Re: [ccp4bb] Crystals Disappearing Overnight
*** This message has been scanned by the InterScan for CSC SSM by IICT security policy and found to be free of known security risks. *** Maria, From my experience with co-crystallization experiments, if crystals appear immediately after setting up the drop in presence of small molecules, they most likely are crystals of small molecules and not of protein. Since you have 8% 8K PEG, initially the solution is heterogeneous with pockets of high viscosity that will precipitate the small molecules. Over the period of time, solution becomes homogenous that may dissolve the crystals. To rule out this, set up two crystallization experiments under similar conditions. 1) only the protein 2) only the adenosine Regards Anthony - Dr. Anthony Addlagatta Center for Chemical Biology Indian Institute of Chemical Technology [IICT] Tarnaka, Hyderabad AP-500 607, INDIA Tel:91-40-27191812 Web: https://sites.google.com/site/chembioliict/home/dr-anthony-addlagatta-1 -- Original Message --- From: dusky dew duskyde...@gmail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Wed, 7 May 2014 00:52:22 -0700 Subject: Re: [ccp4bb] Crystals Disappearing Overnight *** This message has been scanned by the InterScan for CSC SSM at IICT and found to be free of known security risks. *** I tried microbatch and the crystals are not stable. They dissolve overnight. I also have reproducibility issue. Can this be due to poor stability of adenosine? Best Maria On Monday, May 5, 2014, Bob Cudney b...@hrmail.com wrote: Try the microbatch first to see if the problem is related to ionic strength. When possible and practical it is good to change only one variable at a time to identify cause and effect. Kind Regards, Bob Cudney Hampton Research 34 Journey Aliso Viejo, CA 92656-3317 USA Telephone 1 949 425 1321 Extension 200 Fax 1 949 425 1611 E-mail b...@hrmail.com Web www.hamptonresearch.com From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of dusky dew Sent: Saturday, May 03, 2014 1:29 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Crystals Disappearing Overnight Thank you all for getting back! I will set up the drops using microbatch method. Regarding the temp, I set them up in lab and put them in incubator. The lab temp may be slightly higher. So are they not stable at lower temp? Or its the shock? So how can I take care of the temp issue? Thanks again! Maria On Saturday, May 3, 2014, Bob Cudney b...@hrmail.com wrote: Hello Maria, Check to see if there might have been a temperature change between the time the crystals were present and when the crystals disappeared. If your sample has temperature dependent solubility, in this relatively low ionic strength condition, a temperature change could mean the difference between the presence and absence of crystals. That being said, if the experiment is returned to the temperature that produced the crystals, the crystals should/might reappear. If your drop is made by mixing 1 part of protein with 1 part of reagent the initial drop concentration would be 10 mM Tris, 150 mM NaCl, 2.5% w/v PEG 8,000, 50 mM Sodium cacodylate. Is this a vapor diffusion experiment? If yes, then the reservoir would be 5% w/v PEG 8,000, 100 mM Sodium cacodylate. The ionic strength of your drop would initially be higher than the ionic strength in your reservoir. This means water vapor leaves the reservoir and vapor diffuses into the drop, lowering the protein and reagent concentration in your drop. This decrease in relative supersaturation could dissolve a crystal. Your set up would be a reserve vapor diffusion. You say the crystals appeared right after setting the experiment so your crystallization is essentially a batch experiment. Therefore you might want to change your set up from a vapor diffusion to a microbatch experiment under oil. If you need more information about how to perform a microbatch experiment, let me know and I’ll explain. Hope this helps. Kind Regards, Bob Cudney Hampton Research 34 Journey Aliso Viejo, CA 92656-3317 USA Telephone 1 949 425 1321 Extension 200 Fax 1 949 425 1611 E-mail b...@hrmail.com Web www.hamptonresearch.com From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of dusky dew Sent: Friday, May 02, 2014 4:39 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Crystals Disappearing Overnight Dear All, I am trying to crystallize a protein with Adenosine. My protein is in 20 mM Tris, 300 mM NaCl and the crystals appear in a condition with 5 percent PEG8K, 0.1 M Sodium Cacodylate. The protein is incubated with adenosine for 1/2 hr before setting the drop. The crystals appear
Re: [ccp4bb] AW: [ccp4bb] protein polymerization
