Re: [ccp4bb] Stabilization of crystals and ligand exchange
Hi Sabine, The easy experiment to start with, is to take your best conditions (nice looking crystals, no diffraction) and instead of overnight wait 4-8 weeks. Sometimes ligand exchange is slow, or the ligand induces a conformational change which takes a long time to complete in the crystals. There are cases that after a number of weeks, diffraction came back. However, even if the above experiment works, there will be the nagging uncertainty that the crystal packing may have prevented some completely unexpected, nature or science publication worthy conformational change. There will be no way around at least trying to cocrystallize your ligand. Your chance of success will depend on how your protein and ligand behave: -your ligand causes your protein to precipitate. Here your chances are slim. You could try to use the ligand as a precipitant by slowly diffusing it in (e.g. in a capillary with some gel to separate the protein and ligand solutions). -your ligand is poorly soluble. Here you have better chances. As you mentioned, one can add the dilute ligand to a dilute protein solution and then concentrate the complex. The amount of ligand needed depends on the affinity of the ligand for the protein. To get 90% occupancy, you need a free ligand concentration at least 10 times over the Kd (or ~IC50). To give an example: if you use for crystallization 10 mg/ml of a 30 kDa protein, your protein concentration is ~0.33 mM. If your ligand has an affinity of 100 nM, you need a free ligand concentration of 1 µM, which is 300 fold less than what you need to saturate all binding sites in the protein. To account for uncertainties in protein concentrations, I would add 0.5 - 1.0 mM Ligand. If you dilute 10 fold, you have 33 µM protein and I would add 50-100 µM ligand, which is still well above the 1 µM free concentration needed. Even with 100 fold dilution, you still just can dilute the ligand with the same factor as the protein and still be well above the required free concentration and you do not need more ligand. Of course, this only works for high-affinity ligands, for low affinity ligands it is quite a different story. I also would try to use the highest possible ligand concentration, since in many cases, although the ligand should bind in theory, in practise it is quite a different story. Good luck! Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Sabine Schneider Sent: Wednesday, October 17, 2012 6:27 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Stabilization of crystals and ligand exchange Hi everyone, I am trying to get the structure of a protein-ligand complex were I need to exchange the ligand which it co-crystallises nicely with. Problem: either they crack, disolve, turn brown,... OR they still look very nice, well shaped but do not show a single reflection at the synchrotron!!! Here is what I tried so far: 1) initially stabilising with higher precipitant (here PEG1500) before slowly transferring (*) it to the ligand-removal solution (= artifical mother liquor with higher PEG, ethylen glycol or glucose, but without initial ligand) (*) by slow exchange I mean : initially mixing drop solution with stabilising/ligand-removal solution and adding it back to the drop stepwise before fully transferring it. Or calculation wise I have fully exchange the solution to the new solution 2) here I let them ist over night (if they did not disolve, crack or whatever) 3) slow exchange transfer to the artificial ML with the new ligand (10mM), left them over night and directly froze them 'Best' so far (crystals still looking nice but no reflection...) was slow exchange into higher PEG, than to higher PEG with ethylenglycol (30% and also adding ethylenglycol to the reservoir), let them sit for over night, before again slow exchange to the solution with the new ligand in higher PEG and 30% ethylen glycol. As I said here the crystals keep shape, but don't diffract at all anymore. Just freezing them with 30% ethylen glycol they diffract nicely to 2.5A on a home source. But already after step one they are sometimes not happy anymore. Co-crystallisation failed since when I add the ligand, which is not that soluble to the purified protein, everything crashed out of solution. I am thinking about to test adding the ligand to the diluted protein and concentrate it together. But I don't have that much ligand, since the synthesis is quite tedious The ligand can be dissolved in 30% ethylenglycol to ~50mM Thus I was wondering if someone has done successfully ligand exchange with glutaraldehyd stabilised xtals? Or any ideas how to stabilise them? I appreciate any ideas or comments! Sorry for the lengthy email! Best, Sabine
Re: [ccp4bb] unique structures
Thanks ! I got it ! Sandra On Mon, Oct 15, 2012 at 7:23 PM, Das, Debanu deb...@slac.stanford.eduwrote: Hi Sandra, Yes, there are several ways of getting this information. Go to PDB website Advanced Search section. In the Query Type pull down, select All and then select Remove Similar Sequences at 30% identity. You will have to select 30% cut off in the pull down menu. This will result in ~22000 structures out of ~85000 PDB entries. Fine tune the search by searching for only proteins (and xray or NMR). Also note that almost all structures deposited from the various centers of the PSI (Protein Structure Initiative) meet this criteria of novelty (many are actually in the 5-20% seq identity range). From the PDB website, click on Advanced Search. From the drop down menu, select Structural Genomics Project and under Centers select All. You will see ~11500 entries. You can see some PSI metrics at: http://targetdb.pdb.org/Metrics/MilestonesTables.html In addition, the following papers will illustrate the PSI unique structures.: 1) http://www.ncbi.nlm.nih.gov/pubmed/16424331 Science. 2006 Jan 20;311(5759):347-51. The impact of structural genomics: expectations and outcomes. Chandonia JM, Brenner SE. Berkeley Structural Genomics Center, Physical Biosciences Division, Lawrence Berkeley National Laboratory, and Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA. 2) http://www.ncbi.nlm.nih.gov/pubmed/19787035 PLoS Biol. 2009 Sep;7(9):e1000205. Epub 2009 Sep 29. Exploration of uncharted regions of the protein universe. Jaroszewski L, Li Z, Krishna SS, Bakolitsa C, Wooley J, Deacon AM, Wilson IA, Godzik A. Joint Center for Structural Genomics, Bioinformatics Core, Burnham Institute for Medical Research, La Jolla, California, United States of America. 3) http://www.ncbi.nlm.nih.gov/pubmed/19523904 Structure. 2009 Jun 10;17(6):869-81. PSI-2: structural genomics to cover protein domain family space. Dessailly BH, Nair R, Jaroszewski L, Fajardo JE, Kouranov A, Lee D, Fiser A, Godzik A, Rost B, Orengo C. Department of Structural and Molecular Biology, University College of London, London WC1E6BT, UK. ben...@biochem.ucl.ac.uk Hope this helps. Thanks, Debanu. From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Sandra Quarantini [sandraquarant...@gmail.com] Sent: Monday, October 15, 2012 3:53 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] unique structures HI! Does anybody know the number or a likely number of unique structures (solved by Xray) deposited in PDB every year (Unique structures I mean less than 30% identical in sequence to proteins for which structures had already been determined) I could not find this data ın PDB . Is eventually possible to get an estimate of this number by calculating the number of structures solved by MAD/SAD ...? thank you!! -- Dr Sandra Quarantini Department of Biomedical Sciences University of Padua Viale G. Colombo 3 35131 Padova - ITALY Voice: +393494792030 Email: sandraquarant...@gmail.com http://it.linkedin.com/pub/sandra-quarantini/30/b74/88
