[ccp4bb] Researcher position (Structural biology of proteolipid membranes) in Bergen (Norway)
Dear all, we have an opening for a researcher position at the University of Bergen. Funding currently exists for 1.5 years, with a starting date as soon as possible. The project deals with the assembly of proteolipid multilayers, involving studies of integral and peripheral membrane proteins and lipid membranes using methods of structural biology and biophysical assays. The work will be carried out as a part of a larger team funded by the Research Council of Norway and the Faculty of Medicine, and fine details of the project depend also on the background of the candidate. For more information, see the advert: https://www.jobbnorge.no/en/available-jobs/job/262539/researcher-in-structural-biology-of-proteolipid-membranes Applications will only be accepted via the online portal, with all mandatory attachments in place. Application deadline: May 14. With kind regards, Petri Petri Kursula -- Professor -- Department of Biomedicine University of Bergen, Norway https://www.uib.no/en/persons/Petri.Kursula petri.kurs...@uib.no <mailto:petri.kurs...@uib.no> -- Faculty of Biochemistry and Molecular Medicine Biocenter Oulu University of Oulu, Finland -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] open PhD position in Bergen (Norway)
Hi all, in a new interdisciplinary project combining machine learning, psychiatric disorders, drug design, protein science, and structural biology, we are looking for a PhD student into a fully funded 4-year position in Bergen (Norway). https://www.jobbnorge.no/en/available-jobs/job/226673/phd-position-4-years <https://www.jobbnorge.no/en/available-jobs/job/226673/phd-position-4-years> I would be grateful if this information reaches potential candidates with a suitable background. I can be contacted for informal queries, but applications (with all required attachments) must go through the online portal. Best regards, Petri Petri Kursula -- Professor -- Department of Biomedicine University of Bergen, Norway https://www.uib.no/en/persons/Petri.Kursula petri.kurs...@uib.no -- Faculty of Biochemistry and Molecular Medicine Biocenter Oulu University of Oulu, Finland -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] 4-year PhD position in Bergen, Norway
Hi, we have an opening for a fully funded 4-year PhD position in my group at the Unviersity of Bergen, Norway. The position is funded by a recent grant from the Norwegian Research Council, and the broad topic is the assembly and properties of multilayered proteolipid membranes. Please see the full ad below for details. Informal queries are of course welcome, but applications must be made through the link in the advert. Note that all required documents must be submitted for the application to be evaluated. https://www.jobbnorge.no/en/available-jobs/job/221160/phd-position-4-years <https://www.jobbnorge.no/en/available-jobs/job/221160/phd-position-4-years> Best regards, Petri Petri Kursula -- Professor -- Department of Biomedicine University of Bergen, Norway https://link.uib.no/petri <https://link.uib.no/petri> petri.kurs...@uib.no <mailto:petri.kurs...@uib.no> -- Faculty of Biochemistry and Molecular Medicine Biocenter Oulu University of Oulu, Finland -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] 4-year PhD position in Bergen, Norway
Hi, we have an opening for a fully funded 4-year PhD position in my group at hte Unviersity of Bergen, Norway. Please see the full ad below for details. Informal queries are welcome, but applications must be made through the link in the advert. https://www.jobbnorge.no/en/available-jobs/job/213744/phd-position Best regards, Petri Petri Kursula -- Professor -- Department of Biomedicine University of Bergen, Norway https://link.uib.no/petri petri.kurs...@uib.no -- Faculty of Biochemistry and Molecular Medicine Biocenter Oulu University of Oulu, Finland -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Postdoc position in Bergen (Norway)
Hi, we are looking for a postdoc in our project, focusing on a multidisciplinary approach towards formation, structure, and dynamics in proteolipid multilayer structures, such as seen in vertebrate myelin. As we are in the near future hiring several people, we are looking for an optimal combination of expertise, and various backgrounds related to biophysics and structural biology will be considered. The announcement, with a deadline on Oct 10th, can be found at: https://www.jobbnorge.no/en/available-jobs/job/212348/postdoctoral-research-fellow-3-years <https://www.jobbnorge.no/en/available-jobs/job/212348/postdoctoral-research-fellow-3-years> All applications must be done through the online portal (please do attach a CV even though the system does not strictly require it). While applications by email will not be considered, informal queries are welcome. Best regards, Petri Petri Kursula -- Professor -- Department of Biomedicine University of Bergen, Norway https://link.uib.no/petri petri.kurs...@uib.no -- Faculty of Biochemistry and Molecular Medicine Biocenter Oulu University of Oulu, Finland -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] 9 PhD positions in Bergen, Norway
Hi all, our faculty currently has open 9 positions for PhD students at the University of Bergen (Norway): https://www.jobbnorge.no/en/available-jobs/job/211089/phd-positions-9-positions <https://www.jobbnorge.no/en/available-jobs/job/211089/phd-positions-9-positions> Unfortunately, the application deadline is already on Sep 19th, but I wish to point out the Department of Biomedicine at the faculty has several groups working on structural biology and related topics. Any interested, qualified candidates should therefore contact a potential supervisor asap to prepare an application together. Best regards, Petri Petri Kursula -- Professor -- Department of Biomedicine University of Bergen, Norway http://www.uib.no/en/rg/petrikursula petri.kurs...@uib.no -- Faculty of Biochemistry and Molecular Medicine Biocenter Oulu University of Oulu, Finland -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] COOT download site
Could it be because that link is given at least here: https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot <https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot> Petri Petri Kursula -- Professor -- Department of Biomedicine University of Bergen, Norway http://www.uib.no/en/rg/petrikursula petri.kurs...@uib.no -- Faculty of Biochemistry and Molecular Medicine Biocenter Oulu University of Oulu, Finland -- > On 4 Jun 2020, at 17:02, Jurgen Bosch wrote: > > Looks as if Clemens will be jumping straight into the future now with the new > link. Were you on Coot 0.069? > > Jürgen > >> On Jun 4, 2020, at 10:54 AM, Paul Emsley > <mailto:pems...@mrc-lmb.cam.ac.uk>> wrote: >> >> On 04/06/2020 15:41, Clemens Grimm wrote: >>> Dear All, >>> >>> accessing the COOT download pages at >>> >>> http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/ >>> <http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/> >>> >>> >>> gives me an >>> >>> "The requested URL /~emsley/software/binaries/nightlies/pre-release/ was >>> not found on this server." >>> >>> error since a few days. >>> >>> Is the site down or has it moved? >>> >> >> Good grief! I haven't thought about that web site for 10 years. I had no >> idea that it was alive (not that I could do anything about it if it was). >> >> Google finds my Coot pages using "Emsley Coot" - well, it does for me :-) >> >> >> https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ >> <https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/> >> >> >> Paul. >> >> >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 >> <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1> >> >> This message was issued to members of www.jiscmail.ac.uk/CCP4BB >> <http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by >> www.jiscmail.ac.uk <http://www.jiscmail.ac.uk/>, terms & conditions are >> available at https://www.jiscmail.ac.uk/policyandsecurity/ >> <https://www.jiscmail.ac.uk/policyandsecurity/> > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Covalent Cysteine Aduct
