[ccp4bb] Epigenetic symposium, Nov 13/14
Dear All We would like to draw your attention to the forthcoming symposium: "Epigenetics Mechanisms in Health and Disease - From Biology to Medicine" November 13th & 14th 2008 Said Business School, Oxford, UK This symposium will bring together clinical and preclinical scientists at the forefront of epigenetics and chromatin biology research to discuss the latest results. It will explore future trends in epigenetics and related fields of gene regulation, development, molecular recognition and signalling, with an emphasis on prospects of translation into clinical applications. If you would like to attend, and/or present a poster, please find the registration site which contains full details of the symposium including programme at: http://www.sgc.ox.ac.uk/symposium Cheers phx
[ccp4bb] foam dewar usage ?
Dear all, Does anyone in the biocrystallogaphy community use foam dewars for handly liquid nitrogen and freezing/manipulating frozen protein crystals ? We are interested in the following dewar package from Hampton Research : http://www.hamptonresearch.com/products/ProductDetails.aspx?cid=24&sid=187&pid=559 But before purchasing, we would like to have any comments on the advantages and drawbacks from people who already tried those dewars. Thanks in advance for your help and advices. -- Dr JEAN-BAPTISTE REISER - Chargé de recherche CNRS ** Laboratoire de Cristallographie et Cristallogenèse des Protéines (LCCP) et Partnership for Structural Biology (PSB) Institut de Biologie Structural Jean-Pierre Ebel (IBS) - CNRS - CEA - UJF 41, rue Jules Horowitz 38027 Grenoble - France Phone : +33 (0)4 76 20 94 49 Fax : +33 (0)4 76 20 94 80 E-mail : [EMAIL PROTECTED] Web sites : http://www.ibs.fr ; http://psb.esrf.fr ** begin:vcard fn:Jean-Baptiste REISER n:REISER;Jean-Baptiste org:CNRS;IBS/LCCP & PSB adr:;;41 rue Jules Horowitz;Grenoble Cedex;;38027;France email;internet:[EMAIL PROTECTED] title;quoted-printable:Charg=C3=A9 de recherche CNRS tel;work:+33 (0)4 76 20 94 49 tel;fax:+33 (0)4 76 20 94 80 x-mozilla-html:TRUE url:www.ibs.fr version:2.1 end:vcard
Re: [ccp4bb] foam dewar usage ?
Jean-Baptiste, Since these were conceived and developed by Jon Spear when he was a member of my group (at the ALS at the time), I know a bit about these Dewars, their intended usage, and relative benefits. When Jon first made them, the beamline users and staff quickly realized the advantages, they spread around the ALS, and then to other sources. My guess is that for other beamlines that have both these and vacuum-jacketed Dewars, the users prefer these over other options. As with all things, the advantages and disadvantages must be viewed in context of what the use is. The fact that these will not shatter, can be shaped to whatever the needed dimensions are and pockets can be machined in to allow for transport pucks, cryo-tools, etc., they cool and warm rapidly and are inexpensive, are all distinct advantages. Thus for freezing and manipulating crystals at home or the beamline, they are excellent and inexpensive options. Regarding the two comments that followed your post from Uwe and James: Uwe: When using Berkeley-style pucks or Unipucks (which replicated the Berkeley form factor), these are sufficiently dimensioned, and I believe there is a version that accommodates the SSRL cassette. If you want another dimension, I suggest contacting Jon directly and discuss this with him. James: I'm not sure why you think that chemical resistance or autoclaving are relevant to the discussion, as these are for holding and transporting liquid nitrogen and sample cryo-transport units. Also they are machined with a bit more precision than a "carpet knife" would give, and this eliminates the burrs or other bits that may tend to flake off, as well as allowing for shaping to need. - Thomas Thomas Earnest, Ph.D. Senior Scientist and Group Leader Structural Proteomics Development Group Physical Biosciences Division MS64R0121 Lawrence Berkeley National Laboratory Berkeley CA 94720 [EMAIL PROTECTED] 510 486 4603 Jean-Baptiste REISER wrote: Dear all, Does anyone in the biocrystallogaphy community use foam dewars for handly liquid nitrogen and freezing/manipulating frozen protein crystals ? We are interested in the following dewar package from Hampton Research : http://www.hamptonresearch.com/products/ProductDetails.aspx?cid=24&sid=187&pid=559 But before purchasing, we would like to have any comments on the advantages and drawbacks from people who already tried those dewars. Thanks in advance for your help and advices. -- *Dr JEAN-BAPTISTE REISER - Chargé de recherche CNRS* ** *Laboratoire de Cristallographie et Cristallogenèse des Protéines (LCCP)* *et Partnership for Structural Biology (PSB)* *Institut de Biologie Structural Jean-Pierre Ebel (IBS) - CNRS - CEA - UJF* 41, rue Jules Horowitz 38027 Grenoble - France Phone : +33 (0)4 76 20 94 49 Fax : +33 (0)4 76 20 94 80 E-mail : [EMAIL PROTECTED] Web sites : http://www.ibs.fr ; http://psb.esrf.fr **
Re: [ccp4bb] foam dewar usage ?
Yes, we use them all the time and they're great. Stuff does not slip on the bottom like it does in the glass Dewars and the formation of ice is greatly reduced. Plus, they're much easier to dry. Artem > Does anyone in the biocrystallogaphy community use foam dewars for > handly liquid nitrogen and freezing/manipulating frozen protein > crystals ?
Re: [ccp4bb] foam dewar usage ?
