Re: [ccp4bb] design specs/tolerances for crystallization rooms?
My colleague Opher Gileadi gave us an excellent tip when we were designing our 4C harvesting room, over a decade ago: set it to 7C. The crystals are unlikely to mind, but it's SO much more comfortable to be in for hours. I seem to remember he mentioned something like a comfort inflection point as you approach 4C. Install low-flow fans. Fridge people seem to default to installing hurricane machines, you have to tell them that a very very small flow is enough. Get strong light - probably even those daylight things (we don't have them). Being cold is miserable enough already, there's no need to compound it with weak light. Vibration - that dwindles to insignificance if the air flow goes down. Humidity - we installed (at considerable expense) a low humidity air supply - really hard to know just how much it helps, but a few years ago when I had it turned it off to help save energy, very quickly I heard complaints about snow in the liquid nitrogen becoming a major hassle. So based on that set of anecdotes, I conclude it probably is worth having dry air. It's much cheaper though if they can design it into the building's infrastructure, if it's a new building; retrofitting turned out to be super expensive (in our case). As dry as possible. Look at and understand the psychrometric chart (google it): if you're in even vaguely warm or temperate regions (or seasons), cooling the intake air to 4C brings it to below dew point, and then condensation and snow are guaranteed. Size - make it as big as you can get away with, with lots of bench and shelf space. Your students will already be miserably cold, no need for them to be cramped too. Good luck! Frank On 24/09/2019 23:40, Scott, Emily wrote: Anyone out there specifically design rooms for (protein) crystallization at ~22 deg and 4 deg C? If you have successes or failures and can share any design specs with regard to vibration, temperature, and humidity tolerances, it would be much appreciated to pass on to the architects for our new laboratory. Sincerely, Emily Scott -- Emily Scott, Ph.D. Professor, Medicinal Chemistry/Pharmacology/Biophysics Faculty Director, BioNMR Core Lab University of Michigan 428 Church Street Ann Arbor, MI 48109-1065 Phone: 734-764-3530 https://pharmacy.umich.edu/people/scottee Lab webpage: http://scottlab.info ** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues To unsubscribe from the CCP4BB list, click the following link: 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] design specs/tolerances for crystallization rooms?
Anyone out there specifically design rooms for (protein) crystallization at ~22 deg and 4 deg C? If you have successes or failures and can share any design specs with regard to vibration, temperature, and humidity tolerances, it would be much appreciated to pass on to the architects for our new laboratory. Sincerely, Emily Scott -- Emily Scott, Ph.D. Professor, Medicinal Chemistry/Pharmacology/Biophysics Faculty Director, BioNMR Core Lab University of Michigan 428 Church Street Ann Arbor, MI 48109-1065 Phone: 734-764-3530 https://pharmacy.umich.edu/people/scottee Lab webpage: http://scottlab.info ** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Beam time available at upgraded MacCHESS
Got crystals to check out? The Fall 2019 run at CHESS begins October 16, and it's not too late to apply for time. Proposals are accepted any time for beam time at the newly upgraded MacCHESS beamlines: BioSAXS station (formerly G1) - on-site or mail-in BioSAXS, featuring: * 7-14 KeV, standard beam size 250x200 micron, smaller beam available. In commissioning experiment with 50 mA particle beam, 14 KeV X-rays, got 1.4E11 ph/s through 80x80 micron aperture * SAXS/WAXS, loading from multiwell trays or effluent from column (size-exclusion, ion-exchange, high pressure) * in-line DLS/MALS * high-pressure cell * microfluidic cell for time-resolved experiments * user-friendly, flexible, experimental control system * RAW data processing system * excellent staff support * coming in November, in-vacuum EIGER 4M detector FlexX station - on-site or remote macromolecular crystallography, featuring: * 7-14 KeV, undulator source with multilayer monochromator for high flux. In commissioning, with 50 mA particle beam, measured 2E11 ph/s through 100x100 micron aperture * single-axis goniostat, PILATUS3 6M detector, BAM2 automounter * standard crystallography available at start-up, fixed-target serial crystallography in early 2020 * high pressure cryocooling available * data collection at high pressure using a diamond anvil cell under development * excellent staff support * we welcome "non-standard" experiments! Visit http://www.chess.cornell.edu for more information. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Are there any proteins capable of crystallizing at a wide range of pH having the same space group?
I just want add that the redundant PDB got a new site http://pdbflex.org/ (It's pretty cool actually) Thanks to Robyn for pointing that out. El dom., 22 de sep. de 2019 a la(s) 10:18, Robyn Stanfield ( ro...@scripps.edu) escribió: > Hi, > > The Burnham changed names sometime back, that may be why that link > disappeared. Check the Adam Godzik lab page( http://godziklab.org/pages/ > ) else if this info is not there just e-mail Adam and I’ll bet he can fix > you up with the database in question. He is very helpful. > > Good luck, > > Robyn > > > > *From:* CCP4 bulletin board * On Behalf Of *David > Waterman > *Sent:* Friday, September 20, 2019 4:09 PM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] Are there any proteins capable of crystallizing > at a wide range of pH having the same space group? > > > > archive.org suggests the database existed up to December 2018, but > appears to be no more. > > > > What to do when scientific resources associated with published papers > disappear like this? It seems to be a problem that is not very well > addressed. > > > > Cheers > > David > > > > On Fri, 20 Sep 2019, 04:26 Murpholino Peligro, > wrote: > > Following my last question I was searching for a redundant PDB and found > this paper https://doi.org/10.1016/j.str.2007.07.012. I went to the > methods section and found out that the link to the database of redundant > protein structures is now gone (http://dper.burnham.org/). Anyone knows > of a similar database? Or anyone knows how to make one? > > > > Thanks again for your help. > > > > > > Murph > > > > El jue., 19 de sep. de 2019 a la(s) 19:04, Dale Tronrud ( > de...@daletronrud.com) escribió: > > >My recollection is that gamma-chymotrypsin crystals will persist in > pHs all the way from 3 to 9. I don't know if the crystals will grow > over that range. > >There are a fair number of phage T4 lysozymes variants in the PDB. I > don't think this is considered "overpopulation" but a valuable > contribution to humanity. ;-) > > Dale Tronrud > > On 9/19/2019 4:03 PM, Murpholino Peligro wrote: > > A quick glance at the entries of hen egg white lysozyme in the PDB show > > that it can be crystallized at different pH values, but the space group > > is not always the same. I still have to refine the analysis but I was > > wondering that maybe there are a few proteins that can crystallize at a > > wide range (maybe not that wide) of pH values and still have the same > > space group? > > > > To refine the analysis a wee further: By any chance do you know any > > proteins overpopulating the PDB (i.e. besides HEWL)? > > > > Lots of thanks as always. > > > > Murphy > > > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > 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 > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > 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] Optimisation of 2D very thin plates to thick plates
Dear Will, if the crystals grow in vapour-diffusion, you can try to overlay the reservoir with oil to slow down the crystallization process. I know at least two cases where this technique helped to get plate-shaped crystals into more 3D shape. http://scripts.iucr.org/cgi-bin/paper?S0021889896013532 Good luck, Sabine > Dear colleagues, > I would like some advice on crystal growth optimisation. I have been trying to crystallise a DNA regulator. I got microcrystals in 1.3M Lithium > Sulphate and 50 mM Cacodylate pH = 6. Through a combination of condition refinement and seeding I have attained crystals with a plate-like habit of > dimension 50micron, 50micron, <1micron. These have very weak (8Ã ) anisotropic diffraction at DLS i24 but as theyâre so wafer thin there has been no improvement. Any suggestions to make them more 3D would be great. The space group is C2221 > Any advice? > Thanks in advance > Regards, > Will > [cid:4D1D54D9-3EAE-46D3-9961-9D17A39FE07C@nottingham.ac.uk] > This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please contact the sender and delete the email and attachment. > Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. Email communications with the University of Nottingham may be monitored where permitted by law. > To unsubscribe from the CCP4BB list, click the following link: > 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] Cryo-EM sample preparation workshop at the ESRF / 5th to 7th of November 2019 (last week before closure of registration)
Dear All, We are pleased to announce a 2.5 day practical winter workshop on sample preparation and negative staining for cryo-EM single particle data collection jointly organised by the ESRF, IBS, ILL and the EMBL Grenoble. This is the third of a series of practical hands-on workshops started in 2018. This workshop is aimed at PhDs, PostDocs and scientists new to the field of single particle cryo-EM and will be held at the European Synchrotron, EMBL Grenoble and the Institut de Biologie Structurale (IBS) in Grenoble, France from *November 5^th to 7^th , 2019*. During the course, participants will learn theoretical and practical aspects of sample preparation for single particle cryo-EM including prior quality control by negative staining. There is *no registration fee* and meals and accommodation during the workshop will be provided free of charge. However, participants are expected to arrange and pay for their own travel to/from Grenoble. A maximum of 12 participants will be selected and we will accept a number of participants’ samples to be tested during the workshop. In the case that you plan to bring your own sample, please clearly mention this in your cover letter, also indicating the importance of the project. Application for the workshop is open using the link http://www.esrf.fr/events/conferences/ and the deadline is *September 29, 2019*. Successful candidates will be informed during the first week after the deadline. Best regards, David Flot. (On behalf of the organizers) -- Dr David FLOT Beam-Line Operation Manager Tel : (+33) 4 76 88 17 63 Structural Biology GroupFax : (+33) 4 76 88 26 24 ESRF e-mail :david.f...@esrf.fr http://www.esrf.eu Room: 30.1.13 Physical addressPostal address ESRF-The European Synchrotron ESRF-The European Synchrotron 71, Avenue des Martyrs CS40220 Grenoble, France38043 Grenoble Cedex 9 France To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