Looks like DTT adduct to me; but then again, if you did not have it, it probably is not. Petri Petri Kursula -- Professor -- Department of Biomedicine University of Bergen, Norway http://www.uib.no/en/rg/petrikursula petri.kurs...@uib.no -- Faculty of Biochemistry and Molecular Medicine Biocenter Oulu University of Oulu, Finland -- > On 27 Mar 2020, at 22:06, Cowan, Richard H. (Dr.) > wrote: > > Hi Robbie et al., > > I'm very sure on the crystallization conditions, but I'll check the > purification for BME, although it seems unlikely, since the crystallized > protein is a Fab. > > What I would be less sure on is the age of the reagents used. Is anyone aware > of significant breakdown products which might be more reactive, particularly > the alcohols? > > Thanks, > > Dr Richard Cowan > Research Associate > <> > HWLSB 1/05 > Department of Biochemistry > University of Leicester > Lancaster Road > Leicester, LE1 <> 9HN <>, U.K. > > Phone +44 (0) 116 229 7077 > > From: robbie_joos...@hotmail.com > Sent: 27 March 2020 20:57 > To: Cowan, Richard H. (Dr.) > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Covalent Cysteine Aduct > > Are you absolutely sure about the conditions? The blob next to the sulfur > looks pretty fat so I would guess BME. > > Cheers, > Robbie > > On 27 Mar 2020 21:32, "Cowan, Richard H. (Dr.)" wrote: > Hi All, > > During the current enforced shutdown, I've been going back over some older > data and spotted this in one of my structures: > > > > > It's what appears to be a covalent aduct onto a cysteine on the surface > (originally modeled as 2 waters!). The condition was optimized from the > Morpheus Screen condition D1, so MES/Imidazole pH 6.5, PEG 500MME, PEG20k and > a mix of 1,6-Hexanediol, 1-Butanol, 1,2-Propanediol, 2-Propanol, > 1,4-Butanediol and 1,3-Propanediol. The data has been cut at 1.7A, with good > stats. > > Has anyone seen anything like this before? what do you think my best bet for > modeling this is? and aduct of 1,3-propanediol? It looks too short for > 1-butanol or 1,4-butandiol, and it's linear so 2-propanol and 1,2-propanediol > seem unlikely. > > Thanks, > > Dr Richard Cowan > Research Associate > > HWLSB 1/05 > Department of Biochemistry > University of Leicester > Lancaster Road > Leicester, LE1 9HN, U.K. > > Phone +44 (0) 116 229 7077 > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DCCP4BB%26A%3D1=02%7C01%7Crc273%40LEICESTER.AC.UK%7Ca21cb2bb3ebe45fdcf8e08d7d2917a35%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C0%7C637209394570788374=i4cJYTIxaA3NqT1u%2FscLnLR3OWxghkRLAiQ2U8zC0kI%3D=0> > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Contradictory result between ITC and cocrystal structure
Hi, a likely scenario is that your mutant crystallises in the same conformation/packing as the wild-type protein, and this conformation is good for ligand binding. In solution, your mutant protein may be more flexible/open than the wild-type and affinity hence lower. We see this quite often. Various solution structure techniques will shed light on this. Another possibility, assuming that you did ITC only at one temperature, is that you are “lucky” enough to be at the temperature where enthalpy for binding is zero for the mutant (but not wild-type). This you can find out by carrying out ITC at different temperatures. Petri Petri Kursula -- Professor -- Department of Biomedicine University of Bergen, Norway http://www.uib.no/en/rg/petrikursula petri.kurs...@uib.no -- Faculty of Biochemistry and Molecular Medicine Biocenter Oulu University of Oulu, Finland -- > On 22 Feb 2020, at 07:31, monika chandravanshi > wrote: > > Dear All, > > I have a situation, where a mutant protein does not exhibit any > heat change upon titration with cognate ligand in the ITC experiment. > However, it co-crystallizes with the respective cognate ligand. Also, the > cocrystal structure reveals the conservation of the hydrogen bonding networks > except for the mutated residues. I would like to know the possible reason for > the no heat change in the ITC experiment. > > Looking forward to hearing from you. > > -- > - > > With Kind Regards > > Monika Chandravanshi > PhD Scholar, > Department of Biosciences and Bioengineering > Indian Institute of Technology Guwahati, Guwahati India > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Cysteine sulfenic acid in coot
I used to always do this in a text editor - old-fashioned by fast and works :) Petri Petri Kursula -- Professor -- Department of Biomedicine University of Bergen, Norway http://www.uib.no/en/rg/petrikursula petri.kurs...@uib.no -- Faculty of Biochemistry and Molecular Medicine University of Oulu, Finland — > On 10 Dec 2019, at 16:11, Sudipta Bhattacharyya > wrote: > > Dear community, > > I would really appreciate your suggestions for linking cysteine sulfenic acid > (one of the active site amino acid residues in my target protein) to rest of > the protein chain. Let me summarize what I did so far in coot - > > 1. I deleted the native cysteine residue at that location, then brought > cysteine sulfenic acid from the monomer library, then fit it in the density > and merged it, then ran refinement by refmac5, the entity fits really well > but the link is not established after the refinement . > > 2. In my version of coot (wincoot) I could not find "Extensions > Modelling > > Replace Residue"...option to change it. > > Thanks in advance for your suggestions and happy holidays! > > Best regards, > Sudipta > > > -- > Sudipta Bhattacharyya, PhD > Assistant Professor, > Department of Bioscience and Bioengineering, > Indian Institute of Technology Jodhpur, > Rajasthan, India. > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] SEC and MALS
Hi, that's typical behaviour for an elongated/disordered molecule, given that SEC separates based on hydrodynamic radius, not MW. Petri Petri Kursula -- Professor -- Department of Biomedicine University of Bergen, Norway http://www.uib.no/en/rg/petrikursula <http://www.uib.no/en/persons/Petri.Kursula> petri.kurs...@uib.no <mailto:petri.kurs...@biomed.uib.no> -- Faculty of Biochemistry and Molecular Medicine University of Oulu, Finland -- > On 27 Aug 2019, at 07:57, Natesh Ramanathan wrote: > > Dear Friends, > > Can you share your experience with examples of MALS giving lower > molecular weight (Eg. Monomer) and SEC giving higher molecular weight (Eg. > Dimer), for the same protein sample? > > If you have/know any published paper, can you please point me to that > reference paper or send me the paper? > > Many thanks. > Best regards, > Natesh > > > -- > -- > "Live Simply and do Serious Things .. " > - Dorothy Mary Crowfoot Hodgkin OM, FRS > > "In Science truth always wins" > - Max Ferdinand Perutz OM FRS > -- > Dr. Ramanathan Natesh > Assistant Professor, > School of Biology, > Indian Institute of Science Education and Research Thiruvananthapuram > (IISER-TVM), > Maruthamala P.O., Vithura, > Thiruvananthapuram, 695551, Kerala, India > > nat...@iisertvm.ac.in <mailto:nat...@iisertvm.ac.in> > http://www.researcherid.com/rid/C-4488-2008 > <http://www.researcherid.com/rid/C-4488-2008> > ORCID: http://orcid.org/-0002-1145-5962 > <http://orcid.org/-0002-1145-5962> > https://publons.com/author/1520837/ramanathan-natesh#profile > <https://publons.com/author/1520837/ramanathan-natesh#profile> > http://faculty.iisertvm.ac.in/natesh <http://faculty.iisertvm.ac.in/natesh> > > Office Ph. 0091- 471-2778087 > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] 4-year PhD position at Biocenter Oulu
Dear colleagues, we have a 4-year PhD position available in our lab at the University of Oulu, Finland. The project will start in January 2020 and end in December 2023. The project will focus on two main topics: the structural basis of mutations causing human hereditary neuropathies and the molecular structure of the myelin membrane. Various structural biology and biophysical techniques will be implemented, and the project is supported by a multidisciplinary network of international collaborators. More information and a link to the online application system can be found through the following link: https://rekry.saima.fi/certiahome/open_job_view.html?did=5600=1=7516=en <https://rekry.saima.fi/certiahome/open_job_view.html?did=5600=1=7516=en> Please feel free to contact me for informal queries; however, applications received by email will NOT be accepted. Best regards, Petri Petri Kursula -- Professor -- Department of Biomedicine University of Bergen, Norway http://www.uib.no/en/rg/petrikursula <http://www.uib.no/en/persons/Petri.Kursula> petri.kurs...@uib.no <mailto:petri.kurs...@biomed.uib.no> -- Faculty of Biochemistry and Molecular Medicine University of Oulu, Finland -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Issue with high Rfree (0.25) for a high-resolution dataset (1.05 Ang)