[ccp4bb] Research Technician Post Doc positions at EMBL Grenoble
Hello, Two positions available in my lab at EMBL Grenoble: 1. Post doc position via the BioStruct-X Joint Research Activity (JRA) workpackage Mammalian cell toolbox for structural biology (collab. with Oxford University). 2. Research technician position. Details pasted below. Further info and online application at www.embl.org/jobs. Thanks, Darren Research technician, High-Throughput Protein Expression Location: Grenoble, France Staff Category: Staff Member Contract Duration: 1 year Grading: 4 or 5, depending on experience and qualifications Closing Date: 31 October 2012 Reference number: GR_00044 Job Description The European Molecular Biology Laboratory (EMBL) is one of the highest ranked scientific research organisations in the world. The Headquarters Laboratory is located in Heidelberg (Germany) and the outstations are in Grenoble (France), Hamburg (Germany), Hinxton (UK) and Monterotondo (Italy). A technician position is available in the High Throughput Protein Technologies laboratory of Darren Hart at EMBL Grenoble. It is funded by P-CUBE and BioStruct-X, European “Research Infrastructures” projects established to provide access to unique high-throughput protein production facilities by visiting international researchers. The candidate will be responsible for molecular biology and automation tasks associated with high throughput screening of expression constructs in bacteria using a new robotic technology, ESPRIT. Projects will be conducted with both local and international visitors, and the candidate will be responsible for the planning of the work and visits, together with experimental supervision. In addition to the project support roles, the candidate will work on a set of defined research activities involving vector design, protocol development and crystallisation studies. Tasks include DNA purification and enzymatic manipulation, PCR, operation of robotics and other advanced instruments, protein expression and purification. Additional tasks include the development of new protocols, testing of new equipment for the facility, keeping accurate records of consumable use on a project basis, ordering of laboratory consumables and monitoring associated budgets, meeting with visiting representatives from suppliers, general maintenance of the robotic laboratory equipment and arranging repairs as necessary. Qualifications and Experience The candidate should hold a Masters degree, or have a good level of previous, relevant work experience. He/she should have a sound experimental background in DNA manipulation methods, E. coli protein expression and protein purification. Experience in high throughput expression, protein engineering, directed evolution and/or laboratory automation would be advantageous.The candidate should have experience of working in an English speaking environment.The ability to work with team members and laboratory visitors is essential. Fluency in English and good computer skills are mandatory Postdoctoral Fellowship in Molecular Biology Location: Grenoble, France Staff Category: Postdoctoral Fellow Contract Duration: up to 18 months Grading: N/A Closing Date: 31.October 2012 Reference number: GR_00045 Job Description The European Molecular Biology Laboratory (EMBL) is one of the highest ranked scientific research organizations in the world. The Headquarters Laboratory is located in Heidelberg (Germany) and the outstations are in Grenoble (France), Hamburg (Germany), Hinxton (UK) and Monterotondo (Italy). EMBL is seeking to recruit a postdoctoral researcher to join the team of Darren Hart. The position is funded by the European Framework 7 BioStruct-X project and is a part of a collaboration to develop a new expression technology for structural biology that can be applied to challenging human proteins. The project will combine random library technologies and high throughput robotics developed at EMBL (PubMed ID: 20206698, 21515383 21364980) with parallelised mammalian expression approaches from the Aricescu lab, University of Oxford (PMID: 17001101). The subjects of the method development will be medically important human proteins where the aim is to initiate structural and functional studies. Qualifications and Experience The successful applicant should hold a Ph.D. in molecular biology and have experience of transfecting and handling mammalian cell lines, as well as being a skilled molecular biologist. He/she should be able to work independently and take responsibility for his/her own project. Strong teamwork and communication skills are required as well as reliability, attention to detail and effective time management. Motivation to work in a multidisciplinary and international environment is fundamental to this position. Good communication and presentation skills and fluency in English are expected. Application Instructions Please apply online through www.embl.org/jobs Please note that appointments on fixed term contracts can be renewed, depending
Re: [ccp4bb] Stabilization of crystals and ligand exchange
Hi Sabine, On top of the excellent suggestions of Herman, I was just wondering. Do you have a structure of the ligand-bound protein? If you do and the ligand bound at crystal contact with another molecule, I would think that it would be hard to get it out without harming the crystals (although not impossible). This may help you decide which way to go for obtaining the ligand-free structure. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of herman.schreu...@sanofi.com [herman.schreu...