Re: [ccp4bb] RFI on access to digital data
Dear Ashley, Excellent find! Within it I see that one of the UK agencies states:- vii. What resources will you require to deliver your (Data management and sharing) plan? Greetings, John On Wed, Nov 9, 2011 at 10:50 PM, Deacon, Ashley M. adea...@slac.stanford.edu wrote: I also found this interesting: http://www.datadryad.org/ Ashley. From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Peter Keller [pkel...@globalphasing.com] Sent: Wednesday, November 09, 2011 8:25 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] RFI on access to digital data On Tue, 8 Nov 2011, Gerard DVD Kleywegt wrote: Relevant to the discussion about archiving image data: http://federalregister.gov/a/2011-28621 Interesting that it quotes MIAME (minimum information about a microarray experiment) as an example of community-driven standardisation. When MIAME was being formulated, it drew in part, and learned from, the history of the PDB. It is also a field where (I am told) the raw data really are useless without metadata about the experiment. Regards, Peter. -- Peter Keller Tel.: +44 (0)1223 353033 Global Phasing Ltd., Fax.: +44 (0)1223 366889 Sheraton House, Castle Park, Cambridge CB3 0AX United Kingdom -- Professor John R Helliwell DSc
[ccp4bb] PhD and Post-doctoral Positions in Membrane Structural Biology at University of Freiburg
A post-doctoral position and a PhD position are open to study structure, mechanism and function of clinically relevant cation/proton antiporters and their integration in signalling processes. The project is part of the Collaborative Research Center 746 (http://www.sfb746.uni-freiburg.de) and is connected to the European Drug Initiative on Channels and Transporters (http://www.edict-project.eu). The Hunte research group is based at the Institute for Biochemistry and Molecular Biology of the University of Freiburg and is member of the BIOSS Centre for Biological Signalling Studies (Cluster of Excellence, http://www.bioss.uni-freiburg.de). Positions are available from January 2012. For more information, please visit the lab web site (http://www.biochemie.uni-freiburg.de/hunte/, go to « Research ») or contact Carola Hunte, to whom applications should be sent by Email. Prof. Dr. Carola Hunte, Institute for Biochemistry and Molecular Biology, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany (http://www.biochemie.uni-freiburg.de/hunte/)
[ccp4bb] crystallization of synthetic peptides
Dear crystallographers, Because of the low cost and speed of synthesizing 40- to 60-mer peptides, I wonder whether anyone has (good or bad) experiences crystalizing such peptides. In literature, I've found up to 34-mer synthetic coiled coils, but no other protein class. I can imagine that a protein sample with a few percent random deletion mutants mixed into it won't crystallize easily, but has anyone actually tried? cheers, Hans
Re: [ccp4bb] crystallization of synthetic peptides
Hans, Most natural toxins from snakes, scorpions etc are 50+/-some peptides. And quite a few of those have been studied and crystallized (see pdb for a list). Having worked on one of these structures as a graduate student, I can share my experience: - Purification is harder than you would think. You are talking about 10kD, usually around 5kD. Many methods (size exclusion, even concentration over a simple membrane) don't work as easily as you would like. - I did not have much of a problem crystallizing (i.e. no worse than other proteins, maybe even a little easier) - Crystals tend to diffract well (maybe better than average) - Structures can be hard to solve; MIR is very difficult because ions tend to not go into such crystals easily (because the molecules are small and tightly packed?); MR is hard because (again) it does not work very well on very small systems - Crystallization is not necessarily purification - if you have a mixture of peptides to start with, it may be harder to crystallize, or not: you might get a crystal that is a (random-ish) mixture. - If you have more than two cysteines in your sequence (natural toxins typically do), the additional problem is to get the correct folding and disulphide bridges; alternatively it is very hard to discriminate between correctly and incorrectly linked disulphides Finally: These sequence should be small enough for NMR. That may or may not answer your questions, but it avoids your original question. Mark -Original Message- From: H. Raaijmakers hraaijmak...@xs4all.nl To: CCP4BB CCP4BB@JISCMAIL.AC.UK Sent: Thu, Nov 10, 2011 8:16 am Subject: [ccp4bb] crystallization of synthetic peptides Dear crystallographers, Because of the low cost and speed of synthesizing 40- to 60-mer peptides, I wonder whether anyone has (good or bad) experiences crystalizing such peptides. In literature, I've found up to 34-mer synthetic coiled coils, but no other protein class. I can imagine that a protein sample with a few percent random deletion mutants mixed into it won't crystallize easily, but has anyone actually tried? cheers, Hans
Re: [ccp4bb] crystallization of synthetic peptides
