Re: [ccp4bb] optimization of dumbbell like crystal
Additives screening. YB 2011-02-21 yybbll 发件人： Bosch, Juergen 发送时间： 2011-02-21 03:46:12 收件人： CCP4BB 抄送： 主题： Re: [ccp4bb] optimization of dumbbell like crystal Seeding ? changing from sitting to hanging drop or under oil ? play with temperature ? Jürgen On Feb 20, 2011, at 9:29 PM, Harvey Rodriguez wrote: Dear CCP4BBers, Recently I got a crystal which appeared in the condition 2.1M DL-Malic Acid, pH 7.0. The crystal looks like a dumbbell but was composed of a cluster of very thin needles as shown in the picture. The crystal can be repeated but the diffraction is poor. I have tried the grid optimization by pH and salt concentration gradients, however there was no improvement in either the shape or the quality of the crystal. Does anyone have some experiences in optimizing this kind of crystals? Any suggestion is appreciated! Harvey dumbbell crystals.jpg .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/
[ccp4bb] Postdoc position at the Gene Center Munich
Dear CCP4ers, on behalf of Patrick Cramer, I send a Postdoc position offer, given below. Please, do not respond to me, but to the e-mail addresses given in the job description. Best regards, Dirk Kostrewa. *** Applications are invited for a RESEARCH SCIENTIST (POSTDOC) POSITION IN CRYSTALLOGRAPHY to work on multi-component complexes and study the mechanisms of gene transcription in the lab of Patrick Cramer at the Gene Center of the University of Munich (www.LMB.uni-muenchen.de/cramer). We look for a collaborative person with a background in X-ray crystallography, documented by at least one significant first-author publication. We offer a stimulating environment on a leading European life science campus, and a longer-term perspective (2-5 years). There are possibilities to join ongoing projects of high scientific significance, to participate in networks of excellence at the national and international level, and to contribute to teaching. Thus this position can prepare for an independent career. Applications including a one-page CV, list of publications, and email addresses of two referees should be sent to R. Menacher (menac...@lmb.uni-muenchen.de). Questions may be sent to Patrick Cramer (cra...@lmb.uni-muenchen.de). Deadline for applications is March 1st, 2011.
Re: [ccp4bb] off-topic: 2 peaks on Cation
In your original mail (2011-02-18; 18:45 GMT), you wrote: Possibly deamidation of the protein, in particluar one or more lysines Hence, my comment was based on your own writing, that is deamiDation. Wishing you a better week. Nadir Pr. Nadir T. Mrabet Structural Molecular Biochemistry Nutrigenex - INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax: +33 (0)3.83.68.32.79 E-mail: Nadir.Mrabetat medecine.uhp-nancy.fr On 18/02/2011 21:07, Soisson, Stephen M wrote: I'll swap you for the deamination, as that pertains to lysines...it's been a long week :) Steve -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Nadir T. Mrabet Sent: Friday, February 18, 2011 2:04 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] off-topic: 2 peaks on Cation Typo! I actually meant deamidation. Nadir Pr. Nadir T. Mrabet Structural Molecular Biochemistry Nutrigenex - INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax: +33 (0)3.83.68.32.79 E-mail: Nadir.Mrabetat medecine.uhp-nancy.fr On 18/02/2011 20:36, Christian Roth wrote: Hi, you did not mention anything about your protein, but if it shows a metal dependency, than different amounts of the metal ion might changen the overall charge and influence the interactions with the ion exchanger. There might be also a modification of an aminoacid f.e. decarboxylation of an aspartate or glutamate. Christian Am Freitag 18 Februar 2011 18:13:36 schrieb Ulli Hain: Hi, I was wondering if anyone had possible explanations for a recombinantly expressed soluble protein that runs as 2 equal, slightly overlapping peaks on a cation exhanger but as one peak on a size exclusion column and same electrophoretic mobility on SDS-PAGE. -Ulli Adelaide Ulricke Hain PhD Candidate Johns Hopkins Bloomberg School of Public Health Department of Biochemistry and Molecular Biology 615 North Wolfe Street Baltimore, MD 21205 Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
Re: [ccp4bb] optimization of dumbbell like crystal
Dear Harvey, Microseeding and adding 1-5% glycerol to the drops helped me when I obtained crystals like these. Good Luck! Bryan From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Harvey Rodriguez Sent: Sunday, February 20, 2011 9:29 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] optimization of dumbbell like crystal Dear CCP4BBers, Recently I got a crystal which appeared in the condition 2.1M DL-Malic Acid, pH 7.0. The crystal looks like a dumbbell but was composed of a cluster of very thin needles as shown in the picture. The crystal can be repeated but the diffraction is poor. I have tried the grid optimization by pH and salt concentration gradients, however there was no improvement in either the shape or the quality of the crystal. Does anyone have some experiences in optimizing this kind of crystals? Any suggestion is appreciated! Harvey -- 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.
