[ccp4bb] Rfree set for twinned data
Hi all, Is there anything that needed to pay attention to while choosing Rfree set for twinned data set? Or we can choose Rfree set randomly as untwined data set? Thanks! Best wishes! Yamei Yu
Re: [ccp4bb] Selenomethionine crystals
Can I remind everyone that animals scattering is in reality *anisotropic* and therefore in some crystals, depending on the distribution of the anomalous scatterers in the protein and the symmetry of the space group, there may be relative orientations of beam and crystal in which one has lots of anomalous signal and others in which there is little. See the Templetons' work and also: Bricogne, G., Capelli, S.C., Evans, G., Mitschler, A., Pattison, P., Roversi, P., Schiltz, M. X-ray absorption, refraction and resonant scattering tensors in selenated protein crystals: implications for data collection strategies in macromolecular crystallography J. Appl. Cryst., 38, 168-182, 2005 I suspect there have been times in which lack of signal or lots of signal have been attributed to oxidation/reduction of Se atoms, when in fact it may have been the luck of the draw of how the crystal went up into the beam. Ciao Pietro Sent from my Desktop Dr. Pietro Roversi Oxford University Biochemistry Department - Glycobiology Division South Parks Road Oxford OX1 3QU England - UK Tel. 0044 1865 275339 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of James Holton [jmhol...@lbl.gov] Sent: 07 July 2014 00:59 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Selenomethionine crystals I general I agree with Tim, but provided it doesn't kill your protein, oxidation of selenomethionine can actually enhance your anomalous signal considerably (http://dx.doi.org/10.1107/S0907444901008666). The reason for this is because the white line peak in the SeMet x-ray absorption spectrum is actually a pre-edge feature. Although the edge itself represents the point when the incoming photon has just enough energy to completely eject a core electron from the Se atom, it is also possible for the electron to be not exactly ejected but merely promoted to an empty orbital with energy a few eV below that of a free electron in a vacuum. It is because of these extra landing sites that the near-edge structure of the x-ray absorption specturm (XANES or NEXAFS) can be influenced by chemistry. Specifically, the peak of the normal SeMet spectrum is a 1s-4p transition (http://dx.doi.org/10.1021/es9a043 http://dx.doi.org/10.1107/S0909049506048898), and the more oxidized the Se atom is, the less occupied the 4p level becomes and the bigger the while line gets. And, of course, the bigger the while line the more f phasing signal you get. Unfortunately, the extra oxygens stuck on the Se can sterically disrupt the local environment of the SeMet, and fear of this is probably why so many people have not tried it. However, if you're desperate for that extra little boost of phasing signal, it might be a refreshing change to do the opposite of trying to keep your protein from oxidizing all the time. Perhaps even adding a dash of H2O2. The worst your crystals can do is not diffract. -James Holton MAD Scientist On 7/1/2014 8:54 AM, Tim Gruene wrote: Dear Maher, as far as I understand, the anomalous scattering comes from inner shell electrons, not the valence electrons. So while you might notice a slight shift in the peak wavelength, the strength of the signal will only reduce if you crystal order suffered over time, but not from any oxidation of the Se. Best, Tim On Tue, Jul 01, 2014 at 10:51:20AM -0500, Maher Alayyoubi wrote: Hi everyone, Would anyone know for how long Selenomethionine derivative crystals are good if kept in plate at RT. In other words, would SE loose its scattering properties due to oxidation over time? I have SElmet crystals that have been lying in a plate for 2 months by now so I was wondering if they are still worthwhile the effort of collecting new data from them. Thank you very much, Maher
Re: [ccp4bb] Rfree set for twinned data
