Re: [ccp4bb] Cocrystals - should they pop up under native conditions?

Dear Brenda, I am running co crystallisation experiments and have thus far been trying under oil screens with some success (i.e. various hits in various conditions resulting in crystal growth). These conditions have varied from the native condition up until now. Do you already have the s

Re: [ccp4bb] Characterization of common salt crystal forms?

Dear Joe, working with divalent ions, I often get salt crystals (most surely phosphate). I do not have any table available, but can give you the commercial kits & numbers going with it. Just let me know. On Jan 22, 2008, at 6:12 PM, Joe Krahn wrote: Salt crystals are common in macromolecu

Re: [ccp4bb] salt sensitive complex

Dear Jerry, Are there some better ways that I can validate the binding affinity? I think it is possible to calculate the interacting energies by APBS... once you have the complex structure this is! Would be interesting to compare the values of the constants you get from ITC and SPR with

Re: [ccp4bb] Why there are difference density when occupancy is 1.00

Hi Sun, I suggest checking that the b-factors for those residues aren't unexpectedly high compared to those in the flankinh regions. Cheers, James On 1/23/08, Sun Tang <[EMAIL PROTECTED]> wrote: > Hello Everyone, > > When I refined a structure, I found strong difference density Fo-Fc at 3 > sig

[ccp4bb] Why there are difference density when occupancy is 1.00

Hello Everyone, When I refined a structure, I found strong difference density Fo-Fc at 3 sigma contour for the for five residues which already have occupancy of 1. The density is continuous and so strong as if I did not put the residues there. Why was that? Can I put greater than 1 occupan

[ccp4bb] salt sensitive complex

Dear All: Recently I am pursuing the crystallziation of a complex formd by two individual proteins and I met several interesting problems though they are kind of off-topic. Any suggestions for these problems will be highly appreciated. BIAcore showed about submicro

Re: [ccp4bb] differences between Rsym and Rmerge

A cursory analysis of the PDB indicates that resolution in the PDB is reported in shells of 0.05A. Coincidence or design? Artem -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Phil Evans Sent: Tuesday, January 22, 2008 5:02 AM To: CCP4BB@JISCMAIL.AC.UK

Re: [ccp4bb] Cocrystals - should they pop up under native conditions?

Brenda, Generally speaking it is not abnormal to at least *hope* for co-crystals to appear at or around the condition(s) where the native crystals are grown. Therefore many people in fact begin looking for co-crystals by screening a fine grid around the expected crystallization conditions for the

Re: [ccp4bb] antibody crystallization

I want to thank the very many people who responded to my inquiry. I'm overwhelmed and really appreciative. I've still got to read through it all, but a clear (near-unanimous) consensus is emerging. All the best, and again thanks very much for the help. I really appreciate it. Bill

Re: [ccp4bb] Crystal Imaging Systems - possibilities and recommendations

Just an additional small correction : the Imaging system from Formulatrix does handle 24 and 48 wells plates, and it does a great job at it. It can even image capillaries, we gave it a try for fun. Ingrid -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of

Re: [ccp4bb] Cocrystals - should they pop up under native conditions?

Don't call them "co-crystals" until you've actually shot them and seen the density. It will depend not only on the ligand but on the ligor(?) as well. You don't mention the identity of your ligand or ligor(?). You mention that some of your screens are under oil, so I will point out that some non-

Re: [ccp4bb] Crystal Imaging Systems - possibilities and recommendations

Just a FYI, these imagers can be used (and are used) with external chillers to reach a temperature of 4C in a 22C room. If you do not have the chiller option, you can indeed reach +/- 4 deg from ambient. Flip -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf

Re: [ccp4bb] .cif file

Hello Vineet, This seems old one and doesn't have all restraints. you may use refmac dictionary for spermine. I am sure this will work in coot also. you may find it at /ccp4-6.0.2/lib/data/monomers/s/SPM.cif thanks Manish Vineet Gaur <[EMAIL PROTECTED]> wrote: Hi all I am using COOT for

[ccp4bb] Cocrystals - should they pop up under native conditions?

Hello all, I am expecting a somewhat homogeneous reply to this one, but that is fine and welcomed as are anecdotal experiences. I am running co crystallisation experiments and have thus far been trying under oil screens with some success (i.e. various hits in various conditions resulting in cryst

Re: [ccp4bb] .cif file

Your cif-file contains coordinates, but as far as I could see it does not contain bond lengths, and angles and their deviations. That is what coot complains about. Unless your cif-file describes a modified spermine you could use the spermine already described in the refmac5 library: In coot, g

[ccp4bb] .cif file

Hi all I am using COOT for model building and refinement. i have to introducea ligand in my model i have downloaded .cif file from RCSB. However while importing the cif file i m getting the warning message of having No restraints in the CIF file is there any problem in the format of the following

[ccp4bb] Characterization of common salt crystal forms?