Perhaps these were all mentioned already, but here are some points...looking at your statistics, I would definitely process it to even higher resolution, not lower. I understand the detector might not have been close enough for that (happens often nowadays). You might start seeing hydrogens, double bonds, bent aromatic rings, etc., which I personally think is cool :) and often also informative. Your problem might be, as mentioned, in the low-resolution data; overloads, a small overlapping satellite crystal, ...? Your pseudotranslation could be higher than the apparent one, since simultaneous twinning will partially hide it (and vice versa; twin tests may tell your crystal is fine, even when it is not). Your a and b cell edges are nearly identical. Did you try refining using that twin operator? What are the processing/refinement stats if you process in the higher symmetry? Since you have high redundancy, did you try to process only the beginning part of the dataset, up to nice completeness and stats? Do you still get the high R factors in refinement? Are your low-resolution R factors so high already at the beginning of data collection? I would expect those to be around 1-2% for this kind of data. Do you have a very low solvent content? This could increase your R factors. And perhaps not the correct forum for it: did you try processing manually with XDS? Having said all that, if your maps are fine, you can show what you see is reliable, and you can explain the high R factor, everyone should be happy :) even reviewer 2. Petri Petri Kursula -- Professor Department of Biomedicine University of Bergen, Norway http://www.uib.no/en/rg/petrikursula <http://www.uib.no/en/persons/Petri.Kursula> petri.kurs...@uib.no <mailto:petri.kurs...@biomed.uib.no> -- Group Leader, Adjunct Professor Faculty of Biochemistry and Molecular Medicine University of Oulu, Finland -- > On 10 Oct 2018, at 12:18, Barone, Matthias wrote: > > I agree with Pavel... if you got so many observations you dont need TLS but > use anisotropic adps. What I want to add is the dangerous comment to "cutting > back data ... to improve Rfact" Of course, if you lower the amount of > observations while keeping the parameters to fit constant will lower your R > facts. That doesnt necessarily mean you improve your model. It just means > that you incase the param to obs ratio - which says nothing about the > accuracy of your model... > > Dr. Matthias Barone > AG Kuehne, Rational Drug Design > Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) > Robert-Rössle-Strasse 10 > 13125 Berlin > Germany > Phone: +49 (0)30 94793-284 > From: CCP4 bulletin board on behalf of Pavel Afonine > > Sent: Wednesday, October 10, 2018 11:03:49 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Issue with high Rfree (0.25) for a high-resolution > dataset (1.05 Ang) > > Hi Tony, > > I always feel some people are too "greedy" with the resolution they want to > achieve. I mostly find that extremely high density is a pain to work with as > it's usually accompanied by many dual, triple conformers, a lot of noise in > the solvent phase that is often difficult to interpret, etc... Often you > spend more time on a high resolution structure that clearly shows your > protein, as opposed to a low resolution structure where it's difficult to > interpret parts of the map. Also, in most cases you REALLY don't need a 1 Ang > map to clearly show the overall structure of your protein, ligands, first > shell of solvent molecules on the surface of your protein, etc... > > higher resolution typically means you have a chance to obtain a more accurate > atomic model of a crystal structure, which in turn may lead to a more > accurate interpretation of this model. I fully agree that high resolution > requires more modeling effort. There is still a great room for software > developers to provide more automation. > > Your completeness is 90% in your high resolution shell, which is fine, but > have you checked you can clearly see most reflections for h, k and l? Maybe > you're missing many reflections for one of them. I would at least try cutting > your data back to 1.1 or 1.2 Ang, as it might dramatically improve your R > factors and still show everything you want to show. > > Also, did you try TLS refinement? > > At resolutions like 1.2A or better one normally models ADPs as anisotropic > for all atoms (except H), so no need to use TLS. > > Pavel > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > <https://www.jiscmail.ac.uk/cgi-bin/weba
Re: [ccp4bb] Fishing crystals from volatile solvent as precipitant
Hi, you could try picking in the cold room. Provided the temperature change does not kill the crystals, this sometimes worked fine for me in similar cases. Petri Petri Kursula -- Professor Department of Biomedicine University of Bergen, Norway http://www.uib.no/en/rg/petrikursula <http://www.uib.no/en/persons/Petri.Kursula> petri.kurs...@uib.no <mailto:petri.kurs...@biomed.uib.no> -- Group Leader, Adjunct Professor Faculty of Biochemistry and Molecular Medicine University of Oulu, Finland -- > On 14 Aug 2018, at 20:58, Thomas Krey wrote: > > Dear crystallization experts, > > We have 3D protein crystals grown from a microseed matrix screening vapor > diffusion experiment in either > > 15% (v/v) Reagent alcohol > HEPES Na pH 7.5 > 0.2 M MgCl2 > > or in > > 27% Isopropanol > 0.18 M MgCl2 > 90 mM HEPES Na pH 7.5 > 10% Glycerol > > Upon opening the corresponding wells these crystals move quite a bit – > presumably due to the volatility of the alcohols. Does anyone have a good > suggestion to stabilize the swirling movements? Does anyone have experience, > whether these conditions alone can serve as cryo-protectant (i.e., do we > really have to fish, move into cryo solution and fish again)? > Any suggestion or input would be highly welcome. > > Thank you very much in advance. > > Thomas > > > Prof. Dr. Thomas Krey > Hannover Medical School > Institute of Virology > Structural Virology Group > Carl-Neuberg-Str. 1 > D-30625 Hannover > phone: +49 (0) 511 - 532 4308 > email: krey.tho...@mh-hannover.de <mailto:krey.tho...@mh-hannover.de> > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] 2 Open Positions (PhD Student + Post-Doc) in Oulu, Finland
Dear all, I have been informed that the original links will eventually lead to the application system in the Finnish language, which might not be optimal for some. Here are links that will allow to apply in English: post-doc https://rekry.saima.fi/certiahome/open_job_view.html?did=5600=1=5769=en <https://rekry.saima.fi/certiahome/open_job_view.html?did=5600=1=5769=en> PhD student: https://rekry.saima.fi/certiahome/open_job_view.html?did=5600=1=5770=en <https://rekry.saima.fi/certiahome/open_job_view.html?did=5600=1=5770=en> Sorry for the spam, Petri > On 31 May 2018, at 17:33, Petri Kursula wrote: > > Dear All, > > my lab at the University of Oulu, Finland, has two open positions to be > filled in September. The positions are part of a multidisciplinary > collaborative project aiming at a comprehensive understanding of protein > structure/function and disease mechanisms in human hereditary neuropathies. > > The post-doctoral position is open for 2.5 years, and the PhD student > position for 4 years. > > More information about the environment, project, etc., as well as links to > the application system can be found through the web pages below. > > Post-doc: > https://www.saimanet.com/certiahome/open_job_view.html?id=5769 > <https://www.saimanet.com/certiahome/open_job_view.html?id=5769> > > PhD student: > https://www.saimanet.com/certiahome/open_job_view.html?id=5770 > <https://www.saimanet.com/certiahome/open_job_view.html?id=5770> > > Applications must be submitted through the electronic system, and > applications received by email will not be considered. > > Best regards, > Petri > > > Petri Kursula > -- > Professor > Department of Biomedicine > University of Bergen, Norway > http://www.uib.no/en/rg/petrikursula > <http://www.uib.no/en/persons/Petri.Kursula> > petri.kurs...@uib.no <mailto:petri.kurs...@biomed.uib.no> > -- > Group Leader, Adjunct Professor > Faculty of Biochemistry and Molecular Medicine > University of Oulu, Finland > -- > > > > > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] 2 Open Positions (PhD Student + Post-Doc) in Oulu, Finland
Dear All, my lab at the University of Oulu, Finland, has two open positions to be filled in September. The positions are part of a multidisciplinary collaborative project aiming at a comprehensive understanding of protein structure/function and disease mechanisms in human hereditary neuropathies. The post-doctoral position is open for 2.5 years, and the PhD student position for 4 years. More information about the environment, project, etc., as well as links to the application system can be found through the web pages below. Post-doc: https://www.saimanet.com/certiahome/open_job_view.html?id=5769 <https://www.saimanet.com/certiahome/open_job_view.html?id=5769> PhD student: https://www.saimanet.com/certiahome/open_job_view.html?id=5770 <https://www.saimanet.com/certiahome/open_job_view.html?id=5770> Applications must be submitted through the electronic system, and applications received by email will not be considered. Best regards, Petri Petri Kursula -- Professor Department of Biomedicine University of Bergen, Norway http://www.uib.no/en/rg/petrikursula <http://www.uib.no/en/persons/Petri.Kursula> petri.kurs...@uib.no <mailto:petri.kurs...@biomed.uib.no> -- Group Leader, Adjunct Professor Faculty of Biochemistry and Molecular Medicine University of Oulu, Finland -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Open PhD position in Oulu (Finland)
