[ccp4bb] off-topic: PiMS Pro
PiMS now has a commercial partner, Emerald Bio. They will distribute PiMS Pro(TM) for commercial use. STFC will use the royalties from this agreement to continue supporting PiMS for use both in industry and in universities, and proposals by academics for support for new methods will keep PiMS current for industrial use. PiMS will continue to be available free for academic use, to support data management in academic protein production and structural biology laboratories. The interests of academic users of PiMS will be represented by a board consisting of: Peter Nollert (Emerald Bio, co-chair), Chris Morris (STFC, co-chair), Ray Owens (OPPF-UK), Mark Mixon (Emerald Bio) I would like to thank CCP4 for its generous support of PiMS over the years. This has enabled us to reach this point, which makes PiMS truly sustainable for the first time. There are more details in this press release: http://pims.structuralbiology.eu/docs/PiMS%20Press%20Release%20Final.pdf regards, Chris Chris Morris chris.mor...@stfc.ac.uk Tel: +44 (0)1925 603689 Fax: +44 (0)1925 603634 Mobile: 07921-717915 Skype: chrishgmorris http://pims.structuralbiology.eu/ http://www.citeulike.org/blog/chrishmorris STFC, Daresbury Laboratory, Sci-Tech Daresbury, Keckwick Lane, Daresbury, Warrington, WA4 4AD UK -- Scanned by iCritical.
[ccp4bb] CCP4 Study Weekend 2013
Dear All, A quick reminder that these next few days are the last chance to register for next month's CCP4 Study Weekend. Registration will close next Monday the 10th of December. The meeting will take place at the East Midlands Conference Centre in Nottingham, UK from the 3rd to the 5th of January and is entitled "Molecular Replacements", focusing on the presentation and discussion of advanced methods and techniques in this important field. For more information about the meeting and to register please visit the Study Weekend website at: http://www.cse.scitech.ac.uk/events/CCP4_2013/ We look forward to seeing you in Nottingham. Best wishes, Ronan -- Scanned by iCritical.
[ccp4bb] Pseudo translational symmetry Problem or Wrong Spacegroup
Dear All, Recently, I collected a dataset of a protein-DNA complex and indexed in spacegroup P212121 to 3.4 Å. However, Phenix.Xtriage indicated the presence of a very high pseudotranslational symmetry peak. I scaled the data in spacegroup P222. When I used the protein heterotetramer as search model to do the MR, solutions are suggested in P22121, P212121, P2212, P21212 and all with a TFZ score higher than 15, LLG higher than 570. Then I used phenix.refine to refine those solutions; however the Rfree is as high as 0.54-0.56. The refinement strategy that I used for the refinement is rigid body, group B-factors and XYZ coordinates. How to deal with this pseudotranslational symmetry problem? Does a solution with such high TFZ scores mean that the correct one has been found? How to solve the spacegroup problem in such situation? Do you have any suggestions? Thank you very much. Greetings, Yurong
Re: [ccp4bb] Pseudo translational symmetry Problem or Wrong Spacegroup
Dear Yurong, your approach to individually refine each potential solution is correct. I do not know how things are implemented in phenix.refine, but the first thing to check is that your are using the correct space group as obtained from the MR program. Some refinement programs use the space group from the reflection file (MTZ), which may be the space group used for the processing instead of the space group from the pdb file found by the MR program. >From what you write, you must have non-crystallographic translations of almost >0.5 in x and z direction. This means that you will have along these axis >either exact 21 symmetry, where the ~0.5 shift will generate a pseudo 2-fold, >or you have exact 2-fold symmetry where the pseudo symmetry will produce a >pseudo 21 axis. With your low resolution data, this explains why you get >solutions in all these space groups. You really have to try all combinations >of crystallographic and non-crystallographic symmetry. Good luck! Herman From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Yurong Wen Sent: Monday, December 03, 2012 12:49 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Pseudo translational symmetry Problem or Wrong Spacegroup Dear All, Recently, I collected a dataset of a protein-DNA complex and indexed in spacegroup P212121 to 3.4 Å. However, Phenix.Xtriage indicated the presence of a very high pseudotranslational symmetry peak. I scaled the data in spacegroup P222. When I used the protein heterotetramer as search model to do the MR, solutions are suggested in P22121, P212121, P2212, P21212 and all with a TFZ score higher than 15, LLG higher than 570. Then I used phenix.refine to refine those solutions; however the Rfree is as high as 0.54-0.56. The refinement strategy that I used for the refinement is rigid body, group B-factors and XYZ coordinates. How to deal with this pseudotranslational symmetry problem? Does a solution with such high TFZ scores mean that the correct one has been found? How to solve the spacegroup problem in such situation? Do you have any suggestions? Thank you very much. Greetings, Yurong
[ccp4bb] Perfluoropolyether as cryoprotectant for membrane proteins ?
Dear crystallographers, does anyone have experience using Perfluoropolyether (Hampton Research) as cryoprotectant for membrane proteins ? Cheers, Ulrike
Re: [ccp4bb] To cryo or not to cryo...
Hi Yuri, I've had a very similar experience last week which ended badly. I opted to cryo my new crystals using my favourite cryo. Diffraction showed at least the crystals were protein but not much more. A classic example of cryo killing crystals. I mounted the remaining tiny fragment from the drop in a room temperature mount and got 15 images before it died. From this I got a cell and lattice even though it only diffracted to 6Ang. If had mounted a larger piece of crystal first off I might of been able to get a dataset with much shorter exposures. I would encourage either an in-situ test you have the equipment or use a capillary in whichever way suits. There are methods that allow recovery of the crystal after the test. At least this way you can (a) feel satisfied when you crush it up afterwards for seed because it didn't diffract at all or (b) successfully cryo your nicely diffracting crystal. Good Luck! David Hargreaves Associate Principal Scientist _ AstraZeneca DECS, CP&SS Mereside, 50F49, Alderley Park, Cheshire, SK10 4TF Tel +44 (0)01625 518521 Fax +44 (0) 1625 232693 David.Hargreaves @astrazeneca.com Please consider the environment before printing this e-mail -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged 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 unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Yuri Pompeu Sent: 01 December 2012 01:23 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] To cryo or not to cryo... Dear community, I have what seems to be a pretty decent single crystal that grew from a screen set up 2 weeks ago. I am trying to reproduce it but so far I have not succeeded. I am however afraid the crystal that did form will start to deteriorate. So this brings me to dilemma, I feel like I should try and mount this crystal and shoot it. But since I only have 1 sample, I do not want to mess this up... I am inclined to try cryo conditions, but I am afraid the addition of a cryo such as glycerol could destroy the little guy. The crystal formed in 30% PEG 4000, 0.1M NaCitrate pH5.6 and 0.2M NH4AcO, I wonder if this is a cryo condition already? Any suggestions would be appreciated. best,
Re: [ccp4bb] Perfluoropolyether as cryoprotectant for membrane proteins ?
Ulrike, I usually suggest it as the second try (the first try is mother liquor alone), as it does not involve mixing any new buffer concoctions. I do not have hard data, but I'd estimate it worked in about 50% of cases; it seemed not to matter if you try it on a soluble or membrane protein crystal. In my hands it performs better than mineral oil, silicon oil or paratone. Problematic cases are crystals in heavy precipitate, which has to be removed prior to transfer into the oil, otherwise it sticks around the crystal and you can't get the crystal "dry". hth, Jens On Mon, 2012-12-03 at 13:07 +, Ulrike Demmer wrote: > Dear crystallographers, > > does anyone have experience using Perfluoropolyether (Hampton Research) as > cryoprotectant for membrane proteins ? > > Cheers, > > Ulrike
