Re: [ccp4bb] Phasing at Low Resolution

I like PIP (di-mu-iodo-bis-ethylenediamine-di-platinum (II) nitrate). At low resolution it offers you 4 heavy atoms (I2Pt2), a choice of anomalous signal, and at higher resolution if you can resolve the 4 heavy atoms you then instantly get higher resolution phases. It likes binding as a low-res

[ccp4bb] Post-Doctoral Position in Ubiquitin Research

Post-Doctoral Position in Ubiquitin Research Applications are sought for a Post-Doctoral position in the Dhe-Paganon laboratory in the Department of Physiology a

Re: [ccp4bb] Crystallizing Fluorescent Molecules

You're not the only one to have had exactly that problem with exactly that system! A good ad for the potential utility of JDF (Journal of Dismal Failure). Phoebe Original message >Date: Thu, 14 May 2009 19:20:58 -0400 >From: matthew.frank...@imclone.com >Subject: Re: [ccp4bb] Cr

Re: [ccp4bb] Crystallizing Fluorescent Molecules

CCP4 bulletin board wrote on 05/14/2009 03:42:05 PM: > Dear Crystallographers, > > I have exactly two spherulite crystals of a protein-peptide complex which > have a fluorescently-labelled peptide in them, and are therefore nicely > colorful in both the light and fluorescence microscopes, making

Re: [ccp4bb] Phasing at Low Resolution

Maybe I'm wrong. Myself solved structure with 1Zn/400aa. In Pete's case 1Zn/570 aa structure was solved at low resolution. I also heard some other cases of 1Zn for > 400 aa. But for Se, I never heard 1se for > 300aa. Se could be partially incorporated or have mixed oxidation state. This could affec

Re: [ccp4bb] Phasing at Low Resolution

Guangyu Zhu wrote: > Zn and Se have similar f' and f''. Why Zn seems have much better phasing > powder in practice? Is it just because Zn always binds tightly on protein > but Se might have higher b-factor? I don't have a better explanation than tighter binding for Zn, although I suppose that it's

Re: [ccp4bb] Phasing at Low Resolution

Dear Martin You can either add the cluster as a powder, just dip the tip of a needle in the powder and gently approach the drop with the needle, the Ta6Br12 crystals will spray itself onto the drop. Then you just wait for the crystal to turn green, I usually marked the position where the

Re: [ccp4bb] Phasing at Low Resolution

Regarding question 1, see: Acta Cryst. (2008). D64, 354-367  Towards a rational approach for heavy-atom derivative screening in protein crystallography J. Agniswamy, M. G. Joyce, C. H. Hammer and P. D. Sun Cheers. riya doreen wrote: I have two questions regarding derivatization:  

Re: [ccp4bb] Crystallizing Fluorescent Molecules

Exposure to light during crystal growth should not have any effect unless the fluorophore is destroyed by ambient light, which is unlikely. V. Nagarajan JANSi http://janscientific.com -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Jacob Keller Sen

[ccp4bb] Crystallizing Fluorescent Molecules

Dear Crystallographers, I have exactly two spherulite crystals of a protein-peptide complex which have a fluorescently-labelled peptide in them, and are therefore nicely colorful in both the light and fluorescence microscopes, making it easier to know that at least the peptide is in the crysta

Re: [ccp4bb] Phasing at Low Resolution

I have two questions regarding derivatization: (i) Is there a pH dependence to making derivatives ? i.e. effectiveness of getting derivatives at low vs high pH ? (ii) Any thoughts on the effectiveness of Barium for phasing low resolution structures (especially for magnesium binding proteins ) ???

[ccp4bb] March 15, 2009 deadline- User proposal submission for Collaborative Crystallography at BCSB

Dear Users, The deadline for July/August 2009 Collaborative Crystallography proposals will be May 15, 2009. = Thumbnail Description: Through the Collaborative Crystallography Program (CC) at the Advanced Light Source (ALS), scientists can send protein crystals to Berkeley Center

Re: [ccp4bb] Phasing at Low Resolution

Zn and Se have similar f' and f''. Why Zn seems have much better phasing powder in practice? Is it just because Zn always binds tightly on protein but Se might have higher b-factor? Guangyu On 5/14/09 2:31 PM, "Pete Meyer" wrote: > You might find Structure 14, 973-982 Jun 2006 of interest. >

Re: [ccp4bb] Na/K Phosphate

On a side note, I have created a web server that, based on your sample buffer, makes a crude attempt at prediciting conditions within a screen that may form salt crystals (though this probably should be taken with a grain of. salt, ahem!). http://www.pageforaday.com/xtalwizard/salt.php

Re: [ccp4bb] Phasing at Low Resolution

Dear all Now that tantalum clusters have been mentioned I have recently had issues with the solubility of the Ta6Br12 cluster (obtained from Jena Bioscience) in PEG-based crystallisation conditions at pH 8.0-8.5. Has anybody also experienced this? Is there a trick to getting the compound to di

Re: [ccp4bb] Phasing at Low Resolution

You might find Structure 14, 973-982 Jun 2006 of interest. Larger protein, Zn instead of Se (although only 8 sites), roughly comparable to slightly lower resolution. This was mainly testing to confirm that there was enough anomalous signal to phase off of, so the model was essentially known; howe

Re: [ccp4bb] Source Ta6Br12 for phasing

Try here Jena Scientific or Ryan Scientific in the US http://www.jenabioscience.com/cms/en/1/catalog/1166_tantalum_cluster_derivatization_kit.html Gabriel Birrane Beth Israel Deaconess Medical Center RN325 99 Brookline Ave Boston, MA 02215 USA -Original Message- From: CCP4 bulletin b

[ccp4bb] Source Ta6Br12 for phasing

Hi, a follow up question: Which supplier offer Ta6Br12? Thanks, Guenter My post-doc recently produced a splendid (for its resolution) ~5A map of a "medium" sized protein-DNA complex using Ta6Br12 clusters. And he's got a good toehold on a ~340kDa complex using the same clusters. So I'm recentl

Re: [ccp4bb] Phasing at Low Resolution

My post-doc recently produced a splendid (for its resolution) ~5A map of a "medium" sized protein-DNA complex using Ta6Br12 clusters. And he's got a good toehold on a ~340kDa complex using the same clusters. So I'm recently converted to these little nuggets. Phoebe Original message

Re: [ccp4bb] Na/K Phosphate

Hampton Research has a good chart for preparing Na/K phosphate solutions: http://hamptonresearch.com/documents/product/23-000180.pdf 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 > De

[ccp4bb] MALLS equipment

Dear all, we are interested in the multiangle laser light scatterring (MALLS) methodology but we do not know exactly which is the best system on the market. We plan to use it in a cold room (8°C) combined to an Akta Purifer system. Thanks to all in advance for sharing with us your expertise.

Re: [ccp4bb] Glycerol as metal chelator?

I wouldn't use a pH