Dear all, we have an opening for a 4-year PhD student position in our lab in Oulu (Finland), and we are looking for good candidates (see link below). The project deals with structure-function analyses of mutations in several proteins linked to human peripheral neuropathies (Charcot-Marie-Tooth disease). The position can be filled at the beginning of September 2018. More information can be found at: https://rekry.saima.fi/certiahome/open_job_view.html?did=5600=1=5482=en <https://rekry.saima.fi/certiahome/open_job_view.html?did=5600=1=5482=en> Informal queries by email are welcome, but the application must be made through the application system described in the link above. Applications sent by email will not be taken into account in the evaluation. Best regards, Petri Petri Kursula -- Professor Department of Biomedicine University of Bergen, Norway http://www.uib.no/en/rg/petrikursula <http://www.uib.no/en/persons/Petri.Kursula> petri.kurs...@uib.no <mailto:petri.kurs...@biomed.uib.no> -- Group Leader, Adjunct Professor Faculty of Biochemistry and Molecular Medicine University of Oulu, Finland --
[ccp4bb] Open PhD and post-doc positions in Bergen, Norway
Dear all, our faculty in Bergen has currently open 25 PhD and 2 post-doc positions: https://www.jobbnorge.no/en/available-jobs/job/141891/phd-positions-25-positions <https://www.jobbnorge.no/en/available-jobs/job/141891/phd-positions-25-positions> https://www.jobbnorge.no/en/available-jobs/job/141892/postdoctoral-fellow-2-positions <https://www.jobbnorge.no/en/available-jobs/job/141892/postdoctoral-fellow-2-positions> Interested applicants should contact group leaders in the faculty (which includes also structural biology research groups) as soon as possible to plan an application, as CVs need to be pre-screened, and the application must include a detailed research plan, in addition to various other documents. Feel free to distribute the information further to those possibly interested. Greetings from Norway, Petri Petri Kursula -- Professor Department of Biomedicine University of Bergen, Norway http://www.uib.no/en/rg/petrikursula <http://www.uib.no/en/persons/Petri.Kursula> petri.kurs...@uib.no <mailto:petri.kurs...@biomed.uib.no> -- Group Leader, Adjunct Professor Faculty of Biochemistry and Molecular Medicine University of Oulu, Finland --
Re: [ccp4bb] in crystallo enzymatic activity
Hi, apart from the possibilities of conformational flexibility affected by crystal packing, just wondering if this mutation is supposed to actually cause an increase or decrease in the corresponding activity (outside the context of a crystal)? k(cat) and K(M) measured in solution would help here. Is the pH in the crystal far from the optimum of the wild-type protein? Can optimal pH change with the mutation? Petri Petri Kursula -- Professor Department of Biomedicine University of Bergen, Norway http://www.uib.no/en/rg/petrikursula <http://www.uib.no/en/persons/Petri.Kursula> petri.kurs...@uib.no <mailto:petri.kurs...@biomed.uib.no> -- Group Leader, Adjunct Professor Faculty of Biochemistry and Molecular Medicine University of Oulu, Finland -- > On 13 Apr 2017, at 17:27, Pierre Nioche <pierre.nio...@parisdescartes.fr> > wrote: > > Dear CCP4bb, > > We work on an enzyme that we crystallized with two substrates bound in the > active site (the reaction transform two substrates into two products). We > have also the structure with the two products. We are able to see densities > for the substrates when we collect data at different time point > post-crystallization (days or weeks later). There is no change over time and > no in crystallo enzymatic reaction despite the fact that in solution using > the same crystallization solution, the reaction occurs readily. > This is not surprising and there are already many examples in the literature. > However, when we crystallize a single amino acid variant (mutant within the > active site) with the same two substrates, we initially see the substrates > but we then observe in crystallo enzymatic activity and formation of the > final products over time. This structure is identical to the one determined > with the two products co-crystallized with the enzyme. The crystal packing > does not seem to be at play here. > I understand that in crystallo activities are well documented in the > literature and can be induced by addition of ligands, X-rays, change in > oxidative environment, etc? > Here, the substrates are present from the beginning of the crystallization > experiments with the same concentration. Nothing is added to the crystals > later on. Only the time differentiate the two type of crystals: after a > couple of weeks, one has the substrates in the active site (wt) while the > other has the products (variant). > > Is anyone aware of similar examples where a variant induce in crystallo > enzymatic activity without perturbation of the crystal? > > Thanks, > > Pierre > Dept of Pharmacology, Toxicology and cellular signaling > Paris Descartes University
[ccp4bb] Bergen, Norway: 14 PhD and 3 post-doc positions open
Hi all, The Faculty of Medicine and Dentistry in Bergen, Norway has 14 PhD student and 3 post-doc positions available. Bergen is a beautiful, vibrant, modern Scandinavian city with a high standard of living, plenty of opportunities for outdoor activities, and good connections to the rest of Europe. For more details, see: https://www.jobbnorge.no/en/available-jobs/job/134170/phd-positions-14-positions <https://www.jobbnorge.no/en/available-jobs/job/134170/phd-positions-14-positions> and https://www.jobbnorge.no/en/available-jobs/job/134181/postdoctoral-fellow-3-positions <https://www.jobbnorge.no/en/available-jobs/job/134181/postdoctoral-fellow-3-positions> Note: the candidates for all positions must, in addition to other relevant documents, provide a detailed research plan linked to a research group at the faculty, as well as a statement from the supervisor. Hence, prior contact, well in time, to a research group is an absolute pre-requisite. The newly established, ambitious structural biology groups at the Faculty include e.g. projects on structural neurobiology (http://www.uib.no/en/rg/petrikursula <http://www.uib.no/en/persons/Petri.Kursula>) and malaria parasite cytoskeleton and motility (http://www.uib.no/en/rg/inari <http://cc.oulu.fi/~inkursul/lab>). Interested qualified candidates are encouraged to contact one of the the corresponding group leaders with their CVs as soon as possible for pre-screening and possible application preparation, as the application deadline of March 12th is approaching fast. Contact for structural neurobiology: Petri Kursula (petri.kurs...@uib.no <mailto:petri.kurs...@uib.no>) Contact for the malaria project: Inari Kursula (inari.kurs...@uib.no <mailto:inari.kurs...@uib.no>) Petri Kursula -- Professor Department of Biomedicine University of Bergen, Norway http://www.uib.no/en/rg/petrikursula <http://www.uib.no/en/persons/Petri.Kursula> petri.kurs...@uib.no <mailto:petri.kurs...@biomed.uib.no> -- Group Leader, Adjunct Professor Faculty of Biochemistry and Molecular Medicine University of Oulu, Finland --
Re: [ccp4bb] strange X-ray diffraction diagram――RNA Or Complex？
From your picture it looks like you have both these needle clusters and single needle/rod-lke crystals. The diffraction pattern you show is what you expect from a needle cluster (with the ring-like patterns at low resolution), a single needle or a larger optimized single crystal should give you no trouble. Petri Petri Kursula, PhD -- Professor of Biochemistry and Molecular Biology Department of Biomedicine University of Bergen, Norway http://www.uib.no/en/persons/Petri.Kursula <http://www.uib.no/en/persons/Petri.Kursula> petri.kurs...@uib.no <mailto:petri.kurs...@biomed.uib.no> -- Project Leader, Docent Faculty of Biochemistry and Molecular Medicine Biocenter Oulu University of Oulu, Finland petri.kurs...@oulu.fi <mailto:petri.kurs...@oulu.fi> -- > On 12 Oct 2016, at 08:54, Liu Rachel <liuyujie1...@hotmail.com> wrote: > > > Dear everyone: > > Recently, I suffered a problem during my research work. I purified a zinc > finger protein, and crystallized as a beautiful cube in a reservoir solution > only containing phosphate as the precipitant, no other buffer or molecules. > However, regardless of multiple optimization, the crystal diffracted badly > (7~8 Å best). I have also tried co-crystallization with dsRNA because this > protein can bind to dsRNA. Then crystals grow in a new condition（2.5M > (NH4)2SO4，0.1M BTP, pH7.0）and its form change to cluster of needle. But the > X-ray diffraction diagram is very strange（as shown in the picture）. The Data > cannot be processed with HKL2000 either. I want to figure out, could this be > a RNA crystal rather than the complex? Or is there anybody know about the > crystal of RNA molecular？ > > Thank you very much! > > > Yujie Liu > Room 2071, research center in life sciences, > China Agricultural University > No. 2 yuanmingyuan west road, Haidian District, Beijing, 100193 P.R. China > Tel: (86)-10-62734078 > >