Salt crystals are common in macromolecular crystallography. Has anyone tried to tabulate salt crystal forms that commonly occur? I just identified a salt crystal as Mirabilite, made of Na2SO4·10H2O. The high water content makes them rather soft, and may not be recognized as salt right away. In thi

Re: [ccp4bb] protein expression problem

Hi Chen, Since you recognize that this is a protein expression problem, the best way to get return of your investment of efforts is to get soluble expression instead of trying to solubilize the protein down stream. Many good suggestions have been proposed. I just want to add one more thing

Re: [ccp4bb] protein expression problem

Another point not yet brought up is how do you express ? things to check: - different media (LB. TB, auto) - when do you induce (mid log phase, or end log phase) - how long do you induce (before reaching stationary phase, going over night into starvation phase) - how much IPTG do you add - MBP

Re: [ccp4bb] protein expression problem

Chen and David, Before adding detergent, be forewarned that the MPB in many fusions will not bind to an amylose column in the presence of most detergents, particularly maltoside detergents. It has been the bane to us so we have engineered MBP vectors with His tags to deal with this. Wha

Re: [ccp4bb] protein expression problem

I wholly agree with the below. I am not sure how well E.coli can correctly fold snaky misfolded/unfolded protein that are chaperoned by folded tags! Not to rule out that tags do it sometimes... "Folded by association" for insoluble proteins has often not worked well for me. Sometimes, when it '

Re: [ccp4bb] {ccp4bb] CCP4 for bioinformatics?

Hi all, Jacob Keller wrote: Does anyone know of a bioinformatics counterpart of ccp4? It seems like there should really be such an entity, so that folks would not have to write scripts, reinventing the wheel all of the time. I am trying right now to manipulate some sequences into various fo

[ccp4bb] Organic solvent resistent crystallisation plates

Dear all, we are looking to crystallise some hydrophobic peptides in different organic solvents, but find polystyrene plates are not sufficiently resistent. Also, it is not always obvious from which plastic plates are made. In other words, anyone knows of: - cleared polypropylene sitting dro

[ccp4bb] X-ray kit available

Hello, We have some X-ray kit that is now surplus to requirements. We appreciate that it is not state-of-the-art, but if anyone would like it they are very welcome to come and pick it up: The generator is a Nonius FR-591 system with a Enraf-Nonius DIP2000 detector. The MAC X-ray Optical Sy

Re: [ccp4bb] CCP4 for bioinformatics?

A newer one for Ruby is (of course) BioRuby, which I use for simple manipulation of sequences or chopping up structures. It's quite nice for this, but I don't think it's as feature-rich as Bio{Perl,Python,Java} though. http://dev.bioruby.org/wiki/en/?cmd=view&p=How+do+I+get+the+sequence+of+a+chai

Re: [ccp4bb] differences between Rsym and Rmerge

I thought that as author of Scala I might put in my 2 penn'th to this discussion, FWIW 1. I've never been able to find any useful distinction between Rsym & Rmerge, and when filling in the PDBs request for both (undefined by them and irritatingly restricted to < 0.99, at least in Autodep)

Re: [ccp4bb] CCP4 for bioinformatics?

Hi, You can use the on-line software EMBOSS. You can use it at the following site : http://bips.u-strasbg.fr/EMBOSS/ enjoy it ! Claudine Jacob Keller wrote: Dear Crystallographers, Does anyone know of a bioinformatics counterpart of ccp4? It seems like there should really be such an entit

Re: [ccp4bb] protein expression problem

> I have been trying to express a rat protein in bacteria. The MBP-fusion > expressed at very high level (~ 40 mg/L) while the GST-fusion and His-tag > only gave inclusion bodies. The problem is that all protein runs in the void > volume on a size-exclusion column (s-200, hepes, pH 7.4, 200 mM NaCl

Re: [ccp4bb] Crystal Imaging Systems - possibilities and recommendations

> We are currently contemplating the acquisition of > an automated imaging system for crystallization screen plates (96-well). Thanks to Zolt, Renaud and Catherine from Sanofi-Strasbourg, we bought last year a "Formulatrix Rock Imager". The system is composed of a big box, containing your 96 wells