@sanofi.com] Sent: Thursday, October 18, 2012 10:32 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Stabilization of crystals and ligand exchange Hi Sabine, The easy experiment to start with, is to take your best conditions (nice looking crystals, no diffraction) and instead of overnight wait 4-8 weeks. Sometimes ligand exchange is slow, or the ligand induces a conformational change which takes a long time to complete in the crystals. There are cases that after a number of weeks, diffraction came back. However, even if the above experiment works, there will be the nagging uncertainty that the crystal packing may have prevented some completely unexpected, nature or science publication worthy conformational change. There will be no way around at least trying to cocrystallize your ligand. Your chance of success will depend on how your protein and ligand behave: -your ligand causes your protein to precipitate. Here your chances are slim. You could try to use the ligand as a precipitant by slowly diffusing it in (e.g. in a capillary with some gel to separate the protein and ligand solutions). -your ligand is poorly soluble. Here you have better chances. As you mentioned, one can add the dilute ligand to a dilute protein solution and then concentrate the complex. The amount of ligand needed depends on the affinity of the ligand for the protein. To get 90% occupancy, you need a free ligand concentration at least 10 times over the Kd (or ~IC50). To give an example: if you use for crystallization 10 mg/ml of a 30 kDa protein, your protein concentration is ~0.33 mM. If your ligand has an affinity of 100 nM, you need a free ligand concentration of 1 µM, which is 300 fold less than what you need to saturate all binding sites in the protein. To account for uncertainties in protein concentrations, I would add 0.5 - 1.0 mM Ligand. If you dilute 10 fold, you have 33 µM protein and I would add 50-100 µM ligand, which is still well above the 1 µM free concentration needed. Even with 100 fold dilution, you still just can dilute the ligand with the same factor as the protein and still be well above the required free concentration and you do not need more ligand. Of course, this only works for high-affinity ligands, for low affinity ligands it is quite a different story. I also would try to use the highest possible ligand concentration, since in many cases, although the ligand should bind in theory, in practise it is quite a different story. Good luck! Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Sabine Schneider Sent: Wednesday, October 17, 2012 6:27 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Stabilization of crystals and ligand exchange Hi everyone, I am trying to get the structure of a protein-ligand complex were I need to exchange the ligand which it co-crystallises nicely with. Problem: either they crack, disolve, turn brown,... OR they still look very nice, well shaped but do not show a single reflection at the synchrotron!!! Here is what I tried so far: 1) initially stabilising with higher precipitant (here PEG1500) before slowly transferring (*) it to the ligand-removal solution (= artifical mother liquor with higher PEG, ethylen glycol or glucose, but without initial ligand) (*) by slow exchange I mean : initially mixing drop solution with stabilising/ligand-removal solution and adding it back to the drop stepwise before fully transferring it. Or calculation wise I have fully exchange the solution to the new solution 2) here I let them ist over night (if they did not disolve, crack or whatever) 3) slow exchange transfer to the artificial ML with the new ligand (10mM), left them over night and directly froze them 'Best' so far (crystals still looking nice but no reflection...) was slow exchange into higher PEG, than to higher PEG with ethylenglycol (30% and also adding ethylenglycol to the reservoir), let them sit for over night, before again slow exchange to the solution with the new ligand in higher PEG and 30% ethylen glycol. As I said here the crystals keep shape, but don't diffract at all anymore. Just
Re: [ccp4bb] Stabilization of crystals and ligand exchange
Thanks a lot for all the excellent suggestions! Lots more things to try now! Cheers, Sabine On 10/18/2012 12:18 PM, Boaz Shaanan wrote: Hi Sabine, On top of the excellent suggestions of Herman, I was just wondering. Do you have a structure of the ligand-bound protein? If you do and the ligand bound at crystal contact with another molecule, I would think that it would be hard to get it out without harming the crystals (although not impossible). This may help you decide which way to go for obtaining the ligand-free structure. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of herman.schreu...@sanofi.com [herman.schreu...@sanofi.com] Sent: Thursday, October 18, 2012 10:32 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Stabilization of crystals and ligand exchange Hi Sabine, The easy experiment to start with, is to take your best conditions (nice looking crystals, no diffraction) and instead of overnight wait 4-8 weeks. Sometimes ligand exchange is slow, or the ligand induces a conformational change which takes a long time to complete in the crystals. There are cases that after a number of weeks, diffraction came back. However, even if the above experiment works, there will be the nagging uncertainty that the crystal packing may have prevented some completely unexpected, nature or science publication worthy conformational change. There will be no way around at least trying to cocrystallize your ligand. Your chance of success will depend on how your protein and ligand behave: -your ligand causes your protein to precipitate. Here your chances are slim. You could try to use the ligand as a precipitant by slowly diffusing it in (e.g. in a capillary with some gel to separate the protein and ligand solutions). -your ligand is poorly soluble. Here you have better chances. As you mentioned, one can add the dilute ligand to a dilute protein solution and then concentrate the complex. The amount of ligand needed depends on the affinity of the ligand for the protein. To get 90% occupancy, you need a free ligand concentration at least 10 times over the Kd (or ~IC50). To give an example: if you use for crystallization 10 mg/ml of a 30 kDa protein, your protein concentration is ~0.33 mM. If your ligand has an affinity of 100 nM, you need a free ligand concentration of 1 µM, which is 300 fold less than what you need to saturate all binding sites in the protein. To account for uncertainties in protein concentrations, I would add 0.5 - 1.0 mM Ligand. If you dilute 10 fold, you have 33 µM protein and I would add 50-100 µM ligand, which is still well above the 1 µM free concentration needed. Even with 100 fold dilution, you still just can dilute the ligand with the same factor as the protein and still be well above the required free concentration and you do not need more ligand. Of course, this only works for high-affinity ligands, for low affinity ligands it is quite a different story. I also would try to use the highest possible ligand concentration, since in many cases, although the ligand should bind in theory, in practise it is quite a different story. Good luck! Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Sabine Schneider Sent: Wednesday, October 17, 2012 6:27 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Stabilization of crystals and ligand exchange Hi everyone, I am trying to get the structure of a protein-ligand complex were I need to exchange the ligand which it co-crystallises nicely with. Problem: either they crack, disolve, turn brown,... OR they still look very nice, well shaped but do not show a single reflection at the synchrotron!!! Here is what I tried so far: 1) initially stabilising with higher precipitant (here PEG1500) before slowly transferring (*) it to the ligand-removal solution (= artifical mother liquor with higher PEG, ethylen glycol or glucose, but without initial ligand) (*) by slow exchange I mean : initially mixing drop solution with stabilising/ligand-removal solution and adding it back to the drop stepwise before fully transferring it. Or calculation wise I have fully exchange the solution to the new solution 2) here I let them ist over night (if they did not disolve, crack or whatever) 3) slow exchange transfer to the artificial ML with the new ligand (10mM), left them over night and directly froze them 'Best' so far (crystals still looking nice but no reflection...) was slow exchange into higher PEG, than to higher PEG with ethylenglycol (30% and also adding ethylenglycol to the reservoir), let them sit for over night, before again slow exchange to the solution
[ccp4bb] Software Development Posts at Diamond
Please find details below details of software development posts at Diamond. Full details on these posts and others can be found on the web site http://www.diamond.ac.uk/Home/Jobs/Current.html. MX and BioSAXS Automation - Job Title: Software Engineer Post Type: Full Time- Fixed Term- 3 years Salary information Circa £33k Job Reference: DIA0789/CG http://www.diamond.ac.uk/Home/Jobs/Current/DIA0789_CG.html Application deadline 30/11/2012 The successful candidate will contribute to our efforts in software automation in the field of structural biology. In particular, macromolecular crystallography (MX) and biological small angle X-ray scattering techniques (BioSAXS), two highly automated, complementary experiments used to determine 3 dimensional structural information on proteins. Working with existing staff and international collaborators you will enhance and extend our existing fully automatic MX data reduction and structure solution pipelines as well as help develop the equivalent for BioSAXS as part of a European wide initiative, Biostruct-X (http://www.biostruct-x.eu/). MX Data Acquisition --- Job Title: Software Scientist Post Type: Permanent/ Full Time Salary information Circa £33k Job Reference: DIA0774/CB http://www.diamond.ac.uk/Home/Jobs/Current/DIA0774_CB.html Application deadline 16/11/2012 Duties to include: * Share the first line support of the software for MX interacting closely with both beamline staff and external users; * Participate in the implementation of the data acquisition software for one or more Diamond beamlines under the mentoring of more senior group members.(Initially for MX); * Use particular scientific experience to participate actively in the use and direct support of Diamond's Macromolecular Crystallography (MX) beamlines first to establish requirements and then to manage the implementation of software to improve and extend functionality; SR Data --- Job Title: Software Engineer Post Type: Fixed Term- 1 year/ Full Time Salary information Circa £33k Job Reference: DIA0772/CB http://www.diamond.ac.uk/Home/Jobs/Current/DIA0772_CB.html Application deadline 16/11/2012 Duties * Implement updated NeXus standard data format for data acquisition software where appropriate and participate in the development of supporting software within the Data Acquisition and Scientific Computing groups at Diamond; * Development of Eclipse RCP perspective and toolkit; * Contribute to the provision of documentation for software developed within the Data Acquisition and scientific computing groups at Diamond; Alun ___ Alun Ashton, alun.ash...@diamond.ac.uk Tel: +44 1235 778404 Scientific Software Team Leader, http://www.diamond.ac.uk/ Diamond Light Source, Chilton, Didcot, Oxon, OX11 0DE, U.K. -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
Re: [ccp4bb] Stabilization of crystals and ligand exchange
Hi Sabine, Glutaraldehyde crosslinking worked pretty good for various soaks in my experience. J. Appl. Cryst. (1999). 32, 106-112[ doi:10.1107/S002188989801053X ] A gentle vapor-diffusion technique for cross-linking of protein crystals for cryocrystallography C. J. Lusty Best regards, Dmitry On 2012-10-17, at 12:26 PM, Sabine Schneider wrote: Hi everyone, I am trying to get the structure of a protein-ligand complex were I need to exchange the ligand which it co-crystallises nicely with. Problem: either they crack, disolve, turn brown,... OR they still look very nice, well shaped but do not show a single reflection at the synchrotron!!! Here is what I tried so far: 1) initially stabilising with higher precipitant (here PEG1500) before slowly transferring (*) it to the ligand-removal solution (= artifical mother liquor with higher PEG, ethylen glycol or glucose, but without initial ligand) (*) by slow exchange I mean : initially mixing drop solution with stabilising/ligand-removal solution and adding it back to the drop stepwise before fully transferring it. Or calculation wise I have fully exchange the solution to the new solution 2) here I let them ist over night (if they did not disolve, crack or whatever) 3) slow exchange transfer to the artificial ML with the new ligand (10mM), left them over night and directly froze them 'Best' so far (crystals still looking nice but no reflection...) was slow exchange into higher PEG, than to higher PEG with ethylenglycol (30% and also adding ethylenglycol to the reservoir), let them sit for over night, before again slow exchange to the solution with the new ligand in higher PEG and 30% ethylen glycol. As I said here the crystals keep shape, but don't diffract at all anymore. Just freezing them with 30% ethylen glycol they diffract nicely to 2.5A on a home source. But already after step one they are sometimes not happy anymore. Co-crystallisation failed since when I add the ligand, which is not that soluble to the purified protein, everything crashed out of solution. I am thinking about to test adding the ligand to the diluted protein and concentrate it together. But I don't have that much ligand, since the synthesis is quite tedious The ligand can be dissolved in 30% ethylenglycol to ~50mM Thus I was wondering if someone has done successfully ligand exchange with glutaraldehyd stabilised xtals? Or any ideas how to stabilise them? I appreciate any ideas or comments! Sorry for the lengthy email! Best, Sabine
Re: [ccp4bb] Stabilization of crystals and ligand exchange