*** This message has been scanned by the InterScan for CSC SSM by IICT security policy and found to be free of known security risks. *** Dear Lisa, Good think is that your protein is crystallizing and diffracting X-rays. I am not sure if your protein is polymerizing. This could be a simple precipitation. Please check your pH, salt conditions or if you require some co-factors etc in addition to checking with bME as suggested by Herman. Anthony - Dr. Anthony Addlagatta Center for Chemical Biology Indian Institute of Chemical Technology [IICT] Tarnaka, Hyderabad AP-500 607, INDIA Tel:91-40-27191812 Web: https://sites.google.com/site/chembioliict/home/dr-anthony-addlagatta-1 -- Original Message --- From: herman.schreu...@sanofi.com To: CCP4BB@JISCMAIL.AC.UK Sent: Mon, 17 Feb 2014 10:06:18 + Subject: [ccp4bb] AW: [ccp4bb] protein polymerization *** This message has been scanned by the InterScan for CSC SSM at IICT and found to be free of known security risks. *** Dear Lisa, the first thing to check is whether the polymerization is due to disulfide bond formation. If you run a gel of your protein with one sample boiled in the presence of b-mercapto ethanol and one sample boiled in the absence of bME, this should tell you whether disulfide links are the culprit. If disulfide links are the problem you could try adding DTT or TCEP to all your buffers, or to mutate the suspicious cysteines away. Good luck! Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von LISA Gesendet: Montag, 17. Februar 2014 10:58 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] protein polymerization Dear All, My proein is polymerzated and elutate in the void volum when runnning gel filtration Superdex 200. I can get a small crystal after a lot of optimization. But the resolution is still very low (about 8A ). I try to find the sites involved in polymerization. Is there some software to predicat the amino acids which are involved in protein polymerization? And All suggestion to the crystal optimization are welcome. Thank you. Best Regards, Lisa --- End of Original Message --- - Note: The information contained in the e-Mail message and/or attachments to it may contain confidential or privileged information. If you are not the intended recipient, any dissemination, use, review, distribute, prinitng or copying of the information contianed in this e-Mail message and/or attachments to it are strictly prohibited. If you have received this communication in error. Please notify us by reply e-Mail or telephone and immediately and permanently delete the message and any attachment. Thank you.
Re: [ccp4bb] unexplained density
*** This message has been scanned by the InterScan for CSC SSM by IICT security policy and found to be free of known security risks. *** Dear Annemarie, This could be a reaction product of the PMSF with either tris or alanine (as you have modeled, but you should know the source). Anthony - Dr. Anthony Addlagatta Center for Chemical Biology Indian Institute of Chemical Technology [IICT] Tarnaka, Hyderabad AP-500 607, INDIA Tel:91-40-27191812 Web: https://sites.google.com/site/chembioliict/home/dr-anthony-addlagatta-1 -- Original Message --- From: Annemarie Weber annemarie.we...@uni-konstanz.de To: CCP4BB@JISCMAIL.AC.UK Sent: Mon, 3 Feb 2014 17:37:00 +0100 Subject: [ccp4bb] unexplained density *** This message has been scanned by the InterScan for CSC SSM at IICT and found to be free of known security risks. *** Dear all, I am refining a 1.4 A resolution structure and found some well-defined but unfortunately unexplained density. The protein was purified in HEPES buffer with PMSF and protease inhibitor cocktail tablets (Roche) added. It was cocrystallized with AMPPNP in PEG2000MME and Tris. I modelled a molecule into the density, which fits quite well but I do not know what it is and how it got there. Attached are two pictures with the difference density and the molecule I modelled in there. Has anybody seen something like this before? Maybe some degradation product of the buffer/PMSF? Any suggestions will be highly welcome. Thanks a lot Annemarie --- End of Original Message --- - Note: The information contained in the e-Mail message and/or attachments to it may contain confidential or privileged information. If you are not the intended recipient, any dissemination, use, review, distribute, prinitng or copying of the information contianed in this e-Mail message and/or attachments to it are strictly prohibited. If you have received this communication in error. Please notify us by reply e-Mail or telephone and immediately and permanently delete the message and any attachment. Thank you.