Hi, Reflections related by twin operator(s) should have same FreeR flag. FREERFLAG program in CCP4 takes care of it by default. http://www.ccp4.ac.uk/html/freerflag.html if the keyword NOTWIN is not set, all reflections that are equivalent by the symmetry of the point group of the twin lattice (assuming the data is twinned), obtain the same flag. This includes both the possibility of merohedral and pseudomerohedral twinning. Best regards, Takanori Nakane (2014/07/07 7:31), Yamei Yu wrote: Hi all, Is there anything that needed to pay attention to while choosing Rfree set for twinned data set? Or we can choose Rfree set randomly as untwined data set? Thanks! Best wishes! Yamei Yu
Re: [ccp4bb] twin or untwinned
Thanks all for your comments! Yamei Yu On Jul 5, 2014, at 5:10 AM, Nat Echols nathaniel.ech...@gmail.com wrote: On Thu, Jul 3, 2014 at 7:50 AM, Nat Echols nathaniel.ech...@gmail.com wrote: On Thu, Jul 3, 2014 at 6:53 AM, Dirk Kostrewa kostr...@genzentrum.lmu.de wrote: yes - unfortunately, in my hands, phenix.xtriage reads the XDS_ASCII.HKL intensities as amplitudes, producing very different output statistics, compared both to the XDS statistics and to an mtz file with amplitudes created from that XDS file. This is incorrect. It does read it correctly as intensities - the confusion probably arises from the fact that Xtriage internally converts everything to amplitudes immediately, so that when it reports the summary of file information, it will say xray.amplitude no matter what the input type was (the same will also be true for Scalepack and MTZ formats). However, the data will be converted back to intensities as needed for the individual analyses. Obviously this isn't quite ideal either since the original intensities are preferable but for the purpose of detecting twinning I hope it will be okay. In any case the incorrect feedback confused several other users so it's gone as of a few weeks ago, and the current nightly builds will report the true input data type. (The actual results are unchanged.) Tim: I have no reason to think we handle unmerged data poorly; I'm not sure who would have told you that. In most cases they will be merged as needed upon reading the file. I'm a little concerned that you're getting such different results from Xtriage and pointless/aimless, however. Could you please send me the input and log files off-list? Dirk, same thing: if you have an example where XDS and Xtriage are significantly in disagreement, the inputs (and logs) would be very helpful. In both cases, I suspect the difference is in the use of resolution cutoffs and absolute-scaled intensities in Xtriage versus other programs, but I'd like to be certain that there's not something broken. I stand corrected: unmerged XDS files (but not other formats) were not being handled appropriately in Xtriage; this was fixed several weeks ago, so the nightly builds should behave as expected. -Nat
Re: [ccp4bb] Lysine coordinated ions
Hi Kaherine, It seems its a modified lysine in to kcx (Carbamylated lysine) but its only the case if you used during entire purification or crystallization BME in your buffer Best Regards AFSHAN On Wednesday, July 2, 2014 5:38 PM, Katherine Sippel katherine.sip...@gmail.com wrote: At various peoples' urgings (thanks for the contributions all) I went ahead and put in Mg based on the bond valence. If refines very nicely in the context of the density maps (see attached MgCl2_pH6point5_3.png). I ran it through the check my metal server and it clears the coordination geometry and bond distance parameters but is displeased with the coordinating ligands. I am also concerned about the rotamer (big ol' outlier) and the CE-NZ-Mg bond angle. Obviously the density looks good, but it feels weird from a basic chemical standpoint. The crystallization condition for the ion-coordinated lysine was 100 mM Bis Tris pH 6.5, 200 mM MgCl2, 19% PEG 3350. One of the other space groups has 100 mM Tris pH 8.5, 200 mM MgNO3, 27% PEG 1500 and there is no errant density (see attached MgNO3_pH8point5.png). The sodium I mentioned comes from NaCl in the protein storage buffer. Thank you for all of your help thus far. Katherine On Tue, Jul 1, 2014 at 9:35 PM, Nat Echols nathaniel.ech...@gmail.com wrote: On Tue, Jul 1, 2014 at 3:10 PM, Katherine Sippel katherine.sip...