[ccp4bb] Florets- How to improve it
Deal all, Sorry for the non-ccp4 query. I am new to this field and need some suggestions regarding the improvement in the crystallization qual I have crystallized a protein with 65% MPD in 0.1M Acetate buffer pH 3.6 at 4 degree. The florets appear after 2 days and covers the whole drop. What should I do for the optimization. Its a 20kDa protein. The needles are clusters and very long. Please suggest how what are the various tricks one can apply. Thanks in advance for the suggestions. James pruza
Re: [ccp4bb] How to improve crystal which is twinning?
Heng-- Two things you might want to try: 1. Drop ratios with your current conditions and DMSO additive. Use different concentrations of DMSO too. 2. Try using Hampton Crystal Screen and Crystal Screen 2 as additives. I generally do this by adding 5% of XS 1 2 to the wells. Once I find one of these reagents that improves crystal quality/diffraction, I optimize the concentration for that. You can do this with the Mosquito robot for 96 well formator in the 24 well VDX trays. Hope this helps! annie Annie Hassell Glaxo Smithkline 5 Moore Drive RTP, NC 27709 919/483-3228 919/483-0368 (FAX) annie.m.hass...@gsk.com HanJie_HCT Tai chemtai2...@hotmail.com Sent by: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK 17-May-2009 08:27 Please respond to HanJie_HCT Tai chemtai2...@hotmail.com To CCP4BB@JISCMAIL.AC.UK cc Subject [ccp4bb] How to improve crystal which is twinning? Hi, I have a 22kDa protein that the floopy N C terminus have been deleted. It was crystallized in 35%MPD/0.1m Tris (pH 8.5)/0.2M/(NH4)2SO4 in 2 - 3 days. Previously, a few small twining crystals were grown in this condition. I tried Hampton Research 96-additive screen . Additives such as glycerol, dioxane, etc didn't work well to improve/reduce twining issue. The 0.3% DMSO is the best additive I found that can grow a single crystal in the 1(pro)+0.8(buff)+0.2(add) drop. However, If looking careful under microscope it may be some other crystals growing inside that single crystal(hardly see under the microscope, but I can see it in other drops). I conducted the x-ray diffraction experiment for this 0.1x 0.1 mm crystal for which no cryoprotectant is required. The highest resolution is 2A but there are a lot of smear on the diffraction pattern. Thus, the index procedures failed due to the crystal quality. Do you have any brilliant ideas to improve the crystal growing condition in my case in order to get a truly single crystal? regards, Heng Windows Live?: Keep your life in sync. Check it out.
[ccp4bb] Modeling DNA triple helices - MORCAD
Dear, I apologize for the non-ccp4 question. I'm looking for an (alternative) modeling tool for DNA triple helices, such as the earlier Morcad program: MORCAD, and object-oriented molecular modelling package running on IBM RS/6000 and SGI 4Dxxx workstations M. Le Bret, J. Gabarro-Arpa, J.C. Gilbert, C. Lemaréchal J. Chim. Phys. Phys. Chim. Biol. 88, 2489 (1991). Many thanks Kristof -- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 --
Re: [ccp4bb] Florets- How to improve it
Re: 65% MPD in 0.1M Acetate buffer pH 3.6 These conditions can crystallize salt impurities present in the protein buffer. The first step is to ensure that the crystals are protein. If they are protein the next step is to reduce the MPD concentration and seed the drops if no crystals appear. This should allow you to pass from rosettes to single crystals. On Mon, 18 May 2009 12:42:32 +0200, james09 pruza james09x...@gmail.com wrote: Deal all, Sorry for the non-ccp4 query. I am new to this field and need some suggestions regarding the improvement in the crystallization qual I have crystallized a protein with 65% MPD in 0.1M Acetate buffer pH 3.6 at 4 degree. The florets appear after 2 days and covers the whole drop. What should I do for the optimization. Its a 20kDa protein. The needles are clusters and very long. Please suggest how what are the various tricks one can apply. Thanks in advance for the suggestions. James pruza -- Enrico A. Stura D.Phil. (Oxon) ,Tel: 33 (0)1 69 08 4302 Office Room 19, Bat.152, Tel: 33 (0)1 69 08 9449 Lab LTMB, SIMOPRO, IBiTec-S, CEA Saclay, 91191 Gif-sur-Yvette Cedex FRANCE http://www-dsv.cea.fr/en/ibitecs/82 http://www.chem.gla.ac.uk/protein/mirror/stura/index2.html e-mail: est...@cea.fr Fax: 33 (0)1 69 08 90 71
[ccp4bb] BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALOPGRAPHY
BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALLOGRAPHY AT THE TWO ID BEAMLINES OF NE-CAT AT APS. Beamline 24ID-C: Variable energy between 6-18keV, ADSC Q315 Detector, MAD Capable. Beamline 24ID-E: Equipped with MD2 microdiffractometer, delivering beam as small as 5 microns. Single energy (12662eV), ADSC Q315 Detector. http://necat.chem.cornell.edu Contact csalb...@anl.gov for further details.
[ccp4bb] Recompiling REFMAC with larger MAXLINK
Hey Folks, I'm trying to refine a full capsid in REFMAC with about 25 atoms. I haven't been successful and I suspect it's due to the MAXLINKS parameter in atom_com.fh. This is what I observe in the refmac log: WARNING: number of links limit. change parameter MAXLINK in atom_com.fh My attempts to recompile refmac with this parameter increased have also not been successful. I've been getting errors such as: ld: i386 architecture of input file `/usr/local/CCP4/ccp4-6.0.2/lib/libccp4c.a(cmap_open.o)' is incompatible with i386:x86-64 output My question is this: Which parameters are increased in making the precompiled refmac_big for linux executable? Would anyone out there on a linux machine be willing to precompile for me a copy of the latest refmac with MAXLINKS increased to say 20? Cheers, Ed Miller