They work fine and they don't break if you drop them. Bear in mind that they aren't resistant to a lot of chemicals and that you can't autoclave them. Also, the $160 price tag suggests a lucrative market niche for someone who has rudimentary skill with a carpet knife. On Oct 9, 2008, at 1:17 AM, Jean-Baptiste REISER wrote: Dear all, Does anyone in the biocrystallogaphy community use foam dewars for handly liquid nitrogen and freezing/manipulating frozen protein crystals ? We are interested in the following dewar package from Hampton Research : http://www.hamptonresearch.com/products/ProductDetails.aspx?cid=24&sid=187&pid=559 But before purchasing, we would like to have any comments on the advantages and drawbacks from people who already tried those dewars. Thanks in advance for your help and advices. -- Dr JEAN-BAPTISTE REISER - Chargé de recherche CNRS ** Laboratoire de Cristallographie et Cristallogenèse des Protéines (LCCP) et Partnership for Structural Biology (PSB) Institut de Biologie Structural Jean-Pierre Ebel (IBS) - CNRS - CEA - UJF 41, rue Jules Horowitz 38027 Grenoble - France Phone : +33 (0)4 76 20 94 49 Fax : +33 (0)4 76 20 94 80 E-mail : [EMAIL PROTECTED] Web sites : http://www.ibs.fr ; http://psb.esrf.fr ** -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com
[ccp4bb] disulfide bond in coot
Does anyone know how to prevent Coot from establishing a disulfide bond between two adjacent Cys residues? I have reason to suspect that the bond is (at least partially) reduced. Thanks. Klaus - Klaus Fütterer, Ph.D. School of Biosciences P: +44-(0)-121-414 5895 University of Birmingham F: +44-(0)-121-414 5925 Edgbaston E: [EMAIL PROTECTED] Birmingham, B15 2TT, UK W: www.biochemistry.bham.ac.uk/klaus/ -
Re: [ccp4bb] foam dewar usage ?
Hmmm, that's funny. Our experience was quite the opposite. The first time we used one of the darker small dewars we ended up with a lot of burr in the LN2. Those got picked up by the cryo and we ended up with lilac particles embedded inside the cryo. You can imagine the reaction when these particles showed up in the mounting camera We also noticed that the LN2 in these dewars actually ices up more rapidly as compared to the glass dewars. We attribute this to the lower insulating capacity of the foam dewars, which causes a vigorous boiling action and the higher turbulence seems to suck in more ambient air. Needless to say the dewars did not make it past the first use... Carsten -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Behalf Of [EMAIL PROTECTED] Sent: Thursday, October 09, 2008 8:50 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] foam dewar usage ? Yes, we use them all the time and they're great. Stuff does not slip on the bottom like it does in the glass Dewars and the formation of ice is greatly reduced. Plus, they're much easier to dry. Artem > Does anyone in the biocrystallogaphy community use foam dewars for > handly liquid nitrogen and freezing/manipulating frozen protein > crystals ?
[ccp4bb] foam dewar
Jean-Baptiste-- We switched to these foam dewars this year, & everyone in our lab uses them now. After having one of the old style glass ones explode during a late night synchrotron adventure, these foam dewars are a welcome change! annie Annie Hassell Glaxo Smithkline 5 Moore Drive RTP, NC 27709 919/483-3228 919/483-0368 (FAX) [EMAIL PROTECTED]
Re: [ccp4bb] foam dewar usage ?
We've loved them from ages ago when I had our workshop make some. (They didn't like making them, though, so thanks to SPEARLAB for doing it instead!) In fact, spearlab made a green lid on our request which overhangs the edge; I think it'll now be standard, or something like that. He also made us a 4-puck version for us, which may be on the market already...? It's grey and blue, though, I don't know whether there will be objections to this radical colour scheme. But they totally rock. phx. Uwe Mueller wrote: we have those 800ml dewars at our beamlines and I would not by them anymore. The green lid is not really insulating and the working area inside the cylinder is too small. In order to use it for sample manipulations, one has to fill it completely with LN2, which will cause uncontrolled LN2 spilling while moving the dewar. I personally prefer the good old stainless steel dewars together with a self-made metal lid. Best regards, Uwe Jean-Baptiste REISER wrote: Dear all, Does anyone in the biocrystallogaphy community use foam dewars for handly liquid nitrogen and freezing/manipulating frozen protein crystals ? We are interested in the following dewar package from Hampton Research : http://www.hamptonresearch.com/products/ProductDetails.aspx?cid=24&sid=187&pid=559 But before purchasing, we would like to have any comments on the advantages and drawbacks from people who already tried those dewars. Thanks in advance for your help and advices. -- *Dr JEAN-BAPTISTE REISER - Chargé de recherche CNRS* ** *Laboratoire de Cristallographie et Cristallogenèse des Protéines (LCCP)* *et Partnership for Structural Biology (PSB)* *Institut de Biologie Structural Jean-Pierre Ebel (IBS) - CNRS - CEA - UJF* 41, rue Jules Horowitz 38027 Grenoble - France Phone : +33 (0)4 76 20 94 49 Fax : +33 (0)4 76 20 94 80 E-mail : [EMAIL PROTECTED] Web sites : http://www.ibs.fr ; http://psb.esrf.fr **
Re: [ccp4bb] foam dewar usage ?
