordpress.com/
>> which sheds some light on retractions. And also maybe says something about
>> why original data should be available/part of the  review process.
>> J
>> 
>> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gloria
>> Borgstahl [gborgst...@gmail.com]
>> Sent: 11 August 2011 19:32
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] Another paper&  structure retracted
>> 
>> Dale, This is exactly the conversation  I just had with my student Jason,
>> right on!
>> The paper we are writing just now, this is figure 1.
>> But I always get rejected by Nature, so go figure.
>> On Thu, Aug 11, 2011 at 1:25 PM, Dale
>> Tronrudmailto:det...@uoxray.uoregon.edu>>  wrote:
>>I agree with Prof. Tomchick: if the point of your paper is your crystal
>> structure of
>> the binding of a ligand to a protein you should include a figure with the
>> omit map
>> (displayed without a "cover radius") that convinced you that binding took
>> place.  I
>> prefer that map over some simulated, after-the-fact, omit map calculated just
>> for
>> publication.
>> 
>>This is not simply a matter for reviewers to be gatekeepers, it is
>> important for the
>> readers to know what level of confidence to place in this result, and it is
>> instructional
>> for everyone to see what ligand binding density looks like.  Apparently some
>> people don't
>> know what features to look for to distinguish between signal and noise.
>> 
>> Dale Tronrud
>> 
>> On 08/11/11 09:40, Diana Tomchick wrote:
>>> A quick glance at the header of the PDB file shows that there is one glaring
>>> discrepancy between it and the table in the paper that hasn't been mentioned
>>> yet in this forum. The data completeness (for data collection) reported in
>>> the paper is 95.7%, but in the header of the PDB file (actually, in both the
>>> 2QNS and the 3KJ5 depositions) the data completeness (for data collection)
>>> is reported as only 59.4%. The PDB header also contains an inconsistency,
>>> with the data completeness (for refinement) reported as 95.7%. Since the
>>> numbers of reflections reported for refinement versus data collection in the
>>> PDB header differ by less than 1%, it appears that there's been a bit of
>>> magical thinking that took place somewhere along the process from data
>>> processing to final model refinement. Small wonder that the refined geometry
>>> is so poor. Perhaps if these scientists had actually collected a complete
>>> dataset, we would not be having this conversation.
>>> 
>>> Diana
>>> 
>>> P.S. I have, on occasion, provided the coordinates and a map file to
>>> reviewers when they requested it. The last time it was requested was many
>>> years ago; I decided it was safer and easier if I provided as much
>>> information as possible in the manuscript (including better quality electron
>>> density figures than appear in this paper) to allow the reader to determine
>>> whether the work is valid or not.
>>> 
>>> * * * * * * * * * * * * * * * * * * * * * * * * * * * *
>>> Diana R. Tomchick
>>> Associate Professor
>>> University of Texas Southwestern Medical Center
>>> Department of Biochemistry
>>> 5323 Harry Hines Blvd.
>>> Rm. ND10.214B
>>> Dallas, TX 75390-8816, U.S.A.
>>> Email: diana.tomch...@utsouthwestern.edu
>>> 214-645-6383  (phone)
>>> 214-645-6353  (fax)
>>> 
>>> 
>>> 
>>> On Aug 10, 2011, at 5:45 PM, Dale Tronrud wrote:
>>> 
I've made a quick look at the model and the paper - and it doesn't
 need more than a quick look.  The description of the model in
 the paper sounds great.  The problems in the model are clear.  My
 favorite is the quote "Trp-477 of PTH1R makes several van der Waals
 contacts with Trp-339 and Lys-337 of G-beta-1 ...".  They are "contacts"
 all right.  The distances between the 477:CH2 and 337:CE is 2.75 A
 and between 477:NE1 and 339:CH2 is 2.26 A.  There are many more.
 
 

Re: [ccp4bb] Mg2+ or water

[Ibrahim Moustafa]

I agree. It is very unlikely to be Magnesium ion; may be an ordered water!

 I'd recommend to have a look at the following paper which discusses the
different properties of Mg2+, Mn2+, and Zn2+.