@gmail.com wrote: My google-fu has failed me once again so I am turning to the collective knowledge of the bb. I'm working on a blobology challenge at the moment and have hit a wall. Is anyone aware of an ion that coordinates to lysine and prefers octahedral geometry. The mystery ion seems to have perfect octahedral geometry with bond distances of ~2.1 angstrom, but the only direct side chain interaction is to a lysine NZ, the rest are waters. Lysine can coordinate a cation if the chemical environment is favorable - usually this means a high-pH buffer (what was the pH of your crystals?). The same is true for N-termini; I may be able to dig up a published example of this. (I think it is effectively impossible for Arg, however.) These interactions are certainly exceedingly rare (and I doubt they are ever present in vivo), but if the nitrogen loses a proton the lone pair will be able to coordinate a compatible ions. Since magnesium can be coordinated by the nitrogen histidine it seems like the most likely candidate - but I would still be very, very careful before assigning it, especially if the only other coordinating atoms are waters. -Nat -- Nil illegitimo carborundum- Didactylos
[ccp4bb] Postdoctoral positions available at EMBL Hamburg
Dear all, I would like to draw your attention to two postdoctoral Vacancy Notices in the research group of Dr. Matthias Wilmanns at the EMBL Hamburg Unit: *Vacancy Notice: HH_00065* Postdoctoral Fellowship on Structure of Signaling segments in Muscle Filament Proteins Project Outline: Many large muscle filament proteins have extended segments of signaling and kinase domains. In an interdisciplinary approach with proteomics and cell biology collaborators, we wish to investigate the functions of these domains in vitro and an in vivo. We use combined structural biology approaches, with X-ray crystallography being the core method, to characterize their mechanism of action. http://ig14.i-grasp.com//fe/tpl_embl01.asp?newms=jjid=52770aid=15470 * **Vacancy Notice : HH_00067* Postdoctoral Fellowship in Structural and functional relations of the Von Willebond Factor. Project Outline: The Von Willebrand Factor comprises a large multi-domain protein assembly and has crucial roles in blood coagulation. Its function is regulated by shear forces. In collaboration with clinicians, biologists and physicists we are interested in the overall structure of this protein and its domains by hybrid structural biology approaches. http://ig14.i-grasp.com//fe/tpl_embl01.asp?newms=jjid=52784aid=15470 best regards Margret
[ccp4bb] Postdoctoral Fellow in Structural Biology and Chromatin Biology: Brighton (UK)
Postdoctoral Fellow in Structural Biology and Chromatin Biology: Brighton, United Kingdom A Postdoctoral Research Fellow position is available in the newly established group of Erika Mancini at the School of Life Sciences, University of Sussex. The successful candidate will join a multidisciplinary group using structural biology, biochemistry, biophysics and cell biology to characterise complexes involved in chromatin remodelling and the regulation of eukaryotic transcription. More information on our research activities is available at the old lab website: (https://www.strubi.ox.ac.uk/research/erika-mancini) The Fellow will benefit from a multidisciplinary environment and a highly collaborative community with particular strengths in cell biology and cancer (including the MRC Genome Damage and Stability Centre). The School of Life Sciences at Sussex is very well equipped for all aspects of modern structural biology, with state-of-the-art facilities for molecular biology, recombinant expression in bacterial and eukaryotic systems, biochemistry, biophysics and X-ray crystallography. Excellent synchrotron access (~ 2 days/month) is available through rolling beam allocation programmes at Diamond and ESRF, and there is a strong existing structural biology activity in the School. You will have, or expect to soon complete, a PhD (or equivalent) in biochemistry, biophysics, molecular biology or related subject. Experience with recombinant DNA techniques, high-quality protein expression and purification for structure-function studies is essential. Experience in crystallization and X-ray crystallography of protein-protein and protein-DNA complexes and biophysical and biochemical assays to characterize protein-protein and protein-DNA interactions is also required. Experience in other structural biology techniques, such as single particle electron-microscopy, SAXS or NMR would be advantageous. Finally, a background in the cell biology of chromatin and transcription regulation would be a strong asset. For more information, including details on how to apply, please visit http://www.sussex.ac.uk/aboutus/jobs/708 . Informal enquiries should be addressed to Dr. Erika Mancini (er...@strubi.ox.ac.uk). Deadline for applications: 5th August 2014