I say (of course I would!) why not try co-crystallization with random microseeding using the crystals with the original ligand? It usually allows you to control the number of crystals per drop too On 18 October 2012 15:59, Dmitry Rodionov d.rodio...@gmail.com wrote: Hi Sabine, Glutaraldehyde crosslinking worked pretty good for various soaks in my experience. J. Appl. Cryst. (1999). 32, 106-112[ doi:10.1107/S002188989801053X ] A gentle vapor-diffusion technique for cross-linking of protein crystals for cryocrystallography C. J. Lusty Best regards, Dmitry On 2012-10-17, at 12:26 PM, Sabine Schneider wrote: Hi everyone, I am trying to get the structure of a protein-ligand complex were I need to exchange the ligand which it co-crystallises nicely with. Problem: either they crack, disolve, turn brown,... OR they still look very nice, well shaped but do not show a single reflection at the synchrotron!!! Here is what I tried so far: 1) initially stabilising with higher precipitant (here PEG1500) before slowly transferring (*) it to the ligand-removal solution (= artifical mother liquor with higher PEG, ethylen glycol or glucose, but without initial ligand) (*) by slow exchange I mean : initially mixing drop solution with stabilising/ligand-removal solution and adding it back to the drop stepwise before fully transferring it. Or calculation wise I have fully exchange the solution to the new solution 2) here I let them ist over night (if they did not disolve, crack or whatever) 3) slow exchange transfer to the artificial ML with the new ligand (10mM), left them over night and directly froze them 'Best' so far (crystals still looking nice but no reflection...) was slow exchange into higher PEG, than to higher PEG with ethylenglycol (30% and also adding ethylenglycol to the reservoir), let them sit for over night, before again slow exchange to the solution with the new ligand in higher PEG and 30% ethylen glycol. As I said here the crystals keep shape, but don't diffract at all anymore. Just freezing them with 30% ethylen glycol they diffract nicely to 2.5A on a home source. But already after step one they are sometimes not happy anymore. Co-crystallisation failed since when I add the ligand, which is not that soluble to the purified protein, everything crashed out of solution. I am thinking about to test adding the ligand to the diluted protein and concentrate it together. But I don't have that much ligand, since the synthesis is quite tedious The ligand can be dissolved in 30% ethylenglycol to ~50mM Thus I was wondering if someone has done successfully ligand exchange with glutaraldehyd stabilised xtals? Or any ideas how to stabilise them? I appreciate any ideas or comments! Sorry for the lengthy email! Best, Sabine -- patr...@douglas.co.ukDouglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36
[ccp4bb] PNAS on fraud
Dear CCP4 followers, Maybe you are already aware of this interesting study in PNAS regarding the prevalence of fraud vs. 'real' error in paper retractions: Fang FC, Steen RG and Casadevall A (2012) Misconduct accounts for the majority of retracted scientific publications. Proc Natl Acad Sci U S A 109(42): 17028-33. http://www.pnas.org/content/109/42/17028.abstract There were also a few comments on related stuff such as fake peer review in the Chronicle of Higher Education. As not all may have access to that journal, I have put the 3 relevant pdf links on my web http://www.ruppweb.org/CHE_Misconduct_PNAS_Stuft_Oct_2012.pdf http://www.ruppweb.org/CHE_DYI_reviews_Sept_30_2012.pdf http://www.ruppweb.org/CHE_The-Great-Pretender_Oct_8_2012.pdf Best regards, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ -
Re: [ccp4bb] PNAS on fraud
Le Jeudi 18 Octobre 2012 19:16 CEST, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com a écrit: I had a look to this PNAS paper by Fang et al. I am a bit surprised by their interpretation of their Fig. 3: they claim that here exists a highly signficant correlation between Impact factor and number of retractations. Personnaly, I would have concluded to a complete lack of correlation... Should I retract this judgment? Philippe Dumas Dear CCP4 followers, Maybe you are already aware of this interesting study in PNAS regarding the prevalence of fraud vs. 'real' error in paper retractions: Fang FC, Steen RG and Casadevall A (2012) Misconduct accounts for the majority of retracted scientific publications. Proc Natl Acad Sci U S A 109(42): 17028-33. http://www.pnas.org/content/109/42/17028.abstract There were also a few comments on related stuff such as fake peer review in the Chronicle of Higher Education. As not all may have access to that journal, I have put the 3 relevant pdf links on my web http://www.ruppweb.org/CHE_Misconduct_PNAS_Stuft_Oct_2012.pdf http://www.ruppweb.org/CHE_DYI_reviews_Sept_30_2012.pdf http://www.ruppweb.org/CHE_The-Great-Pretender_Oct_8_2012.pdf Best regards, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ -
Re: [ccp4bb] PNAS on fraud
The fit seems to be driven by the high number of points in the area of the graph where many points overlap. The points that catch your eye and establish the visible balance probably do not contribute much. Maybe this one should have been plotted as log in the abscissa for appearances. James On Oct 18, 2012, at 11:52 AM, DUMAS Philippe (UDS) wrote: Le Jeudi 18 Octobre 2012 19:16 CEST, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com a écrit: I had a look to this PNAS paper by Fang et al. I am a bit surprised by their interpretation of their Fig. 3: they claim that here exists a highly signficant correlation between Impact factor and number of retractations. Personnaly, I would have concluded to a complete lack of correlation... Should I retract this judgment? Philippe Dumas Dear CCP4 followers, Maybe you are already aware of this interesting study in PNAS regarding the prevalence of fraud vs. 'real' error in paper retractions: Fang FC, Steen RG and Casadevall A (2012) Misconduct accounts for the majority of retracted scientific publications. Proc Natl Acad Sci U S A 109(42): 17028-33. http://www.pnas.org/content/109/42/17028.abstract There were also a few comments on related stuff such as fake peer review in the Chronicle of Higher Education. As not all may have access to that journal, I have put the 3 relevant pdf links on my web http://www.ruppweb.org/CHE_Misconduct_PNAS_Stuft_Oct_2012.pdf http://www.ruppweb.org/CHE_DYI_reviews_Sept_30_2012.pdf http://www.ruppweb.org/CHE_The-Great-Pretender_Oct_8_2012.pdf Best regards, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ -
Re: [ccp4bb] PNAS on fraud