[ccp4bb] post-doc position in Oulu, Finland
Hi, I’d like to bring the following position into the attention of any suitable candidates: - POSTDOCTORAL POSITION IN MOLECULAR MATERIALS RESEARCH, UNIVERSITY OF OULU, FINLAND A two-year interdisciplinary postdoctoral position in molecular materials research is available in the Research Community of Molecular Materials (http://www.oulu.fi/molecularmaterials/node/25636 http://www.oulu.fi/molecularmaterials/node/25636) at the University of Oulu (http://www.oulu.fi/english http://www.oulu.fi/english), Finland. The community consists of seven research groups in physics, biophysics, nanotechnology, chemistry and biochemistry, and pursues both experimental and theoretical/computational work. The successful applicant will conduct research in tight association with at least two of the participating groups. The specific requirements, the contact information of the groups, and the instructions for applying can be found in https://www.saimanet.com/certiahome/open_job_view.html?did=5600jc=1id=867lang=en https://www.saimanet.com/certiahome/open_job_view.html?did=5600jc=1id=867lang=en . The deadline for applications is April 7, 2015. - Best regards, Petri Petri Kursula, PhD -- Professor of Biochemistry and Molecular Biology Department of Biomedicine University of Bergen, Norway http://www.uib.no/en/persons/Petri.Kursula petri.kurs...@biomed.uib.no -- Project Leader, Docent Faculty of Biochemistry and Molecular Medicine Biocenter Oulu University of Oulu, Finland petri.kurs...@oulu.fi --
Re: [ccp4bb] Formulation of my own mother liquor
Well I think some companies make the screens from stocks, the others adjust the pH of the final mixture, so you might want to check the small print for the screen you used in the first place… But when optimizing with your own solutions, you would in general take the easy way out - make good stocks and mix them as you wish. Petri Petri Kursula, PhD -- Professor of Biochemistry and Molecular Biology Department of Biomedicine University of Bergen, Norway http://www.uib.no/en/persons/Petri.Kursula http://www.uib.no/en/persons/Petri.Kursula petri.kurs...@biomed.uib.no mailto:petri.kurs...@biomed.uib.no -- Project Leader, Docent Faculty of Biochemistry and Molecular Medicine Biocenter Oulu University of Oulu, Finland petri.kurs...@oulu.fi mailto:petri.kurs...@oulu.fi -- On 21 Nov 2014, at 17:48, amro selem 03391c09f749-dmarc-requ...@jiscmail.ac.uk wrote: Dear All, first i wish you nice weekend, then i wanna ask about formulation of my own mother liquor, i want to optimize a condition containing 0.2m MgCl2, 0.1m Tris , PH 8; and 20% PEG6K as pricipitant. (PACT) the question is , should i make a stock solution from every ingredient by dissolving it in miliQ water. then mix all stuff together and add water till final concentration with out adjusting final pH. OR dissolve the PEG in pH adjusted buffer and then mix all ingredients , so the final pH will be 8. any suggest any idea or any one knows what the company do. CHEERS Amr
Re: [ccp4bb] Removing PEG3350
Hi, There is a gray area, where you would refrain from talking about low-MW contaminants. PEG3350 will be a highly elongated polymer, with way higher hydrodynamic radius than a globular molecule of the same MW. It also will bind a lot of H2O. Hence, it might not go through concentrators (but could actually get concentrated), and also could still be present in the protein fractions after GF. But I might be wrong, of course. Petri On 20 Aug 2014, at 20:48, Alexander Aleshin aales...@sanfordburnham.org wrote: Dear Remie, I meant application of GF as an ion exchange column. You can use special ion exchange columns, but our lab often uses preparative GF columns for this task. We just load the column, keeping sample volume the void volume. Thus, we do not concentrate a protein before an ion exchange, only after it. But that is inevitable. When I am afraid to loose a protein during its concentrating, I concentrate shoulders of the eluted peak first, then add a central part. My point was that it might be okay to exchange buffers by concentrating a protein, but other molecules like Peg3K would not penetrate the membrane as well as water or salts do, as a result their reduction in concentration will be unreliable. Like, you do a 10 fold concentrating/delusion of a solution, but the final concentration of PEG3K will drop only by 3 fold... Alex On Aug 19, 2014, at 9:42 AM, Remie wrote: Hi Alex, I disagree with you even though GF is always the last step in my purifications. Because it involves concentration before and after the GF so during the concentration you can already be doing the buffer exchange. You use GF when you want to purify other protein impurities if they are different sizes. Of course it has other uses too. But not quite practical for just changing buffer also considering the amount of protein you could be loosing along the process. If one is careful, centripreps are best for concentrating and changing the buffer. I tell you this from experience with large hard to express proteins. Best of luck, Remie On Aug 19, 2014, at 10:45 AM, Alexander Aleshin aales...@sanfordburnham.org wrote: Remie, Actually, concentrating of a protein solution is not the best approach to removing low MW impurities, gel filtration chromatography is more reliable and ... faster. Regards, Alex On Aug 19, 2014, at 7:03 AM, Remie Fawaz-Touma wrote: Hi Reza, I had to do this before. This protocol works for any PEG and any chemical to be removed from a solution: buffer exchange into the new buffer you want your protein to be in. There are ways to do that by 15 mL Amicon concentrators from millipore for large volumes, or if your protein is already concentrated, there are some small 0.5 mL concentrators from millipore as well. The key is to keep your spinning at low speeds (concentrators manuals will tell you) so you don’t precipitate or loose your protein. Check your protein concentration every 2 hours just to make sure you are not loosing it on concentrator surfaces and so on. Good Luck, Remie On Aug 19, 2014, at 9:55 AM, Reza Khayat rkha...@ccny.cuny.edu wrote: Hi, Does anyone have a protocol for getting rid of PEG3350 from a protein sample? Best wishes, Reza Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry, MR-1135 160 Convent Avenue New York, NY 10031 Tel. (212) 650-6070 www.khayatlab.org
[ccp4bb] post-doc/PhD student in Oulu, Finland
Our group at the Faculty of Biochemistry Molecular Medicine, Biocenter Oulu (University of Oulu, Finland) has an opening for a post-doctoral fellow (or an excellent PhD student). Our project focuses on the structure and function of proteins involved in the formation of the vertebrate myelin sheath. Our research covers both high-resolution structure determination of individual proteins and complexes, as well as the binding of these molecules to lipid membranes and the analysis of multilayered membrane assembllies. A multidisciplinary approach is used to link the structural information from single molecules to the properties of the multilayered myelin membrane. As methods we use e.g. X-ray crystallography, X-ray and neutron scattering/diffraction, NMR, electron microscopy, computational methods, and several other biophysical techniques. The exact research project will be planned in detail, once a suitable candidate has been found. Possible projects range from high-resolution structural biology on nervous system proteins and complexes to studies on the structure and dynamics of multilayered membranes. Hands-on and theoretical experience in protein chemistry, structural biology, biophysics, simulations of biomolecular systems, and/or cell biology will be highly advantageous. The ability to work independently and within a group, as well as the willingness to supervise junior colleagues, will be expected. Fluency in English (written and spoken) is required. Initial funding for 1 year is available; extension will be possible upon favourable funding decisions. More information from Petri Kursula (petri.kurs...@oulu.fi) and www.desy.de/~petri/research www.biochem.oulu.fi/kursula. Applications, including CV, publication list, and contact details for 2-3 references should be sent by email to the above address. Screening of applications will begin immediately. --- Petri Kursula, PhD project leader, adjunct professor Department of Biochemistry Biocenter Oulu, University of Oulu, Finland Department of Chemistry, University of Hamburg/DESY, Germany www.biochem.oulu.fi/kursula www.desy.de/~petri/research petri.kurs...@oulu.fi ---