[ccp4bb] Structural Biology Facility Manager--UC Santa Cruz
A full-time research specialist position is available at the University of California Santa Cruz to manage a new Macromolecular Structure-Function Core Facility. Emphasis is on research, training, and equipment management related to x-ray crystallography. For more information see http://apo.ucsc.edu/academic_employment/jobs/JPF00132-15T.pdf Apply at https://recruit.ucsc.edu/apply/JPF00132 Seth M. Rubin Associate Professor of Chemistry and Biochemistry University of California, Santa Cruz 1156 High St. Santa Cruz, CA 95064 PSB 262 831-459-1921 sru...@ucsc.edu http://chemistry.ucsc.edu/~srubin/RubinLab/Home.html
[ccp4bb] Two Molecular Biology Lab Manager Positions
Birkbeck, University of London has two vacancies to mange our Molecular Biology research laboratories. The post holders are responsible for ordering, equipment maintenance and health and safety. They will also be involved in development of teaching laboratory practicals and assisting in research and supervision of Phd and undergraduate and masters projects as their other duties allow. More details and applications can be found at http://www.jobs.ac.uk/job/AJA852/research-laboratory-manager-two-posts/ with a closing date of the 28th July. -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.k...@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G54a Office) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door
[ccp4bb] New app deadline for CSHL X-ray Methods workshop: July 15, 2014
We have extended the application deadline for the CSHL X-ray Methods in Structural Biology Course to be held October 13-28,2014. Our earlier deadline was based on getting all the paperwork completed in time for using NSLS, but since NSLS will not be available*, we can extend the deadline to July 15th. This may be helpful to folks who got caught up in World Cup action and missed the earlier deadline. Below is my previous announcement. Regards, Jim *We will collect diffraction data remotely at the APS and in the homelab at CSHL. Participants are encouraged to bring their own crystals as well. Here's a link to the announcement: http://meetings.cshl.edu/courses/2014 /c-crys14.shtml The course is supported by a grant from the National Institute of General Medical Sciences Some financial assistance is also available for some, see the course announcement on the details of that. I think the course is an outstanding place to learn both the theoretical and practical aspects of Macromolecular Crystallography because of the extensive lectures from world-renowned teachers and the hands-on experiments. This year's course will once again see the return of the long-time instruction team of Alex McPherson, Gary Gilliland, Bill Furey and myself along with many talented experts to help us give the participants an experience in Macromolecular Crystallography learning that cannot be found anywhere else. (The student:teacher ratio ends up to be about 1:1). We expect to have the participants crystallize several proteins and determine their structures all in about two weeks. While an emphasis is placed on proteins that we provide, participants will be able to work on their own macromolecules as well in the 2014 course. The course is limited to 16 participants due to the very hands-on nature of the experiments and the intimate seminar room. Please check the above web site for more details. If anyone has any questions, please send me e-mail, I will be happy to answer all queries. Jim
[ccp4bb] emergency substitute for RT loop cover?
Hi all Pretend you were stuck having to do RT data collection but without access to either Mitegen MicroRT Capillaries or the more old-fashioned quartz capillaries, to pop over the loop. Anybody have suggestions of alternative ways of doing this? I do want to use loops (I never learnt how to suck up crystals in capillaries). I have access to a passably stocked biochemistry teaching lab, and could at a pinch go rifle some more advanced research labs. (No, I'm not at home ;) Thanks! phx
Re: [ccp4bb] emergency substitute for RT loop cover?