   Charles W. Bock, Amy Kaufman Katz, George D. Markham, and Jenny P.
Glusker. Manganese as a replacement for Magnesium and Zinc: Functional
comparison of the divalent ions. (J. Am. Chem. Soc. 1999, 121, 7360-7372)

   Ibrahim

On 12/20/10 6:14 PM, "Dima Klenchin"  wrote:

>> Sorry, the attachment is in here.
> 
> Doesn't look like Mg2+ at all. Distances are too long, Mg is never
> coordinated by amides and if it were Mg you would have seen waters around it.
> 
> Looks like tightly bound water to me.
> 
> - Dima
> 
> 
> 
>> On Mon, Dec 20, 2010 at 4:16 PM, jlliu liu
>> <jlliu20022...@gmail.com> wrote:
>> Hi All,
>> 
>> I am refining a structure and encountered a problem of modeling a
>> difference density as water or Mg2+, and would like to hear opinions from
>> the community. It has the following coordinations (attached): the
>> water/Mg2+ forms salt bridge/H-bonding interaction with a carboxylate
>> group from the ligand, it also forms salt bridge/H-bonding interaction
>> with a Glu residue from the protein, it is also within hydrogen bonding
>> distance to the main chain N of another protein residue. In provious
>> publication, it was modelled as a Mg2+ and the author reasoned the dual
>> salt-bridge stabilizes the liganding binding, also the Mg2+ is present in
>> the protein solution for crystallization. For my case, I have no Mg2+
>> present in the protein buffer, also modelling it with water refines
>> perfectly with no indication of positive difference density even at 2.0
>> sigma cut off. Should I modelled this density as water or as Mg2+. Your
>> opinions are appreciated.
>> 
>> JL
>> 
>> 
>> 
>> Content-type: image/png; name=367-mgtest.png
>> Content-disposition: attachment; filename=367-mgtest.png
>> X-Attachment-Id: f_ghy0k5e31
>> 
> 

Re: [ccp4bb] Fwd: regarding purification of DNA binding protein

[Ibrahim Moustafa]

Hi Arpit,

 You can use PEI (polyethyleneimine). Adding PEI at low conc. (e.g. 0.25%)
after cell lysis should precipitate most of the DNA. Note, it is best to do
the addition step-wise at 4 deg with gentle steering over a period of time
10-15 min or so.

  Ibrahim


On 5/12/10 10:20 AM, "Tim Gruene"  wrote:

> Hello Arpit,
> 
> don't you use DNAse during lysation of the cells? Or do you mean that you want
> to get rid of unspecific DNA and want to add some specific DNA after
> purification? In that case I'd understand you don't want to use DNAse.
> 
> Tim
> On Wed, May 12, 2010 at 06:23:56PM +0530, Arpit Mishra wrote:
>> -- Forwarded message --
>> From: Arpit Mishra 
>> Date: Wed, May 12, 2010 at 6:20 PM
>> Subject: regarding purification of DNA binding protein
>> To: ccp...@jiscmail.ac
>> 
>> 
>> hi all
>> i am trying to purify DNA binding protein, but i couldnt get rid of the DNA
>> after performing hi-trap heparin column, i have also tried high conc salt
>> buffer (upto 1 M NaCl) and also tried o.2 M lithium sulphate, please suggest
>> me some way to get rid of undesired DNA..
>> 
>> thanks
>> 
>> Regards
>> 
>> Arpit

Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....

[Ibrahim Moustafa]

You are absolutely right, more information describing to what extents these
structures were falsified will be valuable to the community. Actually, it
will be more useful if the investigators can publish their report as an
article in Acta D (as a case study for tracking falsified structures).

  I have a suggestion (actually a request) to the expertise in the field to
write a kind of review article about "sources of error in crystallography
and how to hunt these errors". It will be even better if it is written
considering the non-crystallographers (scientists who use the structural
information - like the co-authors on structural papers). This will help to
educate the non-crystallographers how to look at the structures critically.

  Ibrahim

-- 

Ibrahim M. Moustafa, Ph.D.
Biochemistry and Molecular Biology Dept.
201 Althouse Lab., University Park,
Pennsylvania State University
PA 16802

Tel. (814) 863-8703
Fax (814) 865-7927



  


On 12/11/09 4:19 AM, "Tommi Kajander"  wrote:

> Would the exact analysis of how each of these things were wrong and
> fabricated be somewhere
> available Would be fair (apart from the known case of C3b) to have
> the whole analysis available
> instead of just this kind of news feed. I suspect its not obvious by
> five minute check in all cases.
> 
> Perhaps there needs to be ways within PDB in form of automated tools
> that would raise those red
> flags in suspicious cases (e.g. some data analysis --such as the
> contribution by solvent etc now that data beyond 8Å
> is by default used in refinement) - as it appears peer review/editing
> by journals isn't/cant always be(?) stringent enough.
> 
> In any case, some type of  automated analysis of the whole data base
> might be a good idea, as there can be
> other cases (with another couple of thousand papers citing them..).
> 
> tommi
> 
> On Dec 10, 2009, at 4:16 PM, Ibrahim Moustafa wrote:
> 
>> "After a thorough examination of the available data, which included a
>> re-analysis of each structure alleged to have been fabricated, the
>> committee
>> found a preponderance of evidence that structures 1BEF, 1CMW,
>> 1DF9/2QID,
>> 1G40, 1G44, 1L6L, 2OU1, 1RID, 1Y8E, 2A01, and 2HR0 were more likely
>> than not
>> falsified and/or fabricated and recommended that they be removed
>> from the
>> public record," the university said in its statement this week."
> 
> 

[ccp4bb] FW: pdb-l: Retraction of 12 Structures

[Ibrahim Moustafa]

Hi all,

   I want to share the following e-mail received from pdb-l.

  It is sad to see something like that!

  regards,
 Ibrahim


-- Forwarded Message
From: Michael Sadowski 
Date: Thu, 10 Dec 2009 04:22:28 -0800 (PST)
To: 
Subject: pdb-l: Retraction of 12 Structures

Dear All, 

Better check your data!

Apologies to those who have seen this.

S. 

-

"The University of Alabama at Birmingham has issued a statement indicating
that a former UAB researcher may have fabricated or falsified data about
protein structures that are contained in the Protein Data Bank.

The university did not include a name of the researcher, but the Birmingham
News this week reported that the scientist is H.M. Krishna Murthy and an
independent review by BioInform of the PDB shows that Murthy is associated
with all of the proteins that UAB said were falsified.

The newspaper said that a probe of Murthy's research has been underway since
2007.

"After a thorough examination of the available data, which included a
re-analysis of each structure alleged to have been fabricated, the committee
found a preponderance of evidence that structures 1BEF, 1CMW, 1DF9/2QID,
1G40, 1G44, 1L6L, 2OU1, 1RID, 1Y8E, 2A01, and 2HR0 were more likely than not
falsified and/or fabricated and recommended that they be removed from the
public record," the university said in its statement this week."

-
http://www.genomeweb.com/informatics/university-alabama-says-researcher-fabr
icated-protein-structures-now-protein-dat?utm_source=feedburner&utm_medium=f
eed&utm_campaign=Feed%3A+genomeweb%2Fbioinform+%28BioInform%29


http://main.uab.edu/Sites/reporter/articles/71570/

http://blog.al.com/birmingham-news-stories/2009/12/ex-uab_researchers_work_m
ay_be.html


  

TO UNSUBSCRIBE OR CHANGE YOUR SUBSCRIPTION OPTIONS, please see
https://lists.sdsc.edu/mailman/listinfo.cgi/pdb-l .


-- End of Forwarded Message

Re: [ccp4bb] Definition of salt bridge

[Ibrahim Moustafa]

Hi Nader,

By significant, I mean those interactions that withstand the normal
structural fluctuations of the structure. In MD simulation, two ion-pairs at
a distance of 8 A won't stay for long and will disappear early during the
simulation. So, they cannot be considered as non-bonded interactions that
stabilize certain conformation. If you consult any computational chemistry
paper you won't find any quoted salt-bridges at 8 A distance.

  Ibrahim




On 10/16/08 1:58 PM, "Nadir T. Mrabet" <[EMAIL PROTECTED]>
wrote:

> The problem lies with your definition of "significant".
> If it is non null, then any interaction is significant (dual-pan balance
> concept).
> Coulomb's energy is a function of 1/r^2, therefore at 8 Angs, it is
> still 15% of Emax.
> Even H-bonds are sometimes considered relevant up to 5 Angs.
> 
> Nadir Mrabet
> 
> Pr. Nadir T. Mrabet
> Cellular & Molecular Biochemistry
> INSERM U-724
> Nancy University, School of Medicine
> 9, Avenue de la Foret de Haye, BP 184
> 54505 Vandoeuvre-les-Nancy Cedex
> France
> Phone: +33 (0)3.83.68.32.73
> Fax:   +33 (0)3.83.68.32.79
> E-mail: [EMAIL PROTECTED]
> 
> 
> 
> 
> Ibrahim Moustafa wrote:
>> Yes, it is electrostatic interaction. But when searching for a salt-bridge
>> in a protein structure it won't be considered a significant non-bonded
>> interactions at 8 A distance. Also, the electrostatic interaction extends
>> beyond 8 A. For a significant interaction the distance need to be < 8A.
>> 
>>   Ibrahim
>> 
>> 
>> On 10/16/08 12:10 PM, "Nadir T. Mrabet" <[EMAIL PROTECTED]>
>> wrote:
>> 
>>   
>>> --
>>> 
>>> Pr. Nadir T. Mrabet
>>> Cellular & Molecular Biochemistry
>>> INSERM U-724
>>> Nancy University, School of Medicine
>>> 9, Avenue de la Foret de Haye, BP 184
>>> 54505 Vandoeuvre-les-Nancy Cedex
>>> France
>>> Phone: +33 (0)3.83.68.32.73
>>> Fax:   +33 (0)3.83.68.32.79
>>> E-mail: [EMAIL PROTECTED]
>>> 
>>> 
>>> Hi,
>>> 
>>> Salt bridges (or ion pairs) can be long-range (up to 7-8 Ang). They obey
>>> Coulomb's law.
>>> In contrast, H-bonds are short-range and are further anisotropic.
>>> 
>>> For those with general interest in electrostatics, I suggest to go back
>>> to the
>>> 1978 paper of Max Perutz:
>>> Electrostatic Effects in Proteins
>>> Science (1978) 201 (4362), 1187-1191.
>>> 
>>> Nadir Mrabet
>>> 
>>> Jayashankar wrote:
>>> 
>>>> Dear Fransico,
>>>> 
>>>> *Salt bridges are close range electrostatic interaction which depend
>>>> on conformer population.
>>>> 
>>>> *S.Jayashankar
>>>> Research Student
>>>> Institute for Biophysical Chemistry
>>>> Hannover Medical School
>>>> Germany.
>>>> 
>>>> 
>>>> On Thu, Oct 16, 2008 at 8:21 AM, Chavas Leo <[EMAIL PROTECTED]
>>>> <mailto:[EMAIL PROTECTED]>> wrote:
>>>> 
>>>> Dear Francisco --
>>>> 
>>>> On 15 Oct 2008, at 17:05, Francisco J. Enguita wrote:
>>>>   
>>>>> how
>>>>> 
>>>>> can you define a salt-bridge within a protein structure ?
>>>>> 
>>>>> 
>>>> According to Wikipedia:
>>>> a salt bridge in proteins is "a relatively weak ionic bond between
>>>> positively and negatively charged side-chains of proteins."
>>>> 
>>>> Now, at far as I understand (based on "Structure and Mechanism in
>>>> Protein Science - Alan Fersht), you have a salt bridge when two
>>>> groups are making an hydrogen bond that is favored by
>>>> electrostatic interaction, electrostatic energies being weak in
>>>> water. To quote the author of the book, let say you have the
>>>> following equilibrium:
>>>> 
>>>> E-NH3+  ---  OH2   +   OH2  ---  -O2C-S  <==>  E-NH3+
>>>>  ---  -O2C-S   +   H2O  ---  H2O
>>>> 
>>>> The right-hand side equation would be more "favorable", as the
>>>> electrostatic interaction will be more stable than in the
>>>> left-hand side where both ions would be in contact with water
>>>> molecules.
>>>> 
>>>> HTH
>>>> 
>>>> Kind regards.
>>>> 
>>>> -- Leo --
>>>> 
>>>> Chavas Leonard, Ph.D. @ home
>>>> Research Associate
>>>> Marie Curie Actions Fellow
>>>> 
>>>> Faculty of Life Sciences
>>>> The University of Manchester
>>>> The Michael Smith Building
>>>> Oxford Road
>>>> Manchester Lancashire
>>>> M13 9PT
>>>> 
>>>> Tel: +44(0)161-275-1586
>>>> e-mail: [EMAIL PROTECTED]
>>>> <mailto:[EMAIL PROTECTED]>
>>>> http://personalpages.manchester.ac.uk/staff/leonard.chavas/
>>>> 
>>>> 
>>>> 
>>>>   
>> 
>> 
>>   
> 
> 

Re: [ccp4bb] Definition of salt bridge

[Ibrahim Moustafa]

Yes, it is electrostatic interaction. But when searching for a salt-bridge
in a protein structure it won't be considered a significant non-bonded
interactions at 8 A distance. Also, the electrostatic interaction extends
beyond 8 A. For a significant interaction the distance need to be < 8A.