[ccp4bb] PhD positions in Oulu, Finland
Dear all, our university currently has an open call for 107 PhD student positions, out of which 15 are within the Biocenter Oulu Doctoral Programme (see below), including structural biology projects. I would appreciate it, if this information could be brought to the attention of suitable candidates. Best regards, Petri --- Petri Kursula, PhD project leader, adjunct professor Department of Biochemistry Biocenter Oulu, University of Oulu, Finland Department of Chemistry, University of Hamburg/DESY, Germany www.biochem.oulu.fi/kursula www.desy.de/~petri/research petri.kurs...@oulu.fi --- -- The Biocenter Oulu Doctoral Programme (BCO-DP) is an integral part of Biocenter Oulu (BCO), a large multidisciplinary research institute heading the University of Oulu’s (UO) strategic research focus area of Biosciences and Health in Oulu, Finland. The scientific excellence of BCO is guaranteed by selection of the UO’s best bioscience and biomedical projects based on regular international evaluations. The research covers areas of biomedicine, molecular and cell biology, biochemistry, developmental biology, genetics, structural biology and bioinformatics in an inspiring international environment. BCO-DP announces 15 University of Oulu funded doctoral student positions for 2014-2017 in the Biosciences and Health field. BCO-DP CALL A: 12 DOCTORAL STUDENTS 12 PhD positions are available in the current BCO Main Research Projects. For further information, please go to the complete call announcement athttp://www.oulu.fi/uniogs/dppositionscall and choose Sub-call 2 (BCO-DP/A):http://www.oulu.fi/sites/default/files/content/UniOGS_BCO-DP-A.pdf. BCO-DP CALL B: 3 DOCTORAL STUDENTS 3 positions are available for a call of BRIDGE initiatives targeting strategically important new types of BCO or non-BCO-affiliated projects specifically to promote International Cooperation, Interdisciplinary projects, and/or National Cooperation in the Biosciences and Health focus area. For further information, please go to the complete call announcement at http://www.oulu.fi/uniogs/dppositionscall and choose Sub-call 3 (BCO-DP/B): http://www.oulu.fi/sites/default/files/content/UniOGS_BCO-DP-B.pdf. Contact: BCO-DP Coordinator: Dr. Ritva Saastamoinen, e-mail ritva.saastamoinen(at)oulu.fi The deadline for the applications is 16th September, 2013, 15:00 local time. Complete call announcement and application information are available at the University of Oulu Graduate School www page: http://www.oulu.fi/uniogs/dppositionscall and the links therein. To apply, please read carefully both the General Call text and the Sub-call specific text and follow all the instructions. --
Re: [ccp4bb] Intra-molecular interactions
For some starting points, google electrostatic interactions in intrinsically disordered proteins. Of course they occur in IDPs; they even have proportionally more charged residues than folded proteins. Petri On Nov 3, 2012, at 5:06 PM, Xiaodi Yu wrote: Dear All: I have a quick question: how common it is that electrostatic interactions are involved in intra-molecular interactions, particularly in intrinsically disordered proteins? Is this interaction specific and any example? Thanks, Dee Xiaodi Yu, Ph.D. Boston Children's Hospital Dana-Farber Cancer Institute Harvard Medical School 3 Blackfan Boston, MA 02115 --- Petri Kursula, PhD Group Leader, Docent of Neurobiochemistry Department of Biochemistry Biocenter Oulu, University of Oulu, Finland Department of Chemistry, University of Hamburg, Germany Visiting Scientist (CSSB-HZI, DESY, Hamburg, Germany) www.biochem.oulu.fi/kursula www.desy.de/~petri petri.kurs...@oulu.fi petri.kurs...@desy.de ---
[ccp4bb] PhD positions
Dear all, some current openings for PhD students, including those with interests in structural biology: 13 PhD student positions at Biocenter Oulu for 2012-2015 http://www.biocenter.oulu.fi/bcogs_newpositions.html plus a kind-of re-posting of my own ad: --- A PhD student position (3 years, starting January 2012), to use neutron scattering methods for studying proteins from the vertebrate myelin sheath. These proteins have functions e.g. in the interactions between the myelin sheath and the axon, and in the compaction of the multilayered myelin membrane. The project will involve large-scale recombinant expression of myelin proteins and studying their structure and function using mainly neutron scattering. The student will focus on the structure and dynamics of myelin proteins and their complexes, as well as their interactions with membranes. Complementary experiments will be carried out using X-rays and other biochemical/biophysical methods. The ideal candidate will: - have an MSc degree in biochemistry, physics, or a related field - have experience in recombinant protein expression and purification and/or in X-ray and neutron scattering methods - be genuinely interested in using neutrons to study biological macromolecules - be fluent in English The selected candidate will be affiliated with the Department of Biochemistry, University of Oulu, Finland, but a large part of the work is expected to be carried out at the Centre for Structural Systems Biology (CSSB-HZI), on-site the DESY synchrotron campus, Hamburg, Germany. The work will also involve carrying out measurements at international neutron infrastructures, and will be carried out in close collaboration with staff at such facilities, including the ILL (Grenoble). More information about our group can be found at www.biochem.oulu.fi/kursula, and informal queries by email are welcome. To apply, please send your cv, including list of publications, plus the names and email addresses of 2-3 referees by email to petri.kurs...@oulu.fi. The application deadline is October 31st, 2011, but screening of applications will start immediately due to the tight schedule. --- Petri Kursula, PhD Group Leader, Docent of Neurobiochemistry Department of Biochemistry, University of Oulu, Finland Department of Chemistry, University of Hamburg, Germany Visiting Scientist (CSSB-HZI, DESY, Hamburg, Germany) www.biochem.oulu.fi/kursula www.desy.de/~petri petri.kurs...@oulu.fi petri.kurs...@desy.de ---
Re: [ccp4bb] data processing problem with ice rings
Your main problem is not the ice rings but a wrong lattice/indexing solution. R factors are very high for even low res shells and I/sigma very low. To me this tells you are not finding your diffraction spots at all. First thing to try: Take more images for the indexing step and use only the strongest spots. And do not refine distance during indexing, as you probably have a pretty high mosaicity. Petri On Oct 14, 2011, at 7:12 AM, ChenTiantian wrote: Hi there, I am processing a dataset which has bad ice rings (as you can see in the attach png file). I tried both XDS and imosflm, and got similar results, it seems that adding EXCLUDE_RESOLUTION_RANGE cannot get rid of the effects of the ice rings. the following is part of the CORRECT.LP which is the second attached file, you can find more details there. SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE = -3.0 AS FUNCTION OF RESOLUTION RESOLUTION NUMBER OF REFLECTIONSCOMPLETENESS R-FACTOR R-FACTOR COMPARED I/SIGMA R-meas Rmrgd-F Anomal SigAno Nano LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr 4.24 371525537 5545 99.9% 46.9% 52.7% 371502.4850.8%19.4% -28% 0.5135136 3.01 553449002 9840 91.5% 62.7% 65.1% 551161.7668.3%48.1% -28% 0.5207760 2.46 84636 12699 12703 100.0% 67.4% 84.7% 846341.5573.0%54.2% -19% 0.513 12104 2.13 97910 14743 14987 98.4% 254.5%199.3% 979080.16 276.2% 4899.9% -23% 0.473 14037 1.90 110260 16846 16940 99.4% 299.2%303.3% 1102450.06 325.0% -99.9% -17% 0.422 15995 1.74 118354 18629 18744 99.4%1062.0% 1043.6% 118317 -0.20 1156.4% -99.9% -13% 0.380 17414 1.61 122958 20193 20331 99.3% 967.5% 1571.1% 1228680.10 1059.7% 987.3%-2% 0.402 18348 1.51 125075 21554 21794 98.9% 838.9% 1355.1% 1249330.08 922.6% 1116.9%-1% 0.402 18977 1.42 72057 17042 23233 73.4% 640.8%775.3% 703910.08 732.5% 826.7%-8% 0.425 10003 total 823746 136245144117 94.5% 166.4%166.7% 8215620.40 181.1% 296.7% -15% 0.435 119774 Note that I/SIGMA of each resolution shell is 2.5, so how should I do to process the dataset properly? Any suggestion about this super ice rings? Thanks! Tiantian -- Shanghai Institute of Materia Medica, Chinese Academy of Sciences Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, Shanghai, 201203 csrc.pngCORRECT.LP --- Petri Kursula, PhD Group Leader, Docent of Neurobiochemistry Department of Biochemistry, University of Oulu, Finland Department of Chemistry, University of Hamburg, Germany Visiting Scientist (CSSB-HZI, DESY, Hamburg, Germany) www.biochem.oulu.fi/kursula www.desy.de/~petri petri.kurs...@oulu.fi petri.kurs...@desy.de ---
Re: [ccp4bb] Setup pymol in Mac OS X 10.7
