Re: [ccp4bb] Reservoir buffer

Dear Theresa, an interesting question, I think the answer is yes it does, very much. Using Raoult's law we can calculate the equilibrium vapour pressure above a 5M NaCl solution, it is a relative humidity of 82.6%. This is much lower than say a solution of 20% PEG 4000, here we can again

Re: [ccp4bb] Reservoir buffer

/Acta Cryst./ (2005). D*61*, 490-493[ doi:10.1107/S0907444905002726 ] Expanding screening space through the use of alternative reservoirs in vapor-diffusion experiments J. Newman

Re: [ccp4bb] Reservoir buffer

The following could be of use: Newman, J. Expanding screening space through the use of alternative reservoirs in vapor diffusion (2005) Acta Cryst D61(4), 490-493 Cheers, tom From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Felix Frolow Sent: Tuesday, 13 November 2012 5:17

Re: [ccp4bb] Reservoir buffer

You should and can try, but I guess 5 M NaCl will dry your drop quite fast, unless in your drop NaCl concentration is ~2,5 M :-) That is why first mixture of well and protein solution is 1:1 v/v. Other variations such as 1:9, 9:1 etc sometimes help. Dr Felix Frolow Professor of Structural Bio

[ccp4bb] Reservoir buffer

Dear all In *initial screening* using vapor diffusion crystallization, does it matter whether the reservoir buffer is also the precipitant in the drop or just a high salt solution like 5 M NaCl? Thank you. Theresa

Re: [ccp4bb] hkl2000 install

It should be called cr_info you have to : sudo chmod +x cr_info in the directory were it is, I think it should be executable try to activate HKL2000 first of all from there : cd /usr/local/lib HKL2000 FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecul

Re: [ccp4bb] hkl2000 install

Dear everyone: I have got the returned "cr_info.dat" to /usr/local/lib and /usr/local/hklint,when I typing "HKL2000",it still display: dell@ubuntu:~$ HKL2000 ERROR: Not a valid HKL-2000 license: Licence info file (cr_info) not found Error code: -1 So could anyone can help me ? 2012/11/9 王瑞 : >

Re: [ccp4bb] Glass Capillaries

On Nov 12, 2012, at 8:13 AM, Michael Roberts wrote: > Dear All, > > I would be interested to learn of other crystallographers' experience in > their use of glass capillaries for protein crystal growth and X-ray > diffraction clarity. > There are many types of glass available - quartz, soda gla

Re: [ccp4bb] dihedral backbone generator

Ed Pozharski wrote: Does anyone know of a tool that would generate a protein molecule backbone from a set of phi/psi angles? I actually had written my own code to do this eons ago, but those were days of Matlab. My actual question is if in a particular protein the conformational change observed

[ccp4bb] dihedral backbone generator

Does anyone know of a tool that would generate a protein molecule backbone from a set of phi/psi angles? I actually had written my own code to do this eons ago, but those were days of Matlab. My actual question is if in a particular protein the conformational change observed upon substrate bindin

Re: [ccp4bb] Glass Capillaries

I apologise for typing in dark. That is why "know" substitute "no" :-\ Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.i

Re: [ccp4bb] Glass Capillaries

The Triana range of capillaries are very easy to use for screening etc On 12 November 2012 16:13, Michael Roberts wrote: > Dear All, > > I would be interested to learn of other crystallographers' experience in > their use of glass capillaries for protein crystal growth and X-ray > diffraction c

Re: [ccp4bb] Glass Capillaries

Traditional crystallography is difficult to practice, unless you know mathematics, physics, chemistry, computing etc….. :-) If one need to make science with room temperature diffraction, there is know substitution to old type glass capillaries that can be properly sealed :-\ FF Dr Felix Frolow

Re: [ccp4bb] Glass Capillaries

Hi Michael, I would recommend an alternative http://www.mitegen.com/products/micrort/micrort.shtml Traditional capillary is a pain to handle, unless you have a rock sized crystal. Good luck, Nian Huang On Mon, Nov 12, 2012 at 11:13 AM, Michael Roberts wrote: > Dear All, > > I would be interested

Re: [ccp4bb] Glass Capillaries

Light glasses such as borosilicate. Can be purchased from Hampton research. FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.

[ccp4bb] Glass Capillaries

Dear All, I would be interested to learn of other crystallographers' experience in their use of glass capillaries for protein crystal growth and X-ray diffraction clarity. There are many types of glass available - quartz, soda glass, borosilicate, etc. Are there specific types which people pre

Re: [ccp4bb] seleno methionine labelling of protein

thanx all for their nice suggestions On Mon, Nov 12, 2012 at 6:23 PM, Chittaranjan Das wrote: > Tim, > > > My understanding is that the D-isomer does not get incorporated. I could > be wrong though. Bacteria may convert the D to the L-form. > > Chitta > > > > - Original Message - > From

Re: [ccp4bb] Apologies

Hi Matthias, I have not read your attached MS however Figure 2 is very good. Congrats to the first author for a very captive and engaging view of your protein. Jürgen On Nov 12, 2012, at 4:24 AM, Matthias Wilmanns wrote: I am apologizing for sending an unintended email to CCP4 via CC. Matthia

Re: [ccp4bb] seleno methionine labelling of protein

Tim, My understanding is that the D-isomer does not get incorporated. I could be wrong though. Bacteria may convert the D to the L-form. Chitta - Original Message - From: "Tim Gruene" To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, November 12, 2012 4:25:34 AM Subject: Re: [ccp4bb] seleno

Re: [ccp4bb] Problems with PDB validation

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear KS, in addition to what Mark said, you might think about why the torsion angles are this way, i.e. there might be interactions which twist your protein into that conformation. Only because something is reported as off-standard does not mean it is

Re: [ccp4bb] Problems with PDB validation

Also, a very small fraction of amino acids have torsion angles that are really outside normal ranges, as demonstrated by high resolution structures. If the density is convincing, leave them as they are. Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biote

Re: [ccp4bb] Problems with PDB validation

Hello, There are examples of regions (such as loops) where the electron density is rather "poor" and does not allow to build a proper model of the polypeptide chain (the refinement program cannot fit a satisfactory model in that area). Hence you just know that the chain "goes through there" a

[ccp4bb] Problems with PDB validation

Hi all, I am currently validating my protein and experiencing a few issues. I am unable to fix the torsion angles for eight residues no matter what I try. There are 3 models deposited on the PDB website belonging to the same protein. Five of the residues’ torsion angles (of the eight) are cons

Re: [ccp4bb] seleno methionine labelling of protein

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear , I am not up to date, but is there an expression system that allows you to incorporate D-amino acids into proteins? In terms of phasing only the Se-atom is a point or sphere, so the signal won't be altered provided the position of that atom

[ccp4bb] Apologies

I am apologizing for sending an unintended email to CCP4 via CC. Matthias, EMBL Hamburg

[ccp4bb] seleno methionine labelling of protein

Dear All just want to ask the difference between labelling your protein with D L selenomethionine mixture and L selenomethionine alone..will it make difference in anomalous diffraction,detection of Se signal and extraction of phases. Or will be the same for both..? -- Regards Faisal School of L

[ccp4bb] Postdoctoral Position in Structural Immunology at Harvard Medical School

Dear All, On behalf of Dr. Jia-huai Wang, I post this message. For inquiries please contact Dr. Wang directly at jw...@red.dfci.harvard.edu Postdoctoral Position in Structural Biology of Immune Receptors: There is an immediate opening for a postdoctoral position in protein crystallography at t