Re: [ccp4bb] Crystal Optimization
Dear Muhammad, I had a similar case, and the crystals could indeed be optimized. A few things to check first, 1) How long does it take for the needles to appear? Sometimes, if the protein is degraded/ cleaved over time, a small population (possibly a fragment of the whole protein) from the heterogeneous mix can give similar crystals. Like Bryan had suggested, it is also very useful to check the mol wt. of the crystallized species through mass spect/ native page. But do make sure to give the crystals serial washes, so the test accounts for crystallizexd species, not the ones from surrounding condition. 2) If the crystals indeed contain the protein of interest, they can be used for various seeding methods. I've got results from both streak and micro seeding. Best, Tuhin. Tuhin Bhowmick Department of Physics Indian Institute of Science Bangalore: 560012 Email: tuhin.i...@gmail.com On Wed, Jul 11, 2012 at 12:34 AM, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com wrote: Always give up. ** ** ...definitely not the kind of guy I want to sit up front in an airliner…** ** ** ** Best regards, BR - Bernhard Rupp, ATP-B737, CFII-MEI Vienna Air International Professional Aviation Services 001 (925) 209-7429 +43 (676) 571-0536 b...@vienna-air.com b...@ruppweb.org http://www.vienna-air.com/ - It is not your aptitude but your attitude that determines your altitude. (or your crystals) - ** ** ** ** ** ** From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of yybbll Sent: Tuesday, July 10, 2012 11:58 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Crystal Optimization ** ** Hi, In my experience, it is very very very difficult to optimize this needle like crystal. Always give up. Good luck! Dear All; Could somebody give a nice suggestion how the following type crystal could be optimized, I almost tried everything. Crystal Image is attached Crystal condition: 20% w/v PEG3350 and 200mM NaCl. Thanks in advance Bashir -- Muhammad Bashir Khan ** Structural Genome Consortium (SGC). University of Toronto Toronto, Canada
Re: [ccp4bb] DNA/RNA modeling
Hi Jens, You can try NAMOT (Nucleic Acid MOdelling Tool), from the links below. http://namot.sourceforge.net/ http://sourceforge.net/projects/namot/ Best, Tuhin. Tuhin Bhowmick Prof. S. Ramakumar’s Lab Biocrystallography and Computation Department of Physics Indian Institute of Science Bangalore, 560012 India On Wed, May 23, 2012 at 10:18 PM, Francisco Hernandez-Guzman francisco.hernan...@accelrys.com wrote: Hi Jens, ** ** You can try the free DS Visualizer: http://accelrys.com/products/discovery-studio/visualization-download.php** ** ** ** It comes with a free molecular builder for proteins, dna/rna and ligands. Please note that if you do need to make anything more interesting (energy calculations, minimizations, md, etc) will then need a license. ** ** I hope this helps. ** ** Francisco ** ** Full Disclaimer: I do work for Accelrys. ** ** *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *jens j birktoft *Sent:* Wednesday, May 23, 2012 9:32 AM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] DNA/RNA modeling ** ** Hi everybody, ** ** Does anyone know of a (non-commercial) software that are suitable for modeling DNA/RNA structures. Coot is great, however I am looking something that allows more flexibility ** ** Thanks ** ** ** ** -- Jens J. Birktoft e-mail: jens.birkt...@nyu.edu jens.kn...@gmail.com slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025 Phone: 212-749-5057
[ccp4bb] Summary of : Dissolving Hydrophobic ligands for co-crystallization and assays
Dear friends, here I'm summarizing all of your suggestions regarding dissolving a hydrophobic ligand (in this case, containig benzoic acid moities) for crystallization and biochemical assays: 1)Sodium salts of benzoic acid containing molecules can often be soluble in water to high concentration.If material is not limiting, it is a strong possibility to be explored. 2)In case of a ligand with a protonated group (like benzoic acid), increasing the pH of the medium helps the group to donate proton, in turn forming carboxylate anaion, which dissolves better.The need to elevate pH will vary depending upon the ligand. 3)Using low mol. wt. PEGs, such as 200, 300, 350 etc. to dissolve the ligand. PEG mono methyl ether 350, 550 can also be tried. 4) using mild detergents (DDM, OG etc.) 5)(For xtalization, not for activity) Keep prot concentration as low as 1 mg/ml, then add you ligand in low concentration according to molar equivalence as req. After incubation (for whatever time required), concentrate the solution, then use for xtalization.Final conc. of DMSO shouldn't exceed 2 - 5%. Thanks to all for your time, I will try out and let know. Regards, Tuhin. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
[ccp4bb] Dissolving Hydrophobic ligands for co-crystallization and assays
Dear All, does anyone have any clever suggestion/s for handling the solubility problem of highly hydrophobic compound, during co-crystallization or inhibition assays? The ligands I am using are almost insoluble in aquous medium (precipitates out or becomes turbid at ~1 micro molar conc.). In DMSO, the solubility is upto 50mM. Ligands are not soluble in MeOH or EtOH. Besides crystallization, this solubility is also a hindrance for in-vitro or in-vivo assays requiring higher conc. of ligand (keeping in mind, the final DMSO conc. 5%)! Some of the ligands have benzoic acid groups. Does it help to convert them to Na benzoate form? Thanks for your time, Tuhin. Dept. of Physics Indian Institute of Science. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
[ccp4bb] aspherical atom refinement against F and F^2
Dear all: I am working on the aspherical atom refinement of a small molecule using the XD package. The program provides you with the option of selecting a refinement strategy against F or F^2. I have noticed that the R-factors and GOFs calculated based on F^2 are larger in magnitude compared to those computed based on F. Why is it so? Any comments or suggestions in this regard is welcome. Sincerely, Tuhin. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