Re: [ccp4bb] A question on the diffrentiattion of the salt crystal and salt diffraction in the protein metal complex
*** This message has been scanned by the InterScan for CSC SSM by IICT security policy and found to be free of known security risks. *** This link probably may help you with this and other related questions. http://www2.mrc-lmb.cam.ac.uk/groups/JYL/WWWrobots/newsletters/Newsletter_july_2011.pdf Anthony - Dr. Anthony Addlagatta Center for Chemical Biology Indian Institute of Chemical Technology [IICT] Tarnaka, Hyderabad AP-500 607, INDIA Tel:91-40-27191812 Web: https://sites.google.com/site/chembioliict/home/dr-anthony-addlagatta-1 -- Original Message --- From: Acoot Brett acootbr...@yahoo.com To: CCP4BB@JISCMAIL.AC.UK Sent: Sun, 1 Dec 2013 19:16:06 -0800 Subject: [ccp4bb] A question on the diffrentiattion of the salt crystal and salt diffraction in the protein metal complex *** This message has been scanned by the InterScan for CSC SSM at IICT and found to be free of known security risks. *** Dear All, Suppose I have a crystal hit from the protein-metal complex, with the possibility of that the hit is a salt crystal. When I diffract it by X-ray, I got some metal (or salt) diffraction without the protein diffraction (maybe due to too low protein resolution). Will you please tell me how to know whether my diffraction was from a salt crystal or from the diffraction of the metal in my protein-metal complex? I am looking forward to getting your reply. Cheers, Acoot --- End of Original Message --- - Note: The information contained in the e-Mail message and/or attachments to it may contain confidential or privileged information. If you are not the intended recipient, any dissemination, use, review, distribute, prinitng or copying of the information contianed in this e-Mail message and/or attachments to it are strictly prohibited. If you have received this communication in error. Please notify us by reply e-Mail or telephone and immediately and permanently delete the message and any attachment. Thank you.
Re: [ccp4bb] Backbone hydrogen bonds in protein
*** This message has been scanned by the InterScan for CSC SSM by IICT security policy and found to be free of known security risks. *** Dear Mohan, I am not sure if it makes sense to use the C=O...N angle in a C=O...H-N hydrogen bond. Probably you can generate the hydrogen atoms as riding model and measure the O...H-N angle. This have a large bearing on the strength of the hydrogen bond. Larger the angle and shorter the hydrogen bond distance means a stronger hydrogen bond. Anthony - Dr. Anthony Addlagatta Center for Chemical Biology Indian Institute of Chemical Technology [IICT] Tarnaka, Hyderabad AP-500 607, INDIA Tel:91-40-27191812 Web: https://sites.google.com/site/chembioliict/home/dr-anthony-addlagatta-1 -- Original Message --- From: Mohan Pradhan mohan.prad...@ymail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Fri, 29 Mar 2013 23:55:19 -0700 Subject: [ccp4bb] Backbone hydrogen bonds in protein *** This message has been scanned by the InterScan for CSC SSM at IICT and found to be free of known security risks. *** Hi all, I want to calculate all the backbone hydrogen bonds (C=O-H-N) in a protein crystal structure. I am using the donor-acceptor distance cut off as 3.5 Angstrom.. I have not used the C-ON angle cut off. Can anyone tell the significance of this angle constraint? Some groups have used 100, 110 or 120 degrees as the cut off value. Since this angle cut off depends on the hydrogen bond donor, what would be a suitable cut off here? Also, I do not see much difference in the backbone hydrogen bonds calculated with (120 degrees) and without angle constraint. Thanks and Regards, mohan --- End of Original Message --- This Mail Scanned by ClamAV and Spammassassin
Re: [ccp4bb] Off Topic- Cystine Detection
*** This message has been scanned by the InterScan for CSC SSM by IICT security policy and found to be free of known security risks. *** Dear Yuri, If you have access to mass spec, this should be a straight forward experiment. Find the reference here. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2291582/pdf/v010p00017.pdf What was the result in the Ellman´s reaction? Unless you have other reactive cysteines in your protein protein, you should not see any color if the pair of cysteines on surface form disulfide. Anthony - Dr. Anthony Addlagatta Center for Chemical Biology Indian Institute of Chemical Technology [IICT] Tarnaka, Hyderabad AP-500 607, INDIA Tel:91-40-27191812 Web: https://sites.google.com/site/chembioliict/home/dr-anthony-addlagatta-1 -- Original Message --- From: Yuri Pompeu yuri.pom...