The low-form foam dewar is really nice to work with. Fills easily without excessive boiloff, and holds level pretty well while working with crystal loops and vials. Best of all, not much ice will accumulate at the top of the container while working. Best of all, my undergraduates can't break it (easily). We keep one in our lab. I'm less enthusiastic about the tall-form dewars. I used one at CHESS and thought it didn't form any less ice than my traditional tall dewars, seemed to have a rapid boiloff while holding my working sample straws (compared to my normal dewars), and was a little cramped on the inside. I don't own any of these, and prefer the traditional tall dewars. If I was traveling with working dewars, I would still consider the foam simply because of its sturdiness. YMMV -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [EMAIL PROTECTED] Jean-Baptiste REISER wrote: Dear all, Does anyone in the biocrystallogaphy community use foam dewars for handly liquid nitrogen and freezing/manipulating frozen protein crystals ? We are interested in the following dewar package from Hampton Research : http://www.hamptonresearch.com/products/ProductDetails.aspx?cid=24&sid=187&pid=559 But before purchasing, we would like to have any comments on the advantages and drawbacks from people who already tried those dewars. Thanks in advance for your help and advices. -- *Dr JEAN-BAPTISTE REISER - Chargé de recherche CNRS* ** *Laboratoire de Cristallographie et Cristallogenèse des Protéines (LCCP)* *et Partnership for Structural Biology (PSB)* *Institut de Biologie Structural Jean-Pierre Ebel (IBS) - CNRS - CEA - UJF* 41, rue Jules Horowitz 38027 Grenoble - France Phone : +33 (0)4 76 20 94 49 Fax : +33 (0)4 76 20 94 80 E-mail : [EMAIL PROTECTED] Web sites : http://www.ibs.fr ; http://psb.esrf.fr **
Re: [ccp4bb] disulfide bond in coot
Klaus Futterer wrote: Does anyone know how to prevent Coot from establishing a disulfide bond between two adjacent Cys residues? I have reason to suspect that the bond is (at least partially) reduced. It is not possible directly to stop Coot drawing the bond given your atoms. However, you could give one of the S atoms an alt-conf specifier and that will stop the bond being draw. Note that Coot only draws the bond, it doesn't do anything with it (you can't, for example, refine it). So it is an aesthetic issue only. Paul.
[ccp4bb] Unsubscribe from CCP4
Please delete the email id [EMAIL PROTECTED] from your mailing list and BB. Thanks Sadhana Pullalarevu
Re: [ccp4bb] foam dewar usage ?
James, for a LN container like this I don't think people would even consider putting these plastic things into the autoclave for pasteurization. I had used these at GM-CA [EMAIL PROTECTED] more than once and always wish to have one in the lab - less ice formation on the rim, hence in the liquid indeed. I used to bookmark this link http://www.spearlab.com/ and am not sure if they are the same thing, -yong On 10/9/08, James Stroud <[EMAIL PROTECTED]> wrote: > > They work fine and they don't break if you drop them. Bear in mind that > they aren't resistant to a lot of chemicals and that you can't autoclave > them. Also, the $160 price tag suggests a lucrative market niche for someone > who has rudimentary skill with a carpet knife. > > > On Oct 9, 2008, at 1:17 AM, Jean-Baptiste REISER wrote: > > Dear all, >> >> Does anyone in the biocrystallogaphy community use foam dewars for handly >> liquid nitrogen and freezing/manipulating frozen protein crystals ? >> >> We are interested in the following dewar package from Hampton Research : >> http://www.hamptonresearch.com/products/ProductDetails.aspx?cid=24&sid=187&pid=559 >> >> But before purchasing, we would like to have any comments on the >> advantages and drawbacks from people who already tried those dewars. >> >> Thanks in advance for your help and advices. >> >> -- >> Dr JEAN-BAPTISTE REISER - Chargé de recherche CNRS >> >> ** >> Laboratoire de Cristallographie et Cristallogenèse des Protéines (LCCP) >> et Partnership for Structural Biology (PSB) >> Institut de Biologie Structural Jean-Pierre Ebel (IBS) - CNRS - CEA - UJF >> 41, rue Jules Horowitz >> 38027 Grenoble - France >> Phone : +33 (0)4 76 20 94 49 >> Fax : +33 (0)4 76 20 94 80 >> E-mail : [EMAIL PROTECTED] >> Web sites : http://www.ibs.fr ; http://psb.esrf.fr >> >> ** >> >> > > -- > James Stroud > UCLA-DOE Institute for Genomics and Proteomics > Box 951570 > Los Angeles, CA 90095 > > http://www.jamesstroud.com >
[ccp4bb] Foam Dewars Part II
Hi All, I think the foam from these dewars would make excellent flooring in LN2 working areas (where most other flooring cracks). I have seen Judo mats made out of a foam that looks similar. Can anyone tell me what this foam is? Alun. -- Alun R. Coker University College London Division of Medicine, Royal Free Campus Centre for Amyloidosis and Acute Phase Proteins Rowland Hill Street London NW32PF Tel: +44(0)207 433 2764
Re: [ccp4bb] foam dewar usage ?
Funny indeed. Our experience has been as well that icing of the foam dewars seems to be reduced compared to the "classical" ones. Bert -Original Message- From: CCP4 bulletin board on behalf of Schubert, Carsten [PRDUS] Sent: Thu 10/9/2008 9:15 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] foam dewar usage ? Hmmm, that's funny. Our experience was quite the opposite. The first time we used one of the darker small dewars we ended up with a lot of burr in the LN2. Those got picked up by the cryo and we ended up with lilac particles embedded inside the cryo. You can imagine the reaction when these particles showed up in the mounting camera We also noticed that the LN2 in these dewars actually ices up more rapidly as compared to the glass dewars. We attribute this to the lower insulating capacity of the foam dewars, which causes a vigorous boiling action and the higher turbulence seems to suck in more ambient air. Needless to say the dewars did not make it past the first use... Carsten -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Behalf Of [EMAIL PROTECTED] Sent: Thursday, October 09, 2008 8:50 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] foam dewar usage ? Yes, we use them all the time and they're great. Stuff does not slip on the bottom like it does in the glass Dewars and the formation of ice is greatly reduced. Plus, they're much easier to dry. Artem > Does anyone in the biocrystallogaphy community use foam dewars for > handly liquid nitrogen and freezing/manipulating frozen protein > crystals ?