As Mark says, structure solution of smallish peptides is not usually as easy as one might expect. A number of the small (say up to 50 residue) peptides in the PDB were solved by direct methods, but these require native data to 1.2A or (preferably) better. If sulfur is present in the molecule, SAD is a good choice and does not require such a very high resolution, but you need highly redundant data, so a high symmetry space group helps. If even one Met is present in the sequence, since you are synthesizing the peptides anyway, you can replace it with selenomethionine. George On 11/10/2011 09:15 PM, mjvdwo...@netscape.net wrote: Hans, Most natural toxins from snakes, scorpions etc are 50+/-some peptides. And quite a few of those have been studied and crystallized (see pdb for a list). Having worked on one of these structures as a graduate student, I can share my experience: - Purification is harder than you would think. You are talking about 10kD, usually around 5kD. Many methods (size exclusion, even concentration over a simple membrane) don't work as easily as you would like. - I did not have much of a problem crystallizing (i.e. no worse than other proteins, maybe even a little easier) - Crystals tend to diffract well (maybe better than average) - Structures can be hard to solve; MIR is very difficult because ions tend to not go into such crystals easily (because the molecules are small and tightly packed?); MR is hard because (again) it does not work very well on very small systems - Crystallization is not necessarily purification - if you have a mixture of peptides to start with, it may be harder to crystallize, or not: you might get a crystal that is a (random-ish) mixture. - If you have more than two cysteines in your sequence (natural toxins typically do), the additional problem is to get the correct folding and disulphide bridges; alternatively it is very hard to discriminate between correctly and incorrectly linked disulphides Finally: These sequence should be small enough for NMR. That may or may not answer your questions, but it avoids your original question. Mark -Original Message- From: H. Raaijmakers hraaijmak...@xs4all.nl To: CCP4BB CCP4BB@JISCMAIL.AC.UK Sent: Thu, Nov 10, 2011 8:16 am Subject: [ccp4bb] crystallization of synthetic peptides Dear crystallographers, Because of the low cost and speed of synthesizing 40- to 60-mer peptides, I wonder whether anyone has (good or bad) experiences crystalizing such peptides. In literature, I've found up to 34-mer synthetic coiled coils, but no other protein class. I can imagine that a protein sample with a few percent random deletion mutants mixed into it won't crystallize easily, but has anyone actually tried? cheers, Hans
Re: [ccp4bb] How to calculate the percent of the buried hydrohobic surface area in a protein with known structure
Jiyuan, I believe PISA will easily do this for you. C On Thu, Nov 10, 2011 at 5:10 PM, Ke, Jiyuan jiyuan...@vai.org wrote: Dear All, ** ** I have a protein that exists as a dimer in the crystal structure. I want to calculate and compare the area of the buried hydrophobic core of a monomer with that of a dimer? Does anyone know how to do this? Thanks in advance! ** ** Jiyuan Ke, Ph.D. Research Scientist Van Andel Research Institute 333 Bostwick Ave NE Grand Rapids, MI 49503 ** ** -- *The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer.* --
[ccp4bb] Web Seminar: Home Lab SAD phasing with HKL-3000: From data collection to refined models in less than an hour
Dear colleagues, I would like to draw your attention to an upcoming free, educational webinar to be presented by Jim Pflugrath, Ph. D. titled Home Lab SAD phasing with HKL-3000: From data collection to refined models in less than an hour. This interactive tutorial and webinar will demonstrate how to use HKL-3000 to process diffraction images, find the anomalous substructure with SHELXD, phase with SHELXC, MLPHARE, and DM, then build with ARP/wARP and refine with REFMAC (Kudos to all the authors of these programs!). Emphasis will be on practical tips and how to interpret the output. Relatively low redundancy diffraction datasets will be used as examples to dispel some of the myths about sulfur and selenium Home Lab SAD phasing. This webinar is scheduled to occur on Thursday, November 17th 10:00 AM CST (8:00 AM PST / 4:00 PM GMT). You can find more information, including a registration link at: http://www.rigaku.com/protein/webinars.html. Best regards, Angela NOTE: You can watch some of our past webinars at: http://www.rigaku.com/protein/webinars-past.html. This list of webinars includes educational topics, such as data processing with d*TREK, mosflm, XDS and HKL as well as topics on diffraction data collection. Also, don't miss the great talks and historical perspectives from industry experts such as Michael Rossmann, Brian Matthews and Ian Wilson. -- Angela R. Criswell, Ph. D. Rigaku Americas Corporation 9009 New Trails Drive The Woodlands, TX 77381 USA Ph: +1 281 362 2300 ext. 216 Fax: +1 281 364 3628 Email: angela.crisw...@rigaku.com URL: http://www.rigaku.com
[ccp4bb] effect of Izit dye within the crystal structure
Hi crystallographers Has anyone actually collected data on a crystal that has been treated with Izit dye? If so did you see any structural effects or know any structure that presentthis dye? Cheers Adam Campos
Re: [ccp4bb] effect of Izit dye within the crystal structure
I wouldn't be surprised if it is methylene blue. Jürgen On Nov 10, 2011, at 11:34 PM, adam andres wrote: Hi crystallographers Has anyone actually collected data on a crystal that has been treated with Izit dye? If so did you see any structural effects or know any structure that present this dye? Cheers Adam Campos .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://web.mac.com/bosch_lab/
Re: [ccp4bb] crystallization of synthetic peptides
Some HIV protease structures have been done using synthetic HIV protease (99 amino acid monomers). Look at J. Martin et al from UQ in Queensland. I believe this was done with Steve Kent. The protein contains some non-natural amino acids too. Hope this helps -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of H. Raaijmakers Sent: Friday, 11 November 2011 4:17 a.m. To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] crystallization of synthetic peptides Dear crystallographers, Because of the low cost and speed of synthesizing 40- to 60-mer peptides, I wonder whether anyone has (good or bad) experiences crystalizing such peptides. In literature, I've found up to 34-mer synthetic coiled coils, but no other protein class. I can imagine that a protein sample with a few percent random deletion mutants mixed into it won't crystallize easily, but has anyone actually tried? cheers, Hans