On Thursday, October 18, 2012 10:52:48 am DUMAS Philippe (UDS) wrote: Le Jeudi 18 Octobre 2012 19:16 CEST, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com a écrit: I had a look to this PNAS paper by Fang et al. I am a bit surprised by their interpretation of their Fig. 3: they claim that here exists a highly signficant correlation between Impact factor and number of retractations. Personnaly, I would have concluded to a complete lack of correlation... Should I retract this judgment? Fang et al. claim that R^2 = 0.0866, which means that CC = 0.29. While a correlation coefficient of less than 0.3 is not a complete lack of correlation, it's still rather weak. The highly significant must be taken in a purely statistical sense. That is, it doesn't mean the measures are highly correlated, it means the evidence for non-zero correlation is very strong. Ethan Philippe Dumas Dear CCP4 followers, Maybe you are already aware of this interesting study in PNAS regarding the prevalence of fraud vs. 'real' error in paper retractions: Fang FC, Steen RG and Casadevall A (2012) Misconduct accounts for the majority of retracted scientific publications. Proc Natl Acad Sci U S A 109(42): 17028-33. http://www.pnas.org/content/109/42/17028.abstract There were also a few comments on related stuff such as fake peer review in the Chronicle of Higher Education. As not all may have access to that journal, I have put the 3 relevant pdf links on my web http://www.ruppweb.org/CHE_Misconduct_PNAS_Stuft_Oct_2012.pdf http://www.ruppweb.org/CHE_DYI_reviews_Sept_30_2012.pdf http://www.ruppweb.org/CHE_The-Great-Pretender_Oct_8_2012.pdf Best regards, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ - -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] PNAS on fraud
One might include independent prior evidence (Kleywegt, Brown @ Ramaswami) showing that in general most other quality indicators are worse for high impact journals. So, as a frequentist I agree that his correlation is significantly weak, as a Bayesian I say it is reasonably probable. Cheers, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ethan Merritt Sent: Thursday, October 18, 2012 11:11 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PNAS on fraud On Thursday, October 18, 2012 10:52:48 am DUMAS Philippe (UDS) wrote: Le Jeudi 18 Octobre 2012 19:16 CEST, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com a écrit: I had a look to this PNAS paper by Fang et al. I am a bit surprised by their interpretation of their Fig. 3: they claim that here exists a highly signficant correlation between Impact factor and number of retractations. Personnaly, I would have concluded to a complete lack of correlation... Should I retract this judgment? Fang et al. claim that R^2 = 0.0866, which means that CC = 0.29. While a correlation coefficient of less than 0.3 is not a complete lack of correlation, it's still rather weak. The highly significant must be taken in a purely statistical sense. That is, it doesn't mean the measures are highly correlated, it means the evidence for non-zero correlation is very strong. Ethan
Re: [ccp4bb] PNAS on fraud
As much fun as it is to bash Nature, Science and Cell, the evidence that they publish poorer quality structures doesn't actually hold up well. Gerard Kleywegt (cited below) and I tried to use that supposition as the basis of a positive control for our case-controlled validation paper in Acta D, but we were surprised that once you account for the fact that the high-profile journals tend to publish papers on bigger structures that generally diffract to lower resolution, there's actually very little evidence that those structures are worse than comparable lower-resolution structures in lower-impact journals. They probably do have more than their fair share of retractions -- but then it's hard to control for the varying level of scrutiny applied to papers published in different journals. In support of Bayesian reasoning, it's good to see that the data could over-rule our prior belief that Nature/Science/Cell structures would be worse! - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk On 18 Oct 2012, at 19:31, Bernhard Rupp (Hofkristallrat a.D.) wrote: One might include independent prior evidence (Kleywegt, Brown @ Ramaswami) showing that in general most other quality indicators are worse for high impact journals. So, as a frequentist I agree that his correlation is significantly weak, as a Bayesian I say it is reasonably probable. Cheers, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ethan Merritt Sent: Thursday, October 18, 2012 11:11 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PNAS on fraud On Thursday, October 18, 2012 10:52:48 am DUMAS Philippe (UDS) wrote: Le Jeudi 18 Octobre 2012 19:16 CEST, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com a écrit: I had a look to this PNAS paper by Fang et al. I am a bit surprised by their interpretation of their Fig. 3: they claim that here exists a highly signficant correlation between Impact factor and number of retractations. Personnaly, I would have concluded to a complete lack of correlation... Should I retract this judgment? Fang et al. claim that R^2 = 0.0866, which means that CC = 0.29. While a correlation coefficient of less than 0.3 is not a complete lack of correlation, it's still rather weak. The highly significant must be taken in a purely statistical sense. That is, it doesn't mean the measures are highly correlated, it means the evidence for non-zero correlation is very strong. Ethan
Re: [ccp4bb] PNAS on fraud
My two cents: the R-squared for figure 3A is 9%, therefore only a minor proportion of the variation (or random noise) in the data was explained by the fitted model, taking a log scale may reduce that random scatter look but the fit is essentially the same. On Thu, Oct 18, 2012 at 12:10 PM, Ethan Merritt merr...@u.washington.eduwrote: On Thursday, October 18, 2012 10:52:48 am DUMAS Philippe (UDS) wrote: Le Jeudi 18 Octobre 2012 19:16 CEST, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com a écrit: I had a look to this PNAS paper by Fang et al. I am a bit surprised by their interpretation of their Fig. 3: they claim that here exists a highly signficant correlation between Impact factor and number of retractations. Personnaly, I would have concluded to a complete lack of correlation... Should I retract this judgment? Fang et al. claim that R^2 = 0.0866, which means that CC = 0.29. While a correlation coefficient of less than 0.3 is not a complete lack of correlation, it's still rather weak. The highly significant must be taken in a purely statistical sense. That is, it doesn't mean the measures are highly correlated, it means the evidence for non-zero correlation is very strong. Ethan Philippe Dumas Dear CCP4 followers, Maybe you are already aware of this interesting study in PNAS regarding the prevalence of fraud vs. 'real' error in paper retractions: Fang FC, Steen RG and Casadevall A (2012) Misconduct accounts for the majority of retracted scientific publications. Proc Natl Acad Sci U S A 109(42): 17028-33. http://www.pnas.org/content/109/42/17028.abstract There were also a few comments on related stuff such as fake peer review in the Chronicle of Higher Education. As not all may have access to that journal, I have put the 3 relevant pdf links on my web http://www.ruppweb.org/CHE_Misconduct_PNAS_Stuft_Oct_2012.pdf http://www.ruppweb.org/CHE_DYI_reviews_Sept_30_2012.pdf http://www.ruppweb.org/CHE_The-Great-Pretender_Oct_8_2012.pdf Best regards, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ - -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] PNAS on fraud