@ufl.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Wed, 6 Feb 2013 16:10:35 + Subject: [ccp4bb] Off Topic- Cystine Detection *** This message has been scanned by the InterScan for CSC SSM at IICT and found to be free of known security risks. *** Dear All, I am trying to probe the existence of a disulfide bond on the surface of my protein. I have attempted Ellman´s and my results were not as clear as I would have hoped for. I am not a sulfur/cysteine chemist and would appreciate the advice on what experiments to try! Thanks a bunch YAP --- End of Original Message --- This Mail Scanned by ClamAV and Spammassassin
Re: [ccp4bb] electron density assignment
*** This message has been scanned by the InterScan for CSC SSM by IICT security policy and found to be free of known security risks. *** Dear Gang, By chance, P222 is your space group? It seems to be three perpendicular two-fold axes are passing through your central atom which makes them all fall in the same plane. From the density it looks more like a water in the center but anomalous density map should help. Good luck. Anthony - Dr. Anthony Addlagatta Center for Chemical Biology Indian Institute of Chemical Technology [IICT] Tarnaka, Hyderabad AP-500 607, INDIA Tel:91-40-27191812 Web: https://sites.google.com/site/chembioliict/home/dr-anthony-addlagatta-1 -- Original Message --- From: Gang Dong gang.d...@univie.ac.at To: CCP4BB@JISCMAIL.AC.UK Sent: Mon, 4 Feb 2013 13:39:39 +0100 Subject: [ccp4bb] electron density assignment *** This message has been scanned by the InterScan for CSC SSM at IICT and found to be free of known security risks. *** Dear all, Here are some hexmeric densities we observed in our 1.6-A resolution 2Fo-Fc map. They are located in between two dimers. Although 7 waters would fit nicely in the densities, we are not sure whether they might be something else (metals?). Any suggestions are welcome. Thanks! Gang __ Gang Dong, PhD Junior Group Leader Max F. Perutz Laboratories (MFPL) Dr. Bohrgasse 9/3 A-1030 Vienna, Austria Phone: +43-1-4277-61625 FAX: +43-1-4277-9616 http://www.mfpl.ac.at/mfpl-group/group/dong.html --- End of Original Message --- This Mail Scanned by ClamAV and Spammassassin
Re: [ccp4bb] need some suggestions for crystallization
*** This message has been scanned by the InterScan for CSC SSM by IICT security policy and found to be free of known security risks. *** Dave, You can try any or all of these proteins commercially available and all conditions for crystallization and freezing established. LysozymeFerritinGlucose isomerase Myoglobin Proteinase KThaumatin Trypsin You can follow this link. We used some of the conditions mentioned in their successfully. http://www.rigaku.com/products/protein/recipes Disclaimer: I do not have any commercial interest with Rigaku. Anthony - Dr. Anthony Addlagatta Center for Chemical Biology Indian Institute of Chemical Technology [IICT] Tarnaka, Hyderabad AP-500 607, INDIA Tel:91-40-27191812 Web: https://sites.google.com/site/chembioliict/home/dr-anthony-addlagatta-1 -- Original Message --- From: Harry Powell ha...@mrc-lmb.cam.ac.uk To: CCP4BB@JISCMAIL.AC.UK Sent: Mon, 4 Feb 2013 16:10:54 + Subject: Re: [ccp4bb] need some suggestions for crystallization *** This message has been scanned by the InterScan for CSC SSM at IICT and found to be free of known security risks. *** Hi David try going back to the one that started it all,* myoglobin, a recipe is at http://www.rigaku.com/products/protein/recipes (* feel free to argue about this) On 4 Feb 2013, at Mon4 Feb 16:03, David Roberts wrote: So, I know I say this every time I post on this board, but here it goes again. I'm at an undergrad only school, and every 2 years I teach a class in protein crystallography. This year I'm being super ambitious, and I'm going to take a class of 16 to the synchrotron for data collection. It's just an 8 hour thing, to show them the entire process. I'm hoping that we can collect 5-6 good data sets while there. I would like them to grow their own crystals, and go collect data. Then we'd come back and actually do a molecular replacement (pretty easy/standard really). Just to get a feel for how it works. The protein I do research on is not one that I would push on this, as the crystals are hard to grow, they are very soft, and the data just isn't the best (resolution issues). I do have a few that will work on my proteins, but I was thinking of having others in the class grow up classic proteins for data