  Ibrahim


On 10/16/08 12:10 PM, "Nadir T. Mrabet" <[EMAIL PROTECTED]>
wrote:

> --
> 
> Pr. Nadir T. Mrabet
> Cellular & Molecular Biochemistry
> INSERM U-724
> Nancy University, School of Medicine
> 9, Avenue de la Foret de Haye, BP 184
> 54505 Vandoeuvre-les-Nancy Cedex
> France
> Phone: +33 (0)3.83.68.32.73
> Fax:   +33 (0)3.83.68.32.79
> E-mail: [EMAIL PROTECTED]
> 
> 
> Hi,
> 
> Salt bridges (or ion pairs) can be long-range (up to 7-8 Ang). They obey
> Coulomb's law.
> In contrast, H-bonds are short-range and are further anisotropic.
> 
> For those with general interest in electrostatics, I suggest to go back
> to the
> 1978 paper of Max Perutz:
> Electrostatic Effects in Proteins
> Science (1978) 201 (4362), 1187-1191.
> 
> Nadir Mrabet
> 
> Jayashankar wrote:
>> Dear Fransico,
>> 
>> *Salt bridges are close range electrostatic interaction which depend
>> on conformer population.
>> 
>> *S.Jayashankar
>> Research Student
>> Institute for Biophysical Chemistry
>> Hannover Medical School
>> Germany.
>> 
>> 
>> On Thu, Oct 16, 2008 at 8:21 AM, Chavas Leo <[EMAIL PROTECTED]
>> > wrote:
>> 
>> Dear Francisco --
>> 
>> On 15 Oct 2008, at 17:05, Francisco J. Enguita wrote:
>>> 
>>> how
>>> 
>>> can you define a salt-bridge within a protein structure ?
>>> 
>> 
>> According to Wikipedia:
>> a salt bridge in proteins is "a relatively weak ionic bond between
>> positively and negatively charged side-chains of proteins."
>> 
>> Now, at far as I understand (based on "Structure and Mechanism in
>> Protein Science - Alan Fersht), you have a salt bridge when two
>> groups are making an hydrogen bond that is favored by
>> electrostatic interaction, electrostatic energies being weak in
>> water. To quote the author of the book, let say you have the
>> following equilibrium:
>> 
>> E-NH3+  ---  OH2   +   OH2  ---  -O2C-S  <==>  E-NH3+
>>  ---  -O2C-S   +   H2O  ---  H2O
>> 
>> The right-hand side equation would be more "favorable", as the
>> electrostatic interaction will be more stable than in the
>> left-hand side where both ions would be in contact with water
>> molecules. 
>> 
>> HTH
>> 
>> Kind regards.
>> 
>> -- Leo --
>> 
>> Chavas Leonard, Ph.D. @ home
>> Research Associate
>> Marie Curie Actions Fellow
>> 
>> Faculty of Life Sciences
>> The University of Manchester
>> The Michael Smith Building
>> Oxford Road
>> Manchester Lancashire
>> M13 9PT
>> 
>> Tel: +44(0)161-275-1586
>> e-mail: [EMAIL PROTECTED]
>> 
>> http://personalpages.manchester.ac.uk/staff/leonard.chavas/
>> 
>> 
>> 
> 

Re: [ccp4bb] Definition of salt bridge

[Ibrahim Moustafa]

Hi,

You can find more information about salt-bridges in the following
references:

 1) Ion-pairs in Proteins. JMB, 168, 867-885 (1983) - Thornton
2) Investigation of Salt Bridge Stability in a Generalized Born solvent
model. JCTC, 2, 115-127 (2006) - Carlos Simmerling
3) Evaluation of Salt Bridge structure and energetics in peptides. JCTC, 4,
2008 (2008) - Carlos Simmerling

   Salt bridge can be defined as the interaction involving charged groups in
the protein. You¹ll find the cutoff distance to define the salt bridge in a
protein structure varies, but definitely > 3.5 A (used for H-bonds). Using a
cutoff distance of 4.0 A might be too strict and 6.0 A would be too
generous. Something in-between like 4.5 A sounds reasonable.

  The energy of Salt-bridge varies depending on the medium (whether buried
or external). For buried salt bridge the energy can be as high as 30 kJ/mol
(compare to H-bonding of 2 ­ 6 kJ/mole).

 It should be mentioned that Petsko in his ³Protein Structure and Function²
made a distinction between long-range electrostatic interaction between
charged groups and the salt-bridge. He considered the salt bridge as a
strong H-bond between two charged groups (cutoff < 3.5 A, typical distance
2.8 A). 

  But in most of the papers (computational chemistry papers) you will find
the salt bridge defined as mentioned above with variable cutoff distance.