Choice #5: you can purchase a licensed version? Petri On Sep 21, 2011, at 4:38 PM, Pete Meyer wrote: For a fourth choice, you can do a stand-alone build of PyMOL and its dependencies with relatively little problem (at least on 10.6; haven't upgraded yet). Pete Xiaoguang Xue wrote: As I know, you have 3 choices: 1, You can apply a free educational-use-only MacPymol from the company, Schrodinger, LLC. This is the easiest way, just move the MacPymol program into your Program Folder. 2, I think you still can try to install Pymol by Fink. Just follow the wiki page of Pymol.(http://www.pymolwiki.org/index.php/MAC_Install). But there is a compatible problem between Fink and Lion. There is a Lion upgrade notes written by William Scott(http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Lion_upgrade_notes). Maybe it can help you. 3, If Fink doesn't work. I think you can try to use MacPorts. It looks like there is no compatible problem between MacPorts and MacOS Lion. The install process is very simple (http://www.macports.org/install.php). I found MacPorts still contain Pymol package, also include apbs plugin. But there is no other protein xtallography software packages, like CCP4 and coot. And It is impossible to install MacPorts and Fink at the same time. So If you also want install CCP4 or coot from source code, it will be very inconvenient. Best! Xiaoguang Xue On Wed, Sep 21, 2011 at 11:04 AM, Mecy Shi mecy...@gmail.commailto:mecy...@gmail.com wrote: Dear members, I want to setup pymol in Mac OS X 10.7, but I didn't do this before. Who can tell me how to setup and tell me the detail setup procedure. and if need other programs to setup this. Thank you very much! -- Xiaoguang Xue, PhD student Utrecht University Crystal Structural Chemistry Padualaan 8. Room N807 3584 CH Utrecht The Netherlands Tel. +31-30-253-2383 --- Petri Kursula, PhD Group Leader, Docent of Neurobiochemistry Department of Biochemistry, University of Oulu, Finland Department of Chemistry, University of Hamburg, Germany Visiting Scientist (CSSB-HZI, DESY, Hamburg, Germany) www.biochem.oulu.fi/kursula www.desy.de/~petri petri.kurs...@oulu.fi petri.kurs...@desy.de ---
[ccp4bb] PhD student position
Dear colleagues, I would appreciate it if you could bring this off-topic opportunity to the attention of any suitable candidates. Petri --- A PhD student position is available in the group of Dr. Petri Kursula, to use neutron scattering methods to study proteins specifically expressed in the vertebrate myelin sheath. These proteins have functions e.g. in the interactions between the myelin sheath and the axon, and in the compaction of the multilayered myelin membrane. The project will involve large-scale recombinant expression of myelin proteins and studying their structure and function using mainly neutron scattering. The student will focus on the structure and dynamics of myelin proteins and their complexes, as well as their interactions with membranes. Complementary experiments will be carried out using X-rays and other biochemical/biophysical methods. The ideal candidate will: - have an MSc degree in biochemistry, physics, or a related field - have experience in recombinant protein expression and purification and/or in X-ray and neutron scattering methods - be genuinely interested in using neutrons to study biological macromolecules - be fluent in English The selected candidate will be affiliated with the Department of Biochemistry, University of Oulu, Finland, but a large part of the work is expected to be carried out at the Centre for Structural Systems Biology (CSSB-HZI), on-site the DESY synchrotron campus, Hamburg, Germany. The work will also involve performing measurements at international neutron infrastructures, and will be carried out in collaboration with staff at such facilities, including the ILL (Grenoble). The position will be funded by the European Spallation Source (ESS). More information about our group can be found at www.biochem.oulu.fi/kursula, and informal queries by email are also welcome. To apply, please send your cv, including list of publications, plus the names and email addresses of 2-3 referees by email to petri.kurs...@oulu.fi. The application deadline is July 31st, 2011. --- Petri Kursula, PhD Group Leader and Docent of Neurobiochemistry (University of Oulu, Finland) Visiting Scientist (CSSB-HZI, DESY, Hamburg, Germany) www.biochem.oulu.fi/kursula www.desy.de/~petri petri.kurs...@oulu.fi petri.kurs...@desy.de ---
[ccp4bb] Post-doctoral position available
A post-doctoral position is available in the group of Dr. Petri Kursula, to study structure-function relationships in proteins specifically expressed in the myelin sheath. The targets of the project are membrane-associated myelin proteins, which have functions e.g. in the interactions between the myelin sheath and the axon, and in the compaction of the multilayered myelin membrane. We are specifically interested in the structures of these proteins and their complexes, their interactions with macromolecular and small-molecule ligands, as well as membranes. The project will involve e.g. large-scale recombinant expression of myelin proteins or domains thereof, their biophysical characterization, X-ray crystallography and other structural biology methods, as well as more specific methods, such as oriented CD spectroscopy and other membrane interaction assays. The ideal candidate will have: - PhD in biochemistry/structural biology or a closely related field - a good publication record - significant hands-on experience in recombinant protein expression and large-scale purification - a genuine interest in structural biology - fluency in English - experience in supervising junior colleagues Previous work with extracellular domains or peripheral membrane proteins will be considered an asset, as will experience in versatile structural biology and biophysical methods. The position is initially available for 1 year, with possibilities for extension for up to 3 years. The selected candidate will be affiliated with the Department of Biochemistry, University of Oulu, Finland, but a large part of the work is expected to be carried out at the Centre for Structural Systems Biology (CSSB-HZI), on-site the DESY synchrotron campus, Hamburg. More information about our group can be found at www.biochem.oulu.fi/kursula. To apply, please send your cv, including list of publications, plus the names and email addresses of 2-3 referees by email to petri.kurs...@oulu.fi. The application deadline is July 31st, 2011. --- Petri Kursula, PhD Group Leader and Docent of Neurobiochemistry (University of Oulu, Finland) Visiting Scientist (CSSB-HZI, DESY, Hamburg, Germany) www.biochem.oulu.fi/kursula www.desy.de/~petri petri.kurs...@oulu.fi petri.kurs...@desy.de ---
Re: [ccp4bb] xds question
Hi, oh, I'm also surprised people seem to use something else than '-3' as the cutoff, i.e. are throwing away data. This, obviously, brings into new light all the discussions (which I definitely don't wish to restart) on the 'cutoff values' in R(sym) and I/sI which you use to determine the 'resolution limit'...and gives one more thing for referees to think about/require when looking at Table 1. I am sure most of them, and the readers, take it for granted that no data were thrown out before calculating those numbers...and sure, the effects of actually using those data might occasionally be more severe than a drop of, say, 1% in the apparent overall R(sym) or an increase in I/sI. Petri On Feb 8, 2011, at 3:07 PM, Robert Immormino wrote: Hi, I've pasted below the reasons from Dan Gewirth and the HKL2000 manual authors for having a -3 sigma cutoff... I'll add briefly that if you assume the weak data has a Gaussian distribution around zero a -3 sigma cutoff allows you to record ~99.8% of the data. -bob SIGMA CUTOFF Cutoff for rejecting measurements on input. Default = -3.0. Be very careful if you increase this. What is the rationale for using sigma cutoff -3.0 in SCALEPACK? Wouldn't you want to reject all negative intensities? Why shouldn't you use a sigma cutoff 1.0 or zero? The answer to these questions is as follows: The best estimate of I may be negative, due to background subtraction and background fluctuation. Negative measurements typically represent random fluctuations in the detector's response to an X-ray signal. If a measurement is highly negative (= -3[[sigma]]) than it may be more likely the result of a mistake, rather than just random fluctuation. If one eliminates negative fluctuations, but not the positive ones before averaging, the result will be highly biased. In SCALEPACK, sigma cutoff is applied before averaging. If one rejects all negative intensities before averaging a number of things would happen: 1. The averaged intensity would always be positive; 2. For totally random data with redundancy 8, in a shell where there was