[ccp4bb] SUMMARY - crystallization of proteins with His-tag and/or c-myc tags

An example of using MBP as a crystallization tag: Ke A, Wolberger C. Insights into binding cooperativity of MATa1/MATalpha2 from the crystal structure of a MATa1 homeodomain-maltose binding protein chimera. Protein Sci. 2003 Feb;12(2):306-12 Ho

Re: [ccp4bb] X-Ray versus NMR Structure

You might find this review useful: X-ray Crystallography and NMR: Complementary Views of Structure and Dynamics, Nature Structural Biology 4, 862-865 (1997). The pre-publication manuscript is available on my website, publication section. Axel Brunger On Nov 14, 2008, at 3:13 PM, Boaz Shaanan

Re: [ccp4bb] off-topic: soft crystals?

Thanks Boaz, They are protein crystals confirmed by spectra. Deliang - Original Message - From: Boaz Shaanan To: deliang Sent: Friday, November 14, 2008 3:21 PM Subject: Re: [ccp4bb] off-topic: soft crystals? Hi, You might like to check the content of those crystals b

Re: [ccp4bb] X-Ray versus NMR Structure

oops, I forgot to give the reference: Science (1992), vol. 257, p. 961    Boaz - Original Message - From: Young-Tae Lee <[EMAIL PROTECTED]> Date: Friday, November 14, 2008 23:57 Subject: Re: [ccp4bb] X-Ray versus NMR Structure To: CCP4BB@JISCMAIL.AC.UK > Here are some of my thoughts

Re: [ccp4bb] X-Ray versus NMR Structure

Hi,  I don't know what you mean by a systematic comparison between NMR and X-ray structures, but in this paper from 1992 (maybe it's not good enough because it's more than 10 years old - according to a recent paper in Science, articles older than 10 years are referred to much less frequently th

Re: [ccp4bb] X-Ray versus NMR Structure

Here are some of my thoughts and I was also seeking good references pointing out systematic comparison of X-ray and NMR approaches. Both X-ray and NMR structures are models calculated from experimental data. Therefore coordinates from both structures have uncertainty and are inevitably some

Re: [ccp4bb] off-topic: soft crystals?

Hi Deliang, I have an experience with soft crystals: I used to work with a protein which crystallized fine and diffracted fine. However, after opening the crystallization well few times, crystals turned soft and they stopped diffracting. If I remember correctly, letting crystals sit for a long ti

[ccp4bb] off-topic: soft crystals?

Hi there, Do you ever have experience with the diffraction quality of soft crystals? I just harvested some. They are 30K membrane protein, growing 10 months, size ~0.6mm*0.2mm*0.02mm, but as soft as a hair, no sharp surfaces. We don't have synchrotron time in a few months and no experience with

Re: [ccp4bb] X-Ray versus NMR Structure

How about this one: Can't Refine Your Structure To Acceptable Likelihood Typical error bars on crystallographic data are ~5% (R_sym), but with very few exceptions the models in the PDB do not fit their corresponding observations to better than ~40% error (R_cryst for intensities). Gerard? W

Re: [ccp4bb] X-Ray versus NMR Structure

> I've noticed that > several papers describe NMR structures as "atomic resolution > structures" and I'm just wondering what people think of this. I think that "atomic resolution" is one of those terms which mean different things to different people. There are clearly two groups among crystal

Re: [ccp4bb] SUMMARY - crystallization of proteins with His-tag and/or c-myc tags

Here's another paper you might want to have a look at: Carson et al. His-tag impact on structure. Acta Crystallogr D Biol Crystallogr (2007) vol. 63 (Pt 3) pp. 295-301 and here's the Structural Genomics paper (or one of them, I believe there was another one which I originally thought of): Li

Re: [ccp4bb] SUMMARY - crystallization of proteins with His-tag and/or c-myc tags