  HTH,
 Ibrahim 


On 10/16/08 10:39 AM, "Jayashankar" <[EMAIL PROTECTED]> wrote:

> Dear Fransico,
> 
> Salt bridges are close range electrostatic interaction which depend on
> conformer population.
> 
> S.Jayashankar 
> Research Student 
> Institute for Biophysical Chemistry
> Hannover Medical School
> Germany.
> 
> 
> On Thu, Oct 16, 2008 at 8:21 AM, Chavas Leo <[EMAIL PROTECTED]> wrote:
>> Dear Francisco --
>> 
>> On 15 Oct 2008, at 17:05, Francisco J. Enguita wrote:
>>> how
>>>  
>>> 
>>> can you define a salt-bridge within a protein structure ?
>>>  
>> 
>> According to Wikipedia:
>> a salt bridge in proteins is "a relatively weak ionic bond between positively
>> and negatively charged side-chains of proteins."
>> 
>> Now, at far as I understand (based on "Structure and Mechanism in Protein
>> Science - Alan Fersht), you have a salt bridge when two groups are making an
>> hydrogen bond that is favored by electrostatic interaction, electrostatic
>> energies being weak in water. To quote the author of the book, let say you
>> have the following equilibrium:
>> 
>> E-NH3+  ---  OH2   +   OH2  ---  -O2C-S  <==>  E-NH3+  ---
>> -O2C-S   +   H2O  ---  H2O
>> 
>> The right-hand side equation would be more "favorable", as the electrostatic
>> interaction will be more stable than in the left-hand side where both ions
>> would be in contact with water molecules.
>> 
>> HTH
>> 
>>  
>> Kind regards.
>> 
>> -- Leo --
>> 
>> Chavas Leonard, Ph.D. @ home
>> Research Associate
>> Marie Curie Actions Fellow
>> 
>> Faculty of Life Sciences
>> The University of Manchester
>> The Michael Smith Building
>> Oxford Road
>> Manchester Lancashire
>> M13 9PT
>> 
>> Tel: +44(0)161-275-1586
>> e-mail: [EMAIL PROTECTED]
>> http://personalpages.manchester.ac.uk/staff/leonard.chavas/
>> 
>>  
>> 
> 
> 

Re: [ccp4bb] Your opinion about the attached diffraction pattern

[Ibrahim Moustafa]

Hi All,

   Many thanks for those who shared their inputs. And sorry for not giving
more information about how the crystal was tested in the first instance.

   The posted diffraction was obtained using the local resource (new
installed x-ray generator and new CCD Saturn 944+).
The Crystal to detector distance was ³50² with 10 min. exposure. The crystal
was mounted directly into the Cryo stream.

  From the response I got, I think the crystal is a mix of protein and salt
(it is bitty). 
I should try plunging the crystal in Liq. N2 rather than direct mounting in
the cryo stream. 
Further to what mentioned by Jose, I should say that I can see spots below
15 A resolution (not that clear in the posted picture).

 Again, thanks for your inputs...I¹ll keep trying to move away form this
salty crystal.

  Thanks,
 Ibrahim 



On 4/3/08 3:58 PM, "Ibrahim Moustafa" <[EMAIL PROTECTED]> wrote:

> Dear CCP4 users,
> 
>I¹m trying to crystallize a a small protein, 200 aa. Screening showed one
> promising hits which was further optimized by additive screen.
> Finally a beautiful crystal was obtained from conditions: 30% PEG4000 + 0.2 M
> Ammonium sulfate + 10 mM LaCl3. I was optimistic that the crystal
> Is a protein not a salt as the salt conc. is low in the crystallization buffer
> and LaSO4 would be soluble if it is formed. However, testing the
> Crystal on the local source showed a weird diffraction pattern, see the
> attached picture. It is clear that the crystal has a salt, from the strong
> Spots in the diffraction, also depending on the rotation angle, some images
> showed a clear salt. On the other hand there are closer spots
> Suggesting the presence of proteins (may be fibrous). Washing few crystals and
> running a gel revealed the presence of the protein.
> 
> My question is what could be the diffracting object that gave the attached
> pattern? Could it be a salt crystal with a non-ordered protein inside?!
> If it is the case, has any body went through the same experience and got
> success to optimize the condition to get real protein crystal?
> I¹d be appreciated if people want to share their experience and to see what do
> they think of the pattern in the attached pic.
> 
>Thanks in advance for your shared thought.
> 
>   Best,
>  Ibrahim