no signal, , there would be on average 4 positive measurements, with average intensity one sigma. This is because the negative measurements had been thrown out. So the average of the four remaining measurements would be about 2 sigma! This would look like a resolution shell with a meaningful signal; 3. R-merge would be always less than the R-merge with negative measurements included; 4. A SIGMA CUTOFF of 1 would improve R-merge even more, by excluding even more valid measurements. Why should this worry you? Exclusion of valid measurements will deteriorate the final data set. One may notice an inverse relationship between R-merge and data quality as a function of sigma cutoff. So much for using R-merge as any criterion of success. Even the best (averaged) estimate of intensity may be negative. How to use negative I estimates in subsequent phasing and refinement steps is a separate story. The author of SCALEPACK suggests the following: 1. You should never convert I into F. 2. You should square Fcalc and compare it to I. Most, but not all of the crystallography programs do not do this. That is life. In the absence of the proper treatment one can do approximations. One of them is provided by French and also by French and Wilson. An implementation of their ideas is in the CCP4 program TRUNCATE. A very simplified and somewhat imprecise implementation of TRUNCATE is this: if I [[sigma]](I), F=sqrt(I) if I [[sigma]](I), F=sqrt([[sigma]](I)) formatSIGMA CUTOFF value default -3 example SIGMA CUTOFF -2.5 referenced from: http://www.hkl-xray.com/hkl_web1/hkl/Scalepack_Keywords.html --- Petri Kursula, PhD Group Leader and Docent of Neurobiochemistry (University of Oulu, Finland) Visiting Scientist (CSSB-HZI, DESY, Hamburg, Germany) www.biochem.oulu.fi/kursula www.desy.de/~petri petri.kurs...@oulu.fi petri.kurs...@desy.de ---
[ccp4bb] post-doctoral position
A post-doctoral position is available at the Department of Biochemistry, University of Oulu, Finland, in the group of Dr. Petri Kursula. Our work aims at a comprehensive structure-function characterization of the various myelin-specific proteins that play roles in the development and functioning of the vertebrate nervous system. The work will include recombinant expression and purification of challenging myelin protein targets and their biochemical, biophysical, and structural characterization. The methods used will include crystallography, scattering methods, and protein-protein interaction techniques. The suitable candidate is experienced in molecular biology and protein purification, experience with membrane proteins is a definite plus. A keen interest in structural biology is required, as is the ability to work both independently and as a part of a team. Fluency in English and good communication skills are required. The candidate is not afraid to work towards a long-term goal in a challenging project. The University of Oulu is one of the largest universities in Finland, and the Department of Biochemistry harbours a number of research groups and a complete infrastructure for structural biology. Ample beamtime is available at European infrastructures for data collection. Applications should be sent by email to Petri Kursula (petri.kurs...@oulu.fi) by May 12th 2010, and should include a CV, publication list, and the contact details of 2-3 referees. More details on the project can be obtained from www.biochem.oulu.fi/kursula, and informal queries are welcome. --- Petri Kursula, PhD Academy Research Fellow (Academy of Finland) Group Leader and Docent of Neurobiochemistry (University of Oulu, Finland) Visiting Scientist (CSSB-HZI, DESY, Hamburg, Germany) www.biochem.oulu.fi/kursula www.desy.de/~petri petri.kurs...@oulu.fi petri.kurs...@desy.de ---
[ccp4bb] Post-Doctoral Opportunity in Oulu, Finland
Post-Doctoral Opportunity in Oulu, Finland A post-doctoral opportunity, funded by the Sigrid Juselius Foundation, exists in our group for an initial period of approximately 1 year, with possible extension. The work will involve structural studies on proteins important for the function of the human nervous system, mainly proteins from the myelin sheath. The successful candidate will have extensive hands-on experience on at least some of the following: large-scale expression and purification of recombinant proteins, membrane protein purification and characterisation, protein crystallisation, X-ray crystallography, small-angle X-ray scattering. Any further relevant experience will also be considered an asset. A large number of ready-to-use expression clones for the target proteins exists in the lab. The University of Oulu is the largest university in Northern Finland. The Department of Biochemistry is fully equipped for protein structural biology work, and we have frequent access to European synchrotrons for data collection. To apply, please send me an email with a full CV (including list of publications) plus the contact details of at least two scientists for references. More information can be found at www.biochem.oulu.fi/kursula. Informal queries by email are also welcome. Best regards, Petri --- Petri Kursula, Ph.D. Academy Research Fellow Docent of Neurobiochemistry Department of Biochemistry University of Oulu Oulu, Finland [EMAIL PROTECTED] cc.oulu.fi/~pkursula www.biochem.oulu.fi/kursula ---
Re: [ccp4bb] XDS and overlaps
Hi, While on the subject, a related matter that may be of relevance: surprisingly many people do not remove the outliers after XDS processing (via using the REMOVE.HKL file) and this, in certain cases, has its effects on the intensity distribution and 'refinability'. Petri On Feb 21, 2008, at 11:44 AM, Kay Diederichs wrote: Engin Ozkan schrieb: Hi everyone, I have been recently relying on XDS quite a bit, but at the same time worrying about how XDS treats overlaps. We had one dataset that both HKL2000 and Mosflm would show to have severe overlaps, as expected due to unit cell parameters and the unfortunate crystal orientation in the loop. We always ended up with completeness percentages in the 70's. XDS can find the same lattice, index and scale the data, but yields a 100% complete mtz (and a nice structure). Without the HKL/ Mosflm-like GUI, it is difficult to assess the fate of the overlapped observations in XDS. What I could see with VIEW was that some observations were being divided into several ovals, probably different reflections, but I'm not very certain. So, the basic question is, how does XDS treat overlaps? I could not find in the documentation an answer to this question; the single mention of overlaps I could find tells me that XDS can recognize overlaps, but does not tell me if it rejects them, or divvies them up into separate reflections, and if that is the case, how does it divide them, and how reliable is that? Depending on how it divides the overlaps, could that affect commonly-used intensity stats and distributions? Thanks, Engin Engin, the basic answer is: a) each pixel of the detector is assigned to its nearest reflection in reciprocal space b) some of these pixels will mostly allow the background estimation, others will mostly contribute to the integration area (but as they are transformed into a local coordinate system there is not a 1:1 relationship). At this step, pixels which should be background but are higher than expected (due to overlap) are rejected. c) for each reflection, the background is estimated, and the 3D profile is assembled from the pixels contributing to it d) a comparison is made: for a reflection, is the percentage of its observed profile assembled in c) larger than some constant (called MINPK in XDS.INP)? If the answer is no, this reflection will be discarded (you could call this situation overlap). Among other things, this means that: a) the program does _not_ look around each reflection to detect an overlap situation, it just tries to gather the pixels for each reflection b) as a user, when your crystal-detector distance was chosen too low or the reflections are very broad (resulting in generally strong overlap), you may reduce MINPK down to 50. This will result in more completeness, but you should monitor the quality of the resulting data. Conversely, if you raise MINPK over its default of 75 you will discard more reflections, but the resulting dataset will be a bit cleaner. The reference is W. Kabsch (1988) Evaluation of single-crystal X-ray diffraction data from a position-sensitive detector. J. Appl. Cryst. 21, 916-924. (http://dx.doi.org/10.1107/S0021889888007903) HTH, Kay -- Kay Diederichshttp://strucbio.biologie.uni-konstanz.de email: [EMAIL PROTECTED]Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz --- Petri Kursula, Ph.D. Academy Research Fellow Docent of Neurobiochemistry Department of Biochemistry University of Oulu Oulu, Finland [EMAIL PROTECTED] cc.oulu.fi/~pkursula www.biochem.oulu.fi/kursula ---