I think that the jump between fraud and other quality indicators is a bit too steep for me. Poor quality indicators may suggest poor data that the xtal was willing to diffract, a concept that to me is very orthogonal to fraud. Fred [32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred ***[m
Re: [ccp4bb] PNAS on fraud
Randy Read just pointed out to me that in their case-controlled analysis paper http://journals.iucr.org/d/issues/2009/02/00/ba5130/index.html when considering lower resolution and other factors, the vanity journals seem to come out no worse than the rest. In any case I suspect any retractions are underrepresented in those journals because they fight it harder ;-) Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ethan Merritt Sent: Thursday, October 18, 2012 11:11 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PNAS on fraud Fang et al. claim that R^2 = 0.0866, which means that CC = 0.29. While a correlation coefficient of less than 0.3 is not a complete lack of correlation, it's still rather weak. The highly significant must be taken in a purely statistical sense. That is, it doesn't mean the measures are highly correlated, it means the evidence for non-zero correlation is very strong. Ethan
[ccp4bb] imosflm, bad predictions
Hi everyone, I recently switched from HKL2000 to imosflm to get rid of ice rings. The group space and cell unit of the data set are known and perfectly recognized by HKL2000. The predictions are also correct. In imosflm, the unit cell and space group are recognized. However the predictions are terrible, and it even get worse after cell refinenement. I tried to use different images, different resolution range (my data set is at 3.3 A), I placed the beam center using an ice ring. Nothing works. Imosflm also does not seem to allow changes to its defaullt parameters. Does anyone have an idea what I can do, my main goal being to get rid of ice rings in a 3.3 A data set? Thanks,
Re: [ccp4bb] imosflm, bad predictions
since you have already identified the correct beam position through the ice rings I would fix that beam position. My assumption is that the drifting of your predicted spots is due to shifts in the beam position. Also you should probably fix the detector distance at that resolution. Jürgen On Oct 18, 2012, at 3:15 PM, Jan van Agthoven wrote: Hi everyone, I recently switched from HKL2000 to imosflm to get rid of ice rings. The group space and cell unit of the data set are known and perfectly recognized by HKL2000. The predictions are also correct. In imosflm, the unit cell and space group are recognized. However the predictions are terrible, and it even get worse after cell refinenement. I tried to use different images, different resolution range (my data set is at 3.3 A), I placed the beam center using an ice ring. Nothing works. Imosflm also does not seem to allow changes to its defaullt parameters. Does anyone have an idea what I can do, my main goal being to get rid of ice rings in a 3.3 A data set? Thanks, .. 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://lupo.jhsph.edu
Re: [ccp4bb] PNAS on fraud
Just to add in the controversy, with a somewhat related issue: Current crystallographic ethic presumes that a structure is deposited just before the submission of the paper. In a survey we did, we found that while in one journal only 2% of structures are deposited after the paper submission date, on another thats 5%, on another one that is 29% and in yet another one close to 50%. The journals are Nature, Science, ActaD and Proteins in order of decreasing IF. Is there any correlation? To get some guesses first, Robbie can send the answer tomorrow at around noon (as I will be unavailable travelling ...) Tassos On 18 Oct 2012, at 21:13, Bernhard Rupp (Hofkristallrat a.D.) wrote: Randy Read just pointed out to me that in their case-controlled analysis paper http://journals.iucr.org/d/issues/2009/02/00/ba5130/index.html when considering lower resolution and other factors, the vanity journals seem to come out no worse than the rest. In any case I suspect any retractions are underrepresented in those journals because they fight it harder ;-) Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ethan Merritt Sent: Thursday, October 18, 2012 11:11 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PNAS on fraud Fang et al. claim that R^2 = 0.0866, which means that CC = 0.29. While a correlation coefficient of less than 0.3 is not a complete lack of correlation, it's still rather weak. The highly significant must be taken in a purely statistical sense. That is, it doesn't mean the measures are highly correlated, it means the evidence for non-zero correlation is very strong. Ethan
Re: [ccp4bb] PNAS on fraud
Tassos, just to clarify what you are saying in the Journal with 2% deposition after submission, 98% have been deposited prior to submission (the way it should be). Is that what you are saying or am I reading that wrong ? Or are you saying only 2% of structures are deposited in that journal ? Jürgen On Oct 18, 2012, at 3:24 PM, Anastassis Perrakis wrote: Just to add in the controversy, with a somewhat related issue: Current crystallographic ethic presumes that a structure is deposited just before the submission of the paper. In a survey we did, we found that while in one journal only 2% of structures are deposited after the paper submission date, on another thats 5%, on another one that is 29% and in yet another one close to 50%. The journals are Nature, Science, ActaD and Proteins in order of decreasing IF. Is there any correlation? To get some guesses first, Robbie can send the answer tomorrow at around noon (as I will be unavailable travelling ...) Tassos On 18 Oct 2012, at 21:13, Bernhard Rupp (Hofkristallrat a.D.) wrote: Randy Read just pointed out to me that in their case-controlled analysis paper http://journals.iucr.org/d/issues/2009/02/00/ba5130/index.html when considering lower resolution and other factors, the vanity journals seem to come out no worse than the rest. In any case I suspect any retractions are underrepresented in those journals because they fight it harder ;-) Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ethan Merritt Sent: Thursday, October 18, 2012 11:11 AM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PNAS on fraud Fang et al. claim that R^2 = 0.0866, which means that CC = 0.29. While a correlation coefficient of less than 0.3 is not a complete lack of correlation, it's still rather weak. The highly significant must be taken in a purely statistical sense. That is, it doesn't mean the measures are highly correlated, it means the evidence for non-zero correlation is very strong. Ethan .. 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://lupo.jhsph.edu
Re: [ccp4bb] PNAS on fraud