collection. Obviously lysozyme is one, but I was wondering what other standard bulletproof conditions are out there. Can you all suggest some protein crystallization conditions (along with cryo conditions) for some commercially available proteins? I'm looking to get 6-8 different ones (and we'll just take them and see how it goes). I wouldn't mind knowing unit cell parameters as well (just a citation works, I can have them figure it out). I have about 7 weeks to get everything grown and frozen and ready to go. Any help would be greatly appreciated. It always amazes me how helpful this group is. Thank you very much. Dave Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing) --- End of Original Message --- This Mail Scanned by ClamAV and Spammassassin
Re: [ccp4bb] how many metal sites
*** This message has been scanned by the InterScan for CSC SSM by IICT security policy and found to be free of known security risks. *** I agree with Dale that your four metals are not in the density and also don't seem to make sense in terms of chemistry. Based on your residue placement and electron density, it looks more like a non-heme manganese catalase structure where two metal ions bind with very similar environment. This reference may help you. Archives of Biochemistry and Biophysics Volume 525, Issue 2, 15 September 2012, Pages 111–120 Anthony - Dr. Anthony Addlagatta Center for Chemical Biology Indian Institute of Chemical Technology [IICT] Tarnaka, Hyderabad AP-500 607, INDIA Tel:91-40-27191812 Web: https://sites.google.com/site/chembioliict/home/dr-anthony-addlagatta-1 -- Original Message --- From: Dale Tronrud det...@uoxray.uoregon.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Wed, 16 Jan 2013 14:14:50 -0800 Subject: Re: [ccp4bb] how many metal sites *** This message has been scanned by the InterScan for CSC SSM at IICT and found to be free of known security risks. *** Zn is a very electron rich atom so a 2.3 A resolution data set should be a fine experiment to determine the number of fully occupied metal sites. It is always hard to be sure about screen shots of density, but it looks to me that you only have evidence for one zinc here. In my opinion, it is not useful to build models that don't make sense. Your zinc cluster does not make chemical sense to me and the atoms are not in the density. I suspect that you built this cluster, and not the obvious model with fewer zinc atoms, simply because you wanted to match the magic number of four. Use the things you know with confidence as your guide. Dale Tronrud On 01/16/13 11:15, ruisher hu wrote: Hi, Dear All, I recently got a dataset about 2.3 A resolution, however, I got some trouble assigning the metal sites. It suppose to have multiple binding site(possibly four) around those four glu residues in the center (see the attached figure), however, it shows up a huge single positive density ,clustered in the binding center. The signal is pretty strong and I think zn is definitely there. When I tried to put four zns around, the geometry doesn't look very good and there is still some positive density in the center (although get weaker) and the bfactor of metals are high like 100. Does anyone know what's going on?Does it mean only one single site in the middle?Or maybe just metals are too mobile? What's the best way to tell how many metal sites are actually there?Which experiment can I use to test? Thanks very much. Best, R On Wed, Nov 7, 2012 at 9:29 AM, SD Y ccp4...@hotmail.com mailto:ccp4...@hotmail.com wrote: Dear all, I have a related question to the one I have posted low resolution and SG, on which I am still working based on the suggestions I have got. The model I have used, has Zn co-ordinated well in tetrahydral fashion by 3 cys and 1 His residues. They have add Zn in to their experiment. In my 3.4 A structure (I am still working on right SG), initial maps show very strong positive density (sigma=6.5) at the place of Zn ( https://www.dropbox.com/s/4jd6gdor87ab9lj/Zn-coordination.png). I have not used Zn in my experiment. I could only suspect Tryptone and yeast extract which I used to make media. I would like to know how likely this positive density belongs to Zn? How to reason the presence of Zn when its not been used? Is there is any way to confirm if its Zn. If this is not Zn, what else could it be? Any thing I could try to rule out or in Zn or other ions. I appreciate your help and suggestions. Sincerely, SDY --- End of Original Message --- This Mail Scanned by ClamAV and Spammassassin
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....