Also check out the following reviews: Protein Sci. 2003 July; 12(7): 1313–1322. Crystal structures of fusion proteins with large-affinity tags Douglas R. Smyth, Marek K. Mrozkiewicz, William J. McGrath, Pawel Listwan, and Bostjan Kobe1 Gene Volume 281, Issues 1-2, 27 December 2001, Pages 1-9

Re: [ccp4bb] X-Ray versus NMR Structure

Hi David: I haven't read all my email yet so apologize if this has already been mentioned, but Fred Allain and Gabriele Varani did something along these lines specifically for nucleic acids (RNA): F.H.T. Allain and G. Varani. How Accurately and Precisely can RNA Structure be determined by

Re: [ccp4bb] Baubles (re imosflm)

Regarding 64-bit linux, Phil Evans has set up a couple of boxes here at MRC-LMB running 64-bit CentOS. These boxes run a 32-bit firefox and the default gcj (gnu compiler for java) that comes with CentOS. As for the protocol errors you are getting on windows I have never come across them but a prel

Re: [ccp4bb] X-Ray versus NMR Structure

I think we should slowly arrive in the 21st century and realize that methods are complementary to each other. I've never done NMR by myself only some xray stuff and attempts to merge EM data with xray almost 10 years ago to arrive at ab initio phases. Sure one can argue what information can y

Re: [ccp4bb] Choosing TLS groups.

Actually on further thought I see that the problems associated with restraining residual Biso's are even more serious, and even my suggestion of ensuring that there's a flexible linker would not get around it. Suppose you have a domain with an associated TLS group connected to a flexible linker wh

Re: [ccp4bb] X-Ray versus NMR Structure

Dear Tassos, Bernhard and David, If I may push this humourous response (obviously tainted with crystallographic bias) a little further, I would say that my favourite mnemonic for the acronym "NMR" is N eeds M or

Re: [ccp4bb] Baubles (re imosflm)

Google chrome works perfect for this regards spyros O/H Nicholas Keep ??: I have questions about baubles in general. I find that using firefox (3.0.4 windows) baubles logs do not open directly from ccp4i or imosflm and I get an error "i is not a registered protocol" (or c) which I think is

[ccp4bb] Baubles (re imosflm)

I have questions about baubles in general. I find that using firefox (3.0.4 windows) baubles logs do not open directly from ccp4i or imosflm and I get an error "i is not a registered protocol" (or c) which I think is the drive the file is on. However if I open the file in via "open file "then it

Re: [ccp4bb] Choosing TLS groups.

Hi Pavel I think Ethan made my point very nicely, so I don't really have much to add, except maybe a concrete example will help. Let's keep it as simple and ideal as possible: I hope you'll agree that any proposed method has to at least work perfectly in the ideal case before you try to apply i

Re: [ccp4bb] X-Ray versus NMR Structure

But there is a more fundamental difference. Crystallography determines the positions (more or less accurate) whereas NMR measures distances between certain atoms. NMR is local, 1-dimensinal information that -with enough data- can be used to generate a three dimensional model compatible with it,

Re: [ccp4bb] X-Ray versus NMR Structure

although I agree with the statement below, I would say that X-ray crystallography also only generates a molecular model (not "a structure"). Rather than a structure, X-ray crystallography generates an electron density map. The quality of the model based in it depends on the quality of this

Re: [ccp4bb] X-Ray versus NMR Structure

Since I don't like attachments, I will first iterate the title of the attached publication: "Traditional Biomolecular Structure Determination by NMR Spectroscopy Allows for Major Errors " It immediately reminded me of an older one (ehm .. one author in common!), addressed at that time mos

[ccp4bb] PhD Position in Structural Biology in Vienna

*PhD Position: Structural biology of protein-protein interactions in the muscle Z-disk* We are seeking a highly motivated PhD student to work on structural characterization of important protein complexes centered on major players of the Z-disk of striated muscle: alpha-actinin and filamin. Bi