[ccp4bb] Postdoctoral position available at The Institute of Cancer Research
The Institute of Cancer Research Section of Structural Biology / Section of Cancer Therapeutics Post-doctoral Training Fellow Structural elucidation of phosphatase cancer target (Chelsea, London & Sutton, Surrey) The Institute of Cancer Research is one of the world's leading cancer research organisations and is internationally renowned for the quality of its science. Our mission is the relief of human suffering by pursuing excellence in the fight against cancer. An Institute of Cancer Research-funded Postdoctoral position is available immediately in Dr. Rob van Montfort’s Structure-Based Drug Design group. The successful candidate will work on the structure elucidation of a phosphatase implicated in cancer and be involved in subsequent structural studies to investigate the protein-ligand interactions of small molecule inhibitors bound to the protein. The post-doc will be expected to interact closely with biologists, computational chemists and medicinal chemists throughout The Institute and will work across two sites in Chelsea, London and Sutton, Surrey. The Structure-Based Drug Design group is a joint initiative between the Section of Structural Biology and the Section of Cancer Therapeutics at the ICR. The Institute is exceptionally well equipped for all aspects of drug discovery, with state-of-the-art laboratories for molecular biology, recombinant expression in bacterial and eukaryotic systems, biochemistry, X-ray crystallography and medicinal chemistry. Applicants must have a PhD in a biological or physical science, and experience in macromolecular crystallography / crystallisation (to include protein biochemistry, protein crystallisation, & protein crystallography). Experience in molecular biology, protein purification, and/or Structure-Based Drug design will be an advantage. The starting salary for the position will be in the range £29,256 to £31,551 p.a. inclusive (based on previous post-doctoral experience) and the post is offered initially on a fixed term contract of up to 18 months. Informal enquiries to [EMAIL PROTECTED] Please DO NOT send your application to Dr. van Montfort; CVs must be submitted in line with the instructions below. For further particulars and details of how to apply, please visit our website at www.icr.ac.uk. Alternatively you may call our 24 hour recruitment line on 020 7153 5475 quoting reference number C183. Closing date: Friday 31 October 2008 Interviews to be held:Week commencing 17 November 2008 Dr. Rob van Montfort Team Leader Structure-Based Drug Design Sections of Cancer Therapeutics and Structural Biology The Institute of Cancer Research 15 Cotswold Road Sutton SM2 5NG UK Tel: +44-(0)20-8722-4364 (Sutton) +44-(0)20-7153-5142 (Chelsea) Email: [EMAIL PROTECTED] The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Re: [ccp4bb] foam dewar usage ?
we have those 800ml dewars at our beamlines and I would not by them anymore. The green lid is not really insulating and the working area inside the cylinder is too small. In order to use it for sample manipulations, one has to fill it completely with LN2, which will cause uncontrolled LN2 spilling while moving the dewar. I personally prefer the good old stainless steel dewars together with a self-made metal lid. Best regards, Uwe Jean-Baptiste REISER wrote: Dear all, Does anyone in the biocrystallogaphy community use foam dewars for handly liquid nitrogen and freezing/manipulating frozen protein crystals ? We are interested in the following dewar package from Hampton Research : http://www.hamptonresearch.com/products/ProductDetails.aspx?cid=24&sid=187&pid=559 But before purchasing, we would like to have any comments on the advantages and drawbacks from people who already tried those dewars. Thanks in advance for your help and advices. -- *Dr JEAN-BAPTISTE REISER - Chargé de recherche CNRS* ** *Laboratoire de Cristallographie et Cristallogenèse des Protéines (LCCP)* *et Partnership for Structural Biology (PSB)* *Institut de Biologie Structural Jean-Pierre Ebel (IBS) - CNRS - CEA - UJF* 41, rue Jules Horowitz 38027 Grenoble - France Phone : +33 (0)4 76 20 94 49 Fax : +33 (0)4 76 20 94 80 E-mail : [EMAIL PROTECTED] Web sites : http://www.ibs.fr ; http://psb.esrf.fr ** -- ___ Dr. Uwe Müller BESSY-MX group BESSY GmbH Albert-Einstein-Straße-15 D-12489 Berlin Phone: +49-(0)30-6392 4974 Fax : +49-(0)30-6392 4975 email: [EMAIL PROTECTED] url : http://www.psf.bessy.de BESSY GmbH - Mitglied der Leibniz Gemeinschaft Vorsitzender des Aufsichtsrates: Prof. Dr. Dr. h.c. mult Joachim Treusch Geschäftsführer: Prof. Dr. Dr. h.c. Wolfgang Eberhardt, Prof. Dr.Eberhard Jaeschke Sitz Berlin, AG Charlottenburg, HRB 14635
Re: [ccp4bb] foam dewar usage ?
A good cover -- judiciously used -- goes a very long way in reducing ice in dewars whether the dewar is made of foam, glass or stainless steel. If you keep your dewar covered with a lid that extends on the outside of the dewar down a few centimeters below the dewar edge, you will have minimal icing in the dewar. It actually doesn't even matter what the lid is made of. I use the covers of DVD/CDROM packs. I try to remove the cover only for a second or two when plunging crystals and immediately cover the dewar again. From my experience, most folks leave the lids off too often and for too long. Typically, they walk away leaving the lid off. It's no surprise that ice accumulates. If you leave the dewar open to the moist air, you will get ice in the dewar no matter what it is made of. Some simple prophylactic habits will go a long way to practically eliminate ice in the dewar. Jim
Re: [ccp4bb] foam dewar usage ?
I concur with Thomas' comments ... it all depends upon their intended use. We have used it extensively here at SSRL and have shaped three different large (4+ litre capacity) dewars for crystal mounting into the SSRL puck and for loading and unloading Uni-pucks in an adapter cassette for use with the SAM robot system. **Warning, advertising** To new users of SSRL we "give" you one of the big dewars and a full kit of hardware for the robot (incluing a cassette) ... so if you want to try it out, become an SSRL user (that's the advertising part over with!). Anyway, for these purposes the foam works wonderfully. There is definitely only minimal icing and it is possible to fill an entire 96 port cassette without having to change nitrogen ... it's even better if you do this in a fume hood so that the water vapour which condenses on top of the nitrogen is continually drawn off and doesn't get a chance to settle (thanks to Eddie Snell for that little idea ... but this is another story). However for freezing crystals, I still prefer the small open glass vacuum dewars because, as some noted, you can see what is going on much easier ... although you do get considerable icing unless (again per Eddie Snell) you do it in a fume hood. I have used a small foam dewar for this in the past and I have to say icing is not a problem and I din't need to change the N2, just top it up occassionally. If they really do cost $160, your best bet might be to email your friendly local synchrotron group and ask if they will make you something at a fraction of the price ... Clyde - Clyde A. Smith, Ph.D. Staff Scientist Stanford University Stanford Synchrotron Radiation Lab, MS 99 2575 Sand Hill Rd Menlo Park, CA 94025 USA ph (650)926-8544 fax (650)926-3292 cell (650)714-6001 smb.slac.stanford.edu -Original Message- From: CCP4 bulletin board on behalf of Thomas Earnest Sent: Thu 9/10/2008 4:07 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] foam dewar usage ? Jean-Baptiste, Since these were conceived and developed by Jon Spear when he was a member of my group (at the ALS at the time), I know a bit about these Dewars, their intended usage, and relative benefits. When Jon first made them, the beamline users and staff quickly realized the advantages, they spread around the ALS, and then to other sources. My guess is that for other beamlines that have both these and vacuum-jacketed Dewars, the users prefer these over other options. As with all things, the advantages and disadvantages must be viewed in context of what the use is. The fact that these will not shatter, can be shaped to whatever the needed dimensions are and pockets can be machined in to allow for transport pucks, cryo-tools, etc., they cool and warm rapidly and are inexpensive, are all distinct advantages. Thus for freezing and manipulating crystals at home or the beamline, they are excellent and inexpensive options. Regarding the two comments that followed your post from Uwe and James: Uwe: When using Berkeley-style pucks or Unipucks (which replicated the Berkeley form factor), these are sufficiently dimensioned, and I believe there is a version that accommodates the SSRL cassette. If you want another dimension, I suggest contacting Jon directly and discuss this with him. James: I'm not sure why you think that chemical resistance or autoclaving are relevant to the discussion, as these are for holding and transporting liquid nitrogen and sample cryo-transport units. Also they are machined with a bit more precision than a "carpet knife" would give, and this eliminates the burrs or other bits that may tend to flake off, as well as allowing for shaping to need. - Thomas Thomas Earnest, Ph.D. Senior Scientist and Group Leader Structural Proteomics Development Group Physical Biosciences Division MS64R0121 Lawrence Berkeley National Laboratory Berkeley CA 94720 [EMAIL PROTECTED] 510 486 4603 Jean-Baptiste REISER wrote: > Dear all, > > Does anyone in the biocrystallogaphy community use foam dewars for > handly liquid nitrogen and freezing/manipulating frozen protein crystals ? > > We are interested in the following dewar package from Hampton Research > : > http://www.hamptonresearch.com/products/ProductDetails.aspx?cid=24&sid=187&pid=559 > > But before purchasing, we would like to have any comments on the > advantages and drawbacks from people who already tried those dewars. > > Thanks in advance for your help and advices. > > -- > > *Dr JEAN-BAPTISTE REISER - Chargé de recherche CNRS* > > ** > > *Laboratoire de Cristallographie et Cristallogenèse des Protéines (LCCP)* > > *et Partnership for Structural Biology (PSB)* > > *Institut de Biologie Structural Jean-Pierre Ebel (IBS) - CNRS - CEA - > UJF* > > 41, rue Jules Horowitz > > 38027 Grenoble - France > > Phone : +33 (0)4 76 20 94 49 > > Fax : +33
Re: [ccp4bb] Foam Dewars Part II
Hi Alun, The material we use is cross linked polyethylene/EVA foam. We use the 4 PCF (pounds per cubic foot) variety it has tradenames of youngboard, artilon and epilon. (see http://smb.slac.stanford.edu/facilities/hardware/cassette_kit/dewar_schematics.pdf and http://smb.slac.stanford.edu/facilities/hardware/cassette_kit/FabricationDewarAndLid.pdf for how we have the large dewars for the SSRL cassette Clyde described fabricated. ) Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Alun R. Coker Sent: Thursday, October 09, 2008 6:51 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Foam Dewars Part II Hi All, I think the foam from these dewars would make excellent flooring in LN2 working areas (where most other flooring cracks). I have seen Judo mats made out of a foam that looks similar. Can anyone tell me what this foam is? Alun. -- Alun R. Coker University College London Division of Medicine, Royal Free Campus Centre for Amyloidosis and Acute Phase Proteins Rowland Hill Street London NW32PF Tel: +44(0)207 433 2764
Re: [ccp4bb] foam dewar usage ?
> If they really do cost $160, your best bet might be to email your friendly > local synchrotron group and ask if they will make you something at a fraction > of the price ... Or just pay up. 160 USD is not a lot when compared to other consumables likes chemicals or crystal screens. The dewars last quite a while. P
Re: [ccp4bb] foam dewar usage ?
Hi Carsten, since you don't use them anymore I would volunteer to have them shipped to me for free :-) I might cough up the shipping fee. We have both in the lab, for certain purposes I prefer the stainless steel over the foam dewars e.g. freezing protein as 20 µl drops then picking them with tweezers and transferring them into an Eppendorf tube. For use with the robotic equipment the stainless steel are completely useless. Ice formation can be prevented by exchanging the LN2 frequently. Regarding the cane dewars out of foam as seen at ALS I don't like them as they can be accidentally tipped over more easily than the stainless steel dewars. Jürgen On 9 Oct 2008, at 06:15, Schubert, Carsten [PRDUS] wrote: Hmmm, that's funny. Our experience was quite the opposite. The first time we used one of the darker small dewars we ended up with a lot of burr in the LN2. Those got picked up by the cryo and we ended up with lilac particles embedded inside the cryo. You can imagine the reaction when these particles showed up in the mounting camera We also noticed that the LN2 in these dewars actually ices up more rapidly as compared to the glass dewars. We attribute this to the lower insulating capacity of the foam dewars, which causes a vigorous boiling action and the higher turbulence seems to suck in more ambient air. Needless to say the dewars did not make it past the first use... Carsten -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Behalf Of [EMAIL PROTECTED] Sent: Thursday, October 09, 2008 8:50 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] foam dewar usage ? Yes, we use them all the time and they're great. Stuff does not slip on the bottom like it does in the glass Dewars and the formation of ice is greatly reduced. Plus, they're much easier to dry. Artem Does anyone in the biocrystallogaphy community use foam dewars for handly liquid nitrogen and freezing/manipulating frozen protein crystals ? - Jürgen Bosch University of Washington Dept. of Biochemistry, K-426 1705 NE Pacific Street Seattle, WA 98195 Box 357742 Phone: +1-206-616-4510 FAX: +1-206-685-7002 Web: http://faculty.washington.edu/jbosch
Re: [ccp4bb] foam dewar usage ?
For crystal freezing and such we have largely replaced glass and stainless Dewars with foam ones here at the CAMD PX beamline.You can get them directly from www.spearlab.com for USD 100.I agree that the lid supplied with the foam Dewar is not very good but you can easily make a better one.I used 1/4 in thick "Volara" (cross- linked polyethylene) foam from McMaster-Carr. Cut a circle that fits in the cavity and then a bigger one, glue them together and you have a lid that won't slip off. You can cut 1/4 in. sheets with a pair of scissors. You can also cut a notch in the lid to accommodate the handles of tongs or vial clamps. That way the lid is closed except when you are actually manipulating the crystal and ice accumulation in the N2 is minimal. HTH Henry Henry Bellamy Associate Professor - Research Center for Advanced Microstructures and Devices Louisiana State University 6980 Jefferson Hwy. Baton Rouge LA 70806 225-578-9342 (voice) 225-578-6954 (fax) [EMAIL PROTECTED]
Re: [ccp4bb] foam dewar usage ?
Just wanted to clarify the history of the foam Dewars for posterity: - they were developed at the ALS when Gerry McDermott was head of the BCSB group here, and Jon Spear was a member of the group (Gerry was his supervisor at that time) - after we had several glass Dewars implode, Gerry asked Jon specifically to try to make a Dewar out of a different material. Gerry might even have suggested trying the foam (they were originally made from the same material as is used in Yoga mats) - Gerry gave Jon a Spot Award (an internal LBL award) for his efforts - Jon then applied for a patent on the foam Dewars and started his own company to sell them and has done very well (personally, I find them an excellent alternative to the glass dewars) Corie - Original Message - From: Thomas Earnest <[EMAIL PROTECTED]> Date: Thursday, October 9, 2008 4:08 am Subject: Re: [ccp4bb] foam dewar usage ? To: CCP4BB@JISCMAIL.AC.UK > Jean-Baptiste, > > Since these were conceived and developed by Jon Spear when he was a > member of my > group (at the ALS at the time), I know a bit about these Dewars, > their > intended usage, and relative benefits. > When Jon first made them, the beamline users and staff quickly > realized > the advantages, they spread around > the ALS, and then to other sources. My guess is that for other > beamlines > that have both these and > vacuum-jacketed Dewars, the users prefer these over other options. > > As with all things, the advantages and disadvantages must be viewed > in > context of what the use is. The > fact that these will not shatter, can be shaped to whatever the > needed > dimensions are and pockets can be > machined in to allow for transport pucks, cryo-tools, etc., they > cool > and warm rapidly and are inexpensive, are all distinct advantages. > Thus > for freezing and manipulating crystals at home or the beamline, > they are > excellent and > inexpensive options. > > Regarding the two comments that followed your post from Uwe and James: > > Uwe: When using Berkeley-style pucks or Unipucks (which replicated > the > Berkeley form factor), these > are sufficiently dimensioned, and I believe there is a version that > accommodates the SSRL cassette. If > you want another dimension, I suggest contacting Jon directly and > discuss this with him. > > James: I'm not sure why you think that chemical resistance or > autoclaving are relevant to the discussion, as these > are for holding and transporting liquid nitrogen and sample > cryo-transport units. Also they are machined > with a bit more precision than a "carpet knife" would give, and > this > eliminates the burrs or other bits that > may tend to flake off, as well as allowing for shaping to need. > > > - Thomas > > > Thomas Earnest, Ph.D. > Senior Scientist and Group Leader > Structural Proteomics Development Group > Physical Biosciences Division > MS64R0121 > Lawrence Berkeley National Laboratory > Berkeley CA 94720 > > [EMAIL PROTECTED] > 510 486 4603 > > > > Jean-Baptiste REISER wrote: > > Dear all, > > > > Does anyone in the biocrystallogaphy community use foam dewars > for > > handly liquid nitrogen and freezing/manipulating frozen protein > crystals ? > > > > We are interested in the following dewar package from Hampton > Research > > : > > > http://www.hamptonresearch.com/products/ProductDetails.aspx?cid=24&sid=187&pid=559> > > But before purchasing, we would like to have any comments on the > > advantages and drawbacks from people who already tried those dewars. > > > > Thanks in advance for your help and advices. > > > > -- > > > > *Dr JEAN-BAPTISTE REISER - Chargé de recherche CNRS* > > > > > **> > > *Laboratoire de Cristallographie et Cristallogenèse des Protéines > (LCCP)*> > > *et Partnership for Structural Biology (PSB)* > > > > *Institut de Biologie Structural Jean-Pierre Ebel (IBS) - CNRS - > CEA - > > UJF* > > > > 41, rue Jules Horowitz > > > > 38027 Grenoble - France > > > > Phone : +33 (0)4 76 20 94 49 > > > > Fax : +33 (0)4 76 20 94 80 > > > > E-mail : [EMAIL PROTECTED] > > > > Web sites : http://www.ibs.fr ; http://psb.esrf.fr > > > > > **> >
Re: [ccp4bb] foam dewar usage ?
A side note about ice formation... This might have already been mentioned, but I have personally used a shower cap over cryo-bowls and it seems to do a reasonable job - ice seems to form quicker on the shower cap than in the bowl. Covering the bowl with an old Styrofoam lid from a spare shipping box does a decent job too - you can use a craft knife to make it a tight fit. AGS > Date: Thu, 9 Oct 2008 10:18:32 -0500 > From: [EMAIL PROTECTED] > Subject: Re: [ccp4bb] foam dewar usage ? > To: CCP4BB@JISCMAIL.AC.UK > > A good cover -- judiciously used -- goes a very long way in reducing ice > in dewars whether the dewar is made of foam, glass or stainless steel. > > If you keep your dewar covered with a lid that extends on the outside of > the dewar down a few centimeters below the dewar edge, you will have > minimal icing in the dewar. It actually doesn't even matter what the lid > is made of. I use the covers of DVD/CDROM packs. I try to remove the > cover only for a second or two when plunging crystals and immediately > cover the dewar again. From my experience, most folks leave the lids off > too often and for too long. Typically, they walk away leaving the lid > off. It's no surprise that ice accumulates. > > If you leave the dewar open to the moist air, you will get ice in the > dewar no matter what it is made of. > > Some simple prophylactic habits will go a long way to practically > eliminate ice in the dewar. > > Jim _ See how Windows Mobile brings your life together—at home, work, or on the go. http://clk.atdmt.com/MRT/go/msnnkwxp1020093182mrt/direct/01/
[ccp4bb] Potential N-terminal cyclization
Hi All, I am looking for some input regarding an unusual feature in one of our structures. Maybe someone has come across something similar or has some thoughts about it... We have a 1.9 A crystal structure with well-defined density in the N-terminal region. The side chain of His3 is oriented towards the N-terminal amino group of Met1 and there is a nice difference density 'ball' right in between the His and the amino group suggesting that there is an additional atom that is covalently linked. There are two molecules in the asu and both show the same feature (no ncs refinement). My problem is that I cannot come up with a reaction that would result in such a linkage and there is not much to be found in the literature. If I place a hypothetical atom in the difference density peak, I can measure distances and angles. Here are some numbers: Distance from atom X to the N-terminal nitrogen 1.72 (1.64 in chain B). Distance from atom X to His NE2 1.58 (1.45 in chain B; the temperature factors of the His side chain are slightly more consistent with this ring orientation compared to the 180 degree flip that would bring CE1 towards atom X). Atom X is coplanar with the His ring. The angle between NE2 - X - N1 is 95 deg (106 in chain B). The angle between X - N1 - Calpha1 is 111 degrees in both chains. As the N-terminal methionine is still present, it is possible that the methionine formyl-group was present before the hypothetical reaction. However, there is only one 'atom' in the difference density. Any comments or suggestions would be highly welcome. Gerwald
Re: [ccp4bb] Potential N-terminal cyclization
If you're 100% sure that this is only one atom then amination comes to mind. I have no clue what conditions would favor such reactivity but it is possible that the formyl group on the Met was aminated with the cyclic N of the histidine, resulting in either a substituted bis-amine (requires reduction, may not be stable) or in a cyclic amidine (the latter requires four atoms - N1-C=N-Ca - to be in the same plane). This amidine should have some pretty interesting properties (probably more like a Schiff base than an amidine). Could you tell us a bit more about the system you're working with? Artem P.S. The bond lengths you describe are not typical for C-N, however at 1.9A resolution it is not very likely that the values you measured actually correspond to the bond lengths (hopefully, because otherwise you have -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of gerwald jogl Sent: Thursday, October 09, 2008 4:24 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Potential N-terminal cyclization Hi All, I am looking for some input regarding an unusual feature in one of our structures. Maybe someone has come across something similar or has some thoughts about it... We have a 1.9 A crystal structure with well-defined density in the N-terminal region. The side chain of His3 is oriented towards the N-terminal amino group of Met1 and there is a nice difference density 'ball' right in between the His and the amino group suggesting that there is an additional atom that is covalently linked. There are two molecules in the asu and both show the same feature (no ncs refinement). My problem is that I cannot come up with a reaction that would result in such a linkage and there is not much to be found in the literature. If I place a hypothetical atom in the difference density peak, I can measure distances and angles. Here are some numbers: Distance from atom X to the N-terminal nitrogen 1.72 (1.64 in chain B). Distance from atom X to His NE2 1.58 (1.45 in chain B; the temperature factors of the His side chain are slightly more consistent with this ring orientation compared to the 180 degree flip that would bring CE1 towards atom X). Atom X is coplanar with the His ring. The angle between NE2 - X - N1 is 95 deg (106 in chain B). The angle between X - N1 - Calpha1 is 111 degrees in both chains. As the N-terminal methionine is still present, it is possible that the methionine formyl-group was present before the hypothetical reaction. However, there is only one 'atom' in the difference density. Any comments or suggestions would be highly welcome. Gerwald
Re: [ccp4bb] foam dewar usage ?
Maybe we're not talking about the same kind of container? We never had any kind of particles** in ours and with the use of a lid the ice does not appear for quite some time. We did not see 'vigorous boiling' either. If one leaves LN2 in the open it would eventually ice up regardless of the nature of storage container :-) Artem * calling foam LN2 container a 'Dewar' is a misnomer, James Dewar would not be happy. ** there is a scenario in which particulates may form - and that is if a wet container (i.e. not dried for long enough after previous use) is subjected to LN2. This would rapidly freeze the water inside the foam layer and bust up the pores, resulting in particulates. _ From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Van Den Berg, Bert Sent: Thursday, October 09, 2008 11:03 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] foam dewar usage ? Funny indeed. Our experience has been as well that icing of the foam dewars seems to be reduced compared to the "classical" ones. Bert -Original Message- From: CCP4 bulletin board on behalf of Schubert, Carsten [PRDUS] Sent: Thu 10/9/2008 9:15 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] foam dewar usage ? Hmmm, that's funny. Our experience was quite the opposite. The first time we used one of the darker small dewars we ended up with a lot of burr in the LN2. Those got picked up by the cryo and we ended up with lilac particles embedded inside the cryo. You can imagine the reaction when these particles showed up in the mounting camera We also noticed that the LN2 in these dewars actually ices up more rapidly as compared to the glass dewars. We attribute this to the lower insulating capacity of the foam dewars, which causes a vigorous boiling action and the higher turbulence seems to suck in more ambient air. Needless to say the dewars did not make it past the first use... Carsten -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Behalf Of [EMAIL PROTECTED] Sent: Thursday, October 09, 2008 8:50 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] foam dewar usage ? Yes, we use them all the time and they're great. Stuff does not slip on the bottom like it does in the glass Dewars and the formation of ice is greatly reduced. Plus, they're much easier to dry. Artem > Does anyone in the biocrystallogaphy community use foam dewars for > handly liquid nitrogen and freezing/manipulating frozen protein > crystals ?
Re: [ccp4bb] foam dewar usage ?
I often use styrofoam boxes from dry ice shipments. Works like a charm if the box is quite new (i.e. not reused too often) -Original Message- From: "Smith, Clyde" <[EMAIL PROTECTED]> Subj: Re: [ccp4bb] foam dewar usage ? Date: Thu Oct 9, 2008 8:26 Size: 2K To: CCP4BB@JISCMAIL.AC.UK I concur with Thomas' comments ... it all depends upon their intended use. We have used it extensively here at SSRL and have shaped three different large (4+ litre capacity) dewars for crystal mounting into the SSRL puck and for loading and unloading Uni-pucks in an adapter cassette for use with the SAM robot system. **Warning, advertising** To new users of SSRL we "give" you one of the big dewars and a full kit of hardware for the robot (incluing a cassette) ... so if you want to try it out, become an SSRL user (that's the advertising part over with!). Anyway, for these purposes the foam works wonderfully. There is definitely only minimal icing and it is possible to fill an entire 96 port cassette without having to change nitrogen ... it's even better if you do this in a fume hood so that the water vapour which condenses on top of the nitrogen is continually drawn off and doesn't get a chance to settle (thanks to Eddie Snell for that little idea ... but this is another story). However for freezing crystals, I still prefer the small open glass vacuum dewars because, as some noted, you can see what is going on much easier ... although you do get considerable icing unless (again per Eddie Snell) you do it in a fume hood. I have used a small foam dewar for this in the past and I have to say icing is not a problem and I din't need to change the N2, just top it up occassionally. If they really do cost $160, your best bet might be to email your friendly local synchrotron group and ask if they will make you something at a fraction of the price ... Clyde - Clyde A. Smith, Ph.D. Staff Scientist Stanford University Stanford Synchrotron Radiation Lab, MS 99 2575 Sand Hill Rd Menlo Park, CA 94025 USA ph (650)926-8544 fax (650)926-3292 cell (650)714-6001 smb.slac.stanford.edu -Original Message- From: CCP4 bulletin board on behalf of Thomas Earnest Sent: Thu 9/10/2008 4:07 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] foam dewar usage ? Jean-Baptiste, Since these were conceived and developed by Jon Spear when he was a member of my group (at the ALS at the time), I know a bit about these Dewars, their intended usage, and relative benefits. When Jon first made them, the beamline users and staff quickly realized the advantages, they spread around the ALS, and then to other sources. My guess is that for other beamlines that have both these and vacuum-jacketed Dewars, the users prefer these over other options. As with all things, the advantages and disadvantages must be viewed in context of what the use is. The fact that these will not shatter, can be shaped to whatever the needed dimensions are and pockets can be machined in to allow for transport pucks, cryo-tools, etc., they cool and warm rapidly and are inexpensive, are all distinct advantages. Thus for freezing and manipulating crystals at home or the beamline, they are excellent and ine --- message truncated ---