Paratone might work. It is thick enough to hold the crystal in place I would think. Small molecule crystallographers use to use it all the time at both room temperature and cryo temperatures. Len Leonard M. Thomas Ph.D. Macromolecular Crystallography Laboratory Manager University of Oklahoma Department of Chemistry and Biochemistry Stephenson Life Sciences Research Center 101 Stephenson Parkway Norman, OK 73019 405-325-1126 lmtho...@ou.edu http://barlywine.chem.ou.edu http://structuralbiology.ou.edu From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Frank von Delft [frank.vonde...@sgc.ox.ac.uk] Sent: Monday, July 07, 2014 11:32 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] emergency substitute for RT loop cover? Hi all Pretend you were stuck having to do RT data collection but without access to either Mitegen MicroRT Capillaries or the more old-fashioned quartz capillaries, to pop over the loop. Anybody have suggestions of alternative ways of doing this? I do want to use loops (I never learnt how to suck up crystals in capillaries). I have access to a passably stocked biochemistry teaching lab, and could at a pinch go rifle some more advanced research labs. (No, I'm not at home ;) Thanks! phx
Re: [ccp4bb] emergency substitute for RT loop cover?
Anyone ever tried a glob of paratone-n for this? I remember it being good for keeping crystals happy during Xe derivatization, but that was for a relatively short time. If this is at the synchrotron, the dataset would only take a few minutes at most, so maybe it would work. JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von Delft Sent: Monday, July 07, 2014 12:33 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] emergency substitute for RT loop cover? Hi all Pretend you were stuck having to do RT data collection but without access to either Mitegen MicroRT Capillaries or the more old-fashioned quartz capillaries, to pop over the loop. Anybody have suggestions of alternative ways of doing this? I do want to use loops (I never learnt how to suck up crystals in capillaries). I have access to a passably stocked biochemistry teaching lab, and could at a pinch go rifle some more advanced research labs. (No, I'm not at home ;) Thanks! phx
Re: [ccp4bb] emergency substitute for RT loop cover?
Hi Frank - How about a gel loading pipet tip as a substitute for the quartz capillary? Suck the crystal into it, then try to get it to stick to the wall. Flame seal the tip end, and use a glob of vacuum grease for the other end (or cut off the skinny part with your crystal using a razor blade). That semi-transparent plastic FPLC tubing (Tefzel?) might work as a substitute for the Mitegen capillary sleeve. Your Xray absorption and background scattering will be really high from all this plastic, but any port in a storm. - Matt On 7/7/14 12:32 PM, Frank von Delft wrote: Hi all Pretend you were stuck having to do RT data collection but without access to either Mitegen MicroRT Capillaries or the more old-fashioned quartz capillaries, to pop over the loop. Anybody have suggestions of alternative ways of doing this? I do want to use loops (I never learnt how to suck up crystals in capillaries). I have access to a passably stocked biochemistry teaching lab, and could at a pinch go rifle some more advanced research labs. (No, I'm not at home ;) Thanks! phx -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374
Re: [ccp4bb] emergency substitute for RT loop cover?
Why not draw out a pasteur pipette using a bunsen burner to the desired thinness? You’ll end up with something rather like an old-fashioned glass capillary. Adrian On 7 Jul 2014, at 17:52, Matthew Franklin mfrank...@nysbc.org wrote: Hi Frank - How about a gel loading pipet tip as a substitute for the quartz capillary? Suck the crystal into it, then try to get it to stick to the wall. Flame seal the tip end, and use a glob of vacuum grease for the other end (or cut off the skinny part with your crystal using a razor blade). That semi-transparent plastic FPLC tubing (Tefzel?) might work as a substitute for the Mitegen capillary sleeve. Your Xray absorption and background scattering will be really high from all this plastic, but any port in a storm. - Matt On 7/7/14 12:32 PM, Frank von Delft wrote: Hi all Pretend you were stuck having to do RT data collection but without access to either Mitegen MicroRT Capillaries or the more old-fashioned quartz capillaries, to pop over the loop. Anybody have suggestions of alternative ways of doing this? I do want to use loops (I never learnt how to suck up crystals in capillaries). I have access to a passably stocked biochemistry teaching lab, and could at a pinch go rifle some more advanced research labs. (No, I'm not at home ;) Thanks! phx -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374 signature.asc Description: Message signed with OpenPGP using GPGMail
Re: [ccp4bb] emergency substitute for RT loop cover?