*** This message has been scanned by the InterScan for CSC SSM by IICT security policy and found to be free of known security risks. *** Bernhard, I would be worried about sending the structure factors and the coordinates along with the manuscript. However, once the scientific merits of the paper are judged and it can be acceptable for the journal, the coordinates and the data have to be reviewed and then only the paper has to be completely accepted. Important, these data either should be directly from the PDB database or the identical set from the authors. This, not only will give confidence to the genuine scientist but will also keep a check on the perpetrators and more responsibility on the reviewers/publishers. Anthony - Dr. Anthony Addlagatta Scientist E1 Indian Institute of Chemical Technology [IICT] Tarnaka, Hyderabad AP-500 607, INDIA Tel:91-40-27191812 -- Original Message --- From: Bernhard Rupp b...@ruppweb.org To: CCP4BB@JISCMAIL.AC.UK Sent: Fri, 11 Dec 2009 11:47:24 -0800 Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures *** This message has been scanned by the InterScan for CSC SSM at IICT and found to be free of known security risks. *** I have to say to the credit of Nature and competent authors that in every case I have requested structure factors and coordinates for review they have arranged to provide these. AFAIK this is their editorial policy, but it requires that at least one of the reviewers knows what to do with the SF as and coordinates. That, however, does not (yet??) seem to be policy, i.e. to pair a technical crystallography review with one that evaluates biological and other relevance. BR From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Prof. Joel L. Sussman Sent: Friday, December 11, 2009 1:31 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures 11-Dec-2009 11:30 Rehovot Dear All, I Agree fully with Tommi, and feel, in parallel, we in the MX community must think of better tools for referees to review papers and insist that these be followed. For example we should insist on getting BOTH the coords and structure factors for papers submitted, so it would be possible to do test on the structures which appear to have 'question marks'. Without this data, it is very difficult to do a serious job in refereeing. Also, any manuscript, submitted to any journal, where BOTH the structure factors and coords are not submitted to the PDB should be rejected immediately without further review. This should be the policy of the reviewer, independent of any particular policy of the journals. It might be worthwhile for the MX community to also consider writing a strong letter to the journals in which published the papers for which the structures have now been retracted, to state just how serious this matter is and that the journals should also take much more responsibility of finding better ways to have these papers and structures reviewed. Joel - Prof. Joel L. Sussman Director, Israel Structural Proteomics Center Dept. of Structural Biology Weizmann Institute of Science Rehovot 76100 ISRAEL Tel: +972 8-934 4531 Fax: +972 8-934 6312 joel.suss...@weizmann.ac.il www.weizmann.ac.il/~joel; www.weizmann.ac.il/ISPC - On 11 Dec 2009, at 11:19, 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
Re: [ccp4bb] video that explains, very simply, what Structural Molecular Biology is about
*** This message has been scanned by the InterScan for CSC SSM by IICT security policy and found to be free of known security risks. *** Nice link. Thanks Anthony - Dr. Anthony Addlagatta Scientist E1 Indian Institute of Chemical Technology [IICT] Tarnaka, Hyderabad AP-500 607, INDIA Tel:91-40-27191583 -- Original Message --- From: Vellieux Frederic frederic.velli...@ibs.fr To: CCP4BB@JISCMAIL.AC.UK Sent: Wed, 11 Nov 2009 10:44:52 +0100 Subject: [ccp4bb] video that explains, very simply, what Structural Molecular Biology is about *** This message has been scanned by the InterScan for CSC SSM at IICT and found to be free of known security risks. *** Dear all, Thought I'd share this with you: I located this through Ms Ines Kahlaoui, from the Beja Higher Institute of Biotechnology in Tunisia (Ines has to teach and locates videos on the internet, which she then downloads and uses for teaching). Ines located this jewel: http://video.google.com/videoplay?docid=7084929825683486794ei=M3b5SvXqD6em2AK3jY33CQq=Plongee+coeur+vivant# This is the French version (explains everything about Structural Molecular Biology, but for the maths :-( , but also shows what we crystallographers have known for a long time, since the first colour ES graphics workstations in fact, that the electron are blue :-) ). Both French and English versions can be downloaded from http://cj.sauter.free.fr/xtal/Film/ No rights associated with the movie, and the Strasbourg group intends to release a higher quality version on DVD soon. Please contact them about that... I am only sharing what I thought was good for educational purposes. 18 minutes of your life, but worth it I think. So feel free to share this. Wish you all a nice day, Fred. --- End of Original Message --- This Mail Scanned by ClamAV and Spammassassin
Re: [ccp4bb] improvement of tiny protein crystals
*** This message has been scanned by the InterScan for CSC SSM by IICT security policy and found to be free of known security risks. *** Atul, Reasons could be so many. Since you say that the His-tag is still present in your protein try to remove it and see if it can make a difference. OR Also, try seeding. You don't say what your protein concentration is. If it is too high, reduce it or vice-versa. Also, in general if crystals appear in one organic acid condition, you can try in others like citric acid and very importantly Sodium MALONATE. Play little bit with pH. Good luck Anthony - Dr. Anthony Addlagatta Scientist E1 Indian Institute of Chemical Technology [IICT] Tarnaka, Hyderabad AP-500 607, INDIA Tel:91-40-27191583 -- Original Message --- From: atul kumar atul.ku...@igib.res.in To: CCP4BB@JISCMAIL.AC.UK Sent: Wed, 30 Sep 2009 12:27:44 +0530 Subject: [ccp4bb] improvement of tiny protein crystals *** This message has been scanned by the InterScan for CSC SSM at IICT and found to be free of known security risks. *** hi all sorry for asking non ccp4bb question. i am trying to crystallise phosphatase protein,it has histag.I am getting very tiny crystals into .1m hepes ph7.4,1m Na-K tartrate.I tried additives(MPD, ethanol,propanol)for improvement of crystals,but didnt get any success.I have tried both sitting and hanging drop conditions.Does anyone have suggestion for the improvement of these crystals? thanks Atul Kumar -Original Message- From: CCP4 bulletin board on behalf of Jessica Gilmore Sent: Wed 9/30/2009 2:44 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Bioinformatics Technician Position - Center for the Study of Systems Biology, Georgia Tech Bioinformatics Technician Position Available - Center for the Study of Systems Biology, Georgia Tech Job Summary Assists research staff in the integration, management and analysis of biological data, with a focus on the development, updating and maintenance of internal and public databases dealing with genome, transcriptome, proteome and metabolome annotation results generated in silico. Job Qualifications Requires a BS, MS, or PhD in Bioinformatics, Computer Science, or related fields. Minimum of two years verifiable experience in web site development and database design. Experience in scripting languages, preferably in a Unix/Linux environment. Familiarity with the use of biological databases. Demonstrated written and verbal communication skills. To apply please email your CV to: skoln...@gatech.edu --- End of Original Message --- This Mail Scanned by ClamAV and Spammassassin
[ccp4bb] Exciting fellowships in India
Sorry for the off topic. DBT New Delhi has announced exiting fellowships for the Scientist of Indian Origin who wish to take up faculty positions in India in the area of Bioenergy. For more details check DBT site at http://dbtindia.nic.in/news_management/PressreleaseDetails.asp?PressId=83button=Edit Last date 15th July 2009. Anthony This Mail Scanned by ClamAV and Spammassassin
[ccp4bb] Exciting postdoctoral fellowships in India
Sorry for the off topic mail Government of India has recently initiated several postdoctoral fellowships with attractive salaries and project contingencies. Those interested can visit the Council of Scientific Industrial Research (CSIR), Department of Science and Technology, New Delhi (DST) and Department of Biotechnology, New Delhi (DBT) web pages. One such fellowships is Nehru Science Postdoctoral Fellowship (http://csirhrdg.res.in/nehru.pdf) sponsored by CSIR. This is aimed at fresh PhD's (within one year of the award) around the world. Up to 20% of the fellowships indeed are reserved for foreign nationals. The fellowship is higher than startup salary of a new faculty in India. This should be an opportunity for those who want to explore India while still working! My lab is a part of the CSIR network and we are centrally (almost) located in India with weather like southern Texas. Anyone interested in molecular, structural and/or cell biology can send in your inquiries to anth...@iict.res.in or addlaga...@yahoo.com. Anthony - Dr. Anthony Addlagatta Scientist E1 and Ramanujan Fellow Center for Chemical Biology Indian Institute of Chemical Technology [IICT] Tarnaka, Hyderabad-607, INDIA Tel:91-40-27191583 This Mail Scanned by ClamAV and Spammassassin --- End of Forwarded Message --- - Dr. Anthony Addlagatta Scientist E1 and Ramanujan Fellow Indian Institute of Chemical Technology [IICT] Tarnaka, Hyderabad-607, INDIA Tel:91-40-27191583 This Mail Scanned by ClamAV and Spammassassin