On 18 Oct 2012, at 21:30, Bosch, Juergen wrote: Tassos, just to clarify what you are saying in the Journal with 2% deposition after submission, 98% have been deposited prior to submission (the way it should be). Is that what you are saying or am I reading that wrong ? Yes, that is what I am saying! 2% is good, 50% is bad. (btw, the 'worse' is close to 70% - any guesses?) A. Or are you saying only 2% of structures are deposited in that journal ? Jürgen On Oct 18, 2012, at 3:24 PM, Anastassis Perrakis wrote: Just to add in the controversy, with a somewhat related issue: Current crystallographic ethic presumes that a structure is deposited just before the submission of the paper. In a survey we did, we found that while in one journal only 2% of structures are deposited after the paper submission date, on another thats 5%, on another one that is 29% and in yet another one close to 50%. The journals are Nature, Science, ActaD and Proteins in order of decreasing IF. Is there any correlation? To get some guesses first, Robbie can send the answer tomorrow at around noon (as I will be unavailable travelling ...) Tassos On 18 Oct 2012, at 21:13, Bernhard Rupp (Hofkristallrat a.D.) wrote: Randy Read just pointed out to me that in their case-controlled analysis paper http://journals.iucr.org/d/issues/2009/02/00/ba5130/index.html when considering lower resolution and other factors, the vanity journals seem to come out no worse than the rest. In any case I suspect any retractions are underrepresented in those journals because they fight it harder ;-) Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ethan Merritt Sent: Thursday, October 18, 2012 11:11 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PNAS on fraud Fang et al. claim that R^2 = 0.0866, which means that CC = 0.29. While a correlation coefficient of less than 0.3 is not a complete lack of correlation, it's still rather weak. The highly significant must be taken in a purely statistical sense. That is, it doesn't mean the measures are highly correlated, it means the evidence for non-zero correlation is very strong. Ethan .. 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://lupo.jhsph.edu
Re: [ccp4bb] PNAS on fraud
That must be an NMR journal :-) Jürgen On Oct 18, 2012, at 3:34 PM, Anastassis Perrakis wrote: On 18 Oct 2012, at 21:30, Bosch, Juergen wrote: Tassos, just to clarify what you are saying in the Journal with 2% deposition after submission, 98% have been deposited prior to submission (the way it should be). Is that what you are saying or am I reading that wrong ? Yes, that is what I am saying! 2% is good, 50% is bad. (btw, the 'worse' is close to 70% - any guesses?) A. Or are you saying only 2% of structures are deposited in that journal ? Jürgen On Oct 18, 2012, at 3:24 PM, Anastassis Perrakis wrote: Just to add in the controversy, with a somewhat related issue: Current crystallographic ethic presumes that a structure is deposited just before the submission of the paper. In a survey we did, we found that while in one journal only 2% of structures are deposited after the paper submission date, on another thats 5%, on another one that is 29% and in yet another one close to 50%. The journals are Nature, Science, ActaD and Proteins in order of decreasing IF. Is there any correlation? To get some guesses first, Robbie can send the answer tomorrow at around noon (as I will be unavailable travelling ...) Tassos On 18 Oct 2012, at 21:13, Bernhard Rupp (Hofkristallrat a.D.) wrote: Randy Read just pointed out to me that in their case-controlled analysis paper http://journals.iucr.org/d/issues/2009/02/00/ba5130/index.html when considering lower resolution and other factors, the vanity journals seem to come out no worse than the rest. In any case I suspect any retractions are underrepresented in those journals because they fight it harder ;-) Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ethan Merritt Sent: Thursday, October 18, 2012 11:11 AM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PNAS on fraud Fang et al. claim that R^2 = 0.0866, which means that CC = 0.29. While a correlation coefficient of less than 0.3 is not a complete lack of correlation, it's still rather weak. The highly significant must be taken in a purely statistical sense. That is, it doesn't mean the measures are highly correlated, it means the evidence for non-zero correlation is very strong. Ethan .. 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://lupo.jhsph.eduhttp://lupo.jhsph.edu/ .. 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://lupo.jhsph.edu
Re: [ccp4bb] Vitamin B12 (cobalamin) geometry issues (help-3615)
Dear Oliver, The representation of B12 has been updated in the wwPDB's Chemical Component Dictionary and related PDB entries. They will be available with next week's update of the archive. Sincerely, Rachel Green *** Rachel Kramer Green, Ph.D. RCSB PDB kra...@rcsb.rutgers.edu On 10/12/2012 4:31 AM, Oliver Smart wrote: If you are working on a protein that binds vitamin B12 (cobalamin) then you may be interested that there appears to be an issue with geometry of the B12 dictionary currently distributed by ccp4. The problem is that atom C19 in the corrin ring is defined as being SP2, planar with no hydrogen atom attached. Small molecule structures of B12 clearly show this atom is tetrahedral (as do high resolution protein complexes). A survey of 53 PDB structures containing B12 reveals that 19 have C19 atoms that are not sufficiently chiral. All are recent - structures prior to 2008 are all OK. The problem also effects the PDB chemical components definition of B12. Please see https://www.globalphasing.com/buster/wiki/index.cgi?B12Dictionary This page provides a dictionary for B12 with the problem fixed. Hope this proves useful. Regards, Oliver | Dr Oliver Smart | | Global Phasing Ltd., Cambridge UK | | http://www.globalphasing.com/people/osmart/ |
Re: [ccp4bb] PNAS on fraud
On curve fitting: http://twitpic.com/8jd081 -- From: DUMAS Philippe (UDS) p.du...@ibmc-cnrs.unistra.fr Sent: Thursday, October 18, 2012 1:52 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PNAS on fraud Le Jeudi 18 Octobre 2012 19:16 CEST, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com a écrit: I had a look to this PNAS paper by Fang et al. I am a bit surprised by their interpretation of their Fig. 3: they claim that here exists a highly signficant correlation between Impact factor and number of retractations. Personnaly, I would have concluded to a complete lack of correlation... Should I retract this judgment? Philippe Dumas
Re: [ccp4bb] imosflm, bad predictions
I had a very similar problem with data collected on a particular beamline. The issue was that I had to reverse the spindle direction in imosflm settings. Also, when I load data from this beamline into imosflm the program rotates the images by 90 degrees for some reason (this does not happen in HKL2000). Because of this rotation, the beam center that I used in HKL2000 was different than the beam center position for imosflm.