Try to put your crystal into oil drop? Sent on a Sprint Samsung Galaxy S® III div Original message /divdivFrom: Frank von Delft frank.vonde...@sgc.ox.ac.uk /divdivDate:07/07/2014 12:32 PM (GMT-05:00) /divdivTo: CCP4BB@JISCMAIL.AC.UK /divdivSubject: [ccp4bb] emergency substitute for RT loop cover? /divdiv /divHi all Pretend you were stuck having to do RT data collection but without access to either Mitegen MicroRT Capillaries or the more old-fashioned quartz capillaries, to pop over the loop. Anybody have suggestions of alternative ways of doing this? I do want to use loops (I never learnt how to suck up crystals in capillaries). I have access to a passably stocked biochemistry teaching lab, and could at a pinch go rifle some more advanced research labs. (No, I'm not at home ;) Thanks! phx
[ccp4bb] PDB Search
Sorry for the off topic post, but I have a relevant question that someone may be able to help me with. I am looking to conduct a PDB search to see how many proteins contain the simple 1 Fe 4 Cys so called rubredoxin like site. Is there a tool that is able to do this that would be based more on structure instead of sequence? Thank you in advance for any and all of your replies! Regards, Ryan Gumpper?
Re: [ccp4bb] emergency substitute for RT loop cover?
One thing you can try is to place modeling clay at the base of the pin. Add some mother liquor to a quartz capillary (1-2mm should work) and under a microscope carefully cover the loop with the capillary, pressing it into the clay to seal the crystal in a closed system. As long as you move or divert the cold stream, you should be ok. I actually collected a full dataset off one precious crystal this way at room temperature, and it diffracted to 2.2 Å. Good luck. Bryan From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ed Pozharski Sent: Monday, July 07, 2014 12:58 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] emergency substitute for RT loop cover? Try to put your crystal into oil drop? Sent on a Sprint Samsung Galaxy S® III -- Confidentiality Notice: This message is private and may contain confidential and proprietary information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful. Original message From: Frank von Delft Date:07/07/2014 12:32 PM (GMT-05:00) To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] emergency substitute for RT loop cover? Hi all Pretend you were stuck having to do RT data collection but without access to either Mitegen MicroRT Capillaries or the more old-fashioned quartz capillaries, to pop over the loop. Anybody have suggestions of alternative ways of doing this? I do want to use loops (I never learnt how to suck up crystals in capillaries). I have access to a passably stocked biochemistry teaching lab, and could at a pinch go rifle some more advanced research labs. (No, I'm not at home ;) Thanks! phx
Re: [ccp4bb] PDB Search
Hi Ryan, You can try the mespeus database that describes ion coordination. You can explicitly search for an iron ion coordinated by cysteine side chains. Cheers, Robbie Original message From: Ryan Henry Gumpper rgumpp...@student.gsu.edu Date:07/07/2014 19:55 (GMT+01:00) To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] PDB Search Sorry for the off topic post, but I have a relevant question that someone may be able to help me with. I am looking to conduct a PDB search to see how many proteins contain the simple 1 Fe 4 Cys so called rubredoxin like site. Is there a tool that is able to do this that would be based more on structure instead of sequence? Thank you in advance for any and all of your replies! Regards, Ryan Gumpper
Re: [ccp4bb] emergency substitute for RT loop cover?
Sorry, forgot you didn’t have any quartz capillaries. If you are in a biochem lab, do you have access to hematocrit capillaries? You might be able to use them to cover the loop in the fashion I posted just a minute ago. Again, good luck! Bryan -- Confidentiality Notice: This message is private and may contain confidential and proprietary information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von Delft Sent: Monday, July 07, 2014 12:33 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] emergency substitute for RT loop cover? Hi all Pretend you were stuck having to do RT data collection but without access to either Mitegen MicroRT Capillaries or the more old-fashioned quartz capillaries, to pop over the loop. Anybody have suggestions of alternative ways of doing this? I do want to use loops (I never learnt how to suck up crystals in capillaries). I have access to a passably stocked biochemistry teaching lab, and could at a pinch go rifle some more advanced research labs. (No, I'm not at home ;) Thanks! phx
Re: [ccp4bb] PDB Search
Dear Ryan Gumpper, entering the keywords 'PDB motif search' at www.ixquick.com led me to the Swiss PDB Viewer Tutorial on 3D motif search (http://spdbv.vital-it.ch/motif3Dsearch_tut.html) which sounds very much like what you are looking for. Regards, Tim On 07/07/2014 07:45 PM, Ryan Henry Gumpper wrote: Sorry for the off topic post, but I have a relevant question that someone may be able to help me with. I am looking to conduct a PDB search to see how many proteins contain the simple 1 Fe 4 Cys so called rubredoxin like site. Is there a tool that is able to do this that would be based more on structure instead of sequence? Thank you in advance for any and all of your replies! Regards, Ryan Gumpper -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: OpenPGP digital signature
Re: [ccp4bb] emergency substitute for RT loop cover?
The quality of glass and thickness may be a problem with the hematocrit caps but definitely worth a try in a pinch. - todd From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Prince, D Bryan [dbryan.pri...@astrazeneca.com] Sent: Monday, July 07, 2014 1:34 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] emergency substitute for RT loop cover? Sorry, forgot you didn’t have any quartz capillaries. If you are in a biochem lab, do you have access to hematocrit capillaries? You might be able to use them to cover the loop in the fashion I posted just a minute ago. Again, good luck! Bryan -- Confidentiality Notice: This message is private and may contain confidential and proprietary information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von Delft Sent: Monday, July 07, 2014 12:33 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] emergency substitute for RT loop cover? Hi all Pretend you were stuck having to do RT data collection but without access to either Mitegen MicroRT Capillaries or the more old-fashioned quartz capillaries, to pop over the loop. Anybody have suggestions of alternative ways of doing this? I do want to use loops (I never learnt how to suck up crystals in capillaries). I have access to a passably stocked biochemistry teaching lab, and could at a pinch go rifle some more advanced research labs. (No, I'm not at home ;) Thanks! phx
[ccp4bb] Postdoctoral Position in Membrane Protein Structural Biology
Two postdoctoral positions in structural biology are available starting in August in my new laboratory within the Biological Sciences department at Purdue University. As part of the Markey Center for Structural Biology, my lab will integrate electron microscopy and X-ray crystallography with biochemical methods to study the biogenesis of beta-barrel membrane proteins in Gram-negative bacteria with a focus on eventual therapeutic development against pathogenic strains of bacteria (See Noinaj et al., Structure (in press, 2014), Nature, 501:385-390 (2013), and Nature, 483:53-58 (2012)). The Markey Center for Structural Biology at Purdue is recognized worldwide for its leadership in structural biology of viruses, membrane proteins, receptors, signaling proteins and enzymes in addition to methods development in crystallography, NMR and electron microscopy. My lab is located within the Hockmeyer Hall of Structural Biology which boasts state-of-the-art shared resources including a Titan Krios cryo-TEM, Bruker Avance-III 800 MHz NMR, Rigaku X-ray generators and detectors, and other advanced instrumentation available at the Bindley Bioscience Center, the Birck Nanotechnology Center, and the new Center for Drug Discovery. In addition, Purdue is in close proximity to the Advanced Photon Source at Argonne National Lab for convenient access to synchrotron data collection. The successful candidate(s) should be highly motivated, have strong written and communication skills, have (or expect) a recent PhD in structural biology, biophysics, biochemistry, or other related field of study and have previous experience in working with membrane proteins and/or X-ray crystallography or electron microscopy. Applicants should send a CV, names of three referees and a statement describing your interests and relevant work experience to Nicholas Noinaj at nicholas.noi...@gmail.commailto:nicholas.noi...@gmail.com. Nicholas Noinaj Purdue University Department of Biological Sciences 333 Hockmeyer Hall 915 W State St West Lafayette, IN 47907
