Re: [ccp4bb] protein turns brown

Hi Sandy, If your protein is soluble (i.e. we're not dealing with brown precipitate), it is possible that the brown color is due to a bound iron-sulfur cluster. In this case, your protein was always brown, but you couldn't see the color when it was very dilute. As a quick test, you could t

Re: [ccp4bb] Cryo Vs crystal size

You've gotten some helpful replies already. I have found the following reference to be helpful in understanding some of the physics behind damage incurred during the crystal cooling process and a general strategy to help avoid it. It expands upon what's already been said - that larger crystal

Re: [ccp4bb] Crystallization of lysine and arginine rich proteins

Umar, Check out: Czepas et al. The impact of Lys-->Arg surface mutations on the crystallization of of the globular domain of RhoGDI, Acta D (2004) 60 275-280. They point out that sulfate ions can help mediate contacts between arginine residues from neighboring molecules in the crystal. Yo

[ccp4bb] [SUMMARY] X-ray diffraction image --> .jpg

To the CCP4 community. As always, I have received a number of very helpful suggestions to my query. I am grateful to all those who replied. My best summary of the suggestions is below. Best Regards, -Andy Torelli A notable consideration (provided by Jim Pflugrath) is that "A JPE

[ccp4bb] X-ray diffraction image --> .jpg

x27;m sure someone must have done this, but I haven't been able to find one. Thanks, Andy Torelli

Re: [ccp4bb] stacked thin plates

James, I think the standard suggestions apply. Try to tweak your crystallization conditions to get a single crystal (i.e. not a series of stacked plates). PEG 400 can be a good substitute for MPD, but you could also try additive screens as well as co-crystallization with products, cofactor

Re: [ccp4bb] problems of co-crystallization of protein-DNA complex

Ru Heng, It is commonly helpful to combine your protein and DNA under dilute conditions and then concentrate the complex. Combining concentrated DNA and protein together has a very good chance of precipitating in my experience. I completely agree that trying different buffer conditions

Re: [ccp4bb] {Spam?} quick purification?

Mark, I agree with Artem in that you may find significant differences in the purity of eluants from the 'high fidelity' IMAC resins (I use pre-packed HisTrap columns). You may also want to have a look at the following reference for a comparison of a variety of different affinity tags in te

Re: [ccp4bb] off topic

Hi Kien, You may also want to try to wash your column with elution buffer (without reducing agents), equilibrate it with binding buffer (plus reducing agents) and then bind your protein. In the case of HisTrap columns (a pre-packed, Ni(II) resin column), this procedure is recommended if y

[ccp4bb] Offtopic: Alscript question

to me directly. Best Regards, -Andy Torelli === Andrew T. Torelli Ph.D. Postdoctoral Associate Department of Chemistry & Chemical Biology Baker Laboratory, Cornell University Ithaca, NY 14853 ===

Re: [ccp4bb] Isomer images

Haitao, The journal Biochemistry (and others no doubt) specifies that the two images should be separated by 5.5 - 6.5 cm as measured between similar points (e.g. the same atom in either image). -Andy === Andrew T. Torelli Ph.D. Postdoctoral Associate

Re: [ccp4bb] SUMMARY:vSystem virtual machine recommendation for crystallography?

using native graphics software/hardware. - You have to reboot the machine to change the memory configuration, but people agreed the software is generally easy to configure for resource allocation. Thanks again to all who replied, -Andy Torelli -- = And

[ccp4bb] System virtual machine recommendation for crystallography?

while running refinement within the guest Linux? My Google and CCP4bb searches have not turned up anything so far. Thanks in advance for any advice or reference material. I will post a summary e-mail as well. Best Regards, -Andy Torelli -- = And

Re: [ccp4bb] Cryo-protectant

Hi Liew, There have already been some very good suggestions. I agree with Tim Gruene that a great starting point is to test the diffraction properties of your crystal at room temperature. This can serve as a baseline for comparing/evaluating cryoprotecting agents and methods. You can als

Re: [ccp4bb] Scaling of intensities

ement that benefit from refining against intensities vs. amplitudes for programs that offer both options? Thanks again, -Andy Torelli George M. Sheldrick wrote: Well, I suppose that it doesn't qualify as a "popular refinement program" but section 2.4 of the SHELX manual

[ccp4bb] Scaling of intensities

at pertains to macromolecular crystallography and the documentation I've looked at for popular refinement programs that offer both targets do not provide guidelines as far as I can tell. If anyone could recommend some literature, I would really appreciate it. Thank you very much for you