Re: [ccp4bb] optimization of dumbbell like crystal
Dear Harvey, I had very good results with low melt agarose and the detergent screen (e.g. Hampton Research). In both cases, the tendency for cluster formation as well as the diffraction power could be improved. Anja Dear CCP4BBers, Recently I got a crystal which appeared in the condition 2.1M DL-Malic Acid, pH 7.0. The crystal looks like a dumbbell but was composed of a cluster of very thin needles as shown in the picture. The crystal can be repeated but the diffraction is poor. I have tried the grid optimization by pH and salt concentration gradients, however there was no improvement in either the shape or the quality of the crystal. Does anyone have some experiences in optimizing this kind of crystals? Any suggestion is appreciated! Harvey Anja Pomowski Universität Freiburg Institut f. Organ. Chemie und Biochemie AK Prof. Einsle Albertstr. 21 79104 Freiburg Tel. 0761 2036088 Fax. 0761 2036161
Re: [ccp4bb] off-topic: Discovery Studio software
Correct, the DS Visualizer is not available for Mac OS at this point, however various emulators such as Parallels or VMWare have been used successfully. Without going into too much detail, there is a new version (3.0) of the visualizer which extends even further the capabilities of our previous free version. Here are some quick points of what is now included in this new version: - Molecular Builders - 3D plot visualization - 2D Protein-ligand interaction plot - Storyboard to capture workflow scenes (no script required) - Forcefield typing for preparation of simulation calculations - Protein reports - and much more... Many of the features that were previously available in the paid version, are now offered for free with this new version. I encourage everyone to give it a try. Thanks, Francisco Francisco Hernandez-Guzman Product Manager Accelrys, San Diego, CA From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Sean Seaver [s...@p212121.com] Sent: Saturday, February 19, 2011 11:11 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] off-topic: Discovery Studio software Hi Padmaja, -Will it work on a Mac OS? No -Is there another program (free or cheaper) that will do everything DS does? Currently, there is a free version that you can use of DS. http://accelrys.com/products/discovery-studio/visualization-download.php Hopefully that will give you a feeling if the program will fit your needs. -Any other comments from users/naysayers about DS We have up put up a couple of blog posts about DS that you may find helpful. Discovery Studio Visualizer 2.5 http://bit.ly/QgvNL 3 Selection Methods in Discovery Studio Visualizer http://bit.ly/4UIzcd Take Care, Sean P212121 http://store.p212121.com/
[ccp4bb] Could someone can help me to explain why EDTA-2Na can formate salt crystals
Dear all, I got a lot of salt crystals in reservior solution (well solution), which contains 0.1 M phosphate/citrate ph 4.2, PEG200 47%, EDTA-2Na 0-22mM. Reservior solution appears crystals from 12mM EDTA. Could someone help me to explain why? Thank you very much! Yibin
Re: [ccp4bb] Could someone can help me to explain why EDTA-2Na can formate salt crystals
The pH is too low and the EDTA is insoluble. You need to be above pH ~8.0. Your best bet is to try another chelator. James On Feb 21, 2011, at 2:22 PM, Yibin Lin wrote: Dear all, I got a lot of salt crystals in reservior solution (well solution), which contains 0.1 M phosphate/citrate ph 4.2, PEG200 47%, EDTA-2Na 0-22mM. Reservior solution appears crystals from 12mM EDTA. Could someone help me to explain why? Thank you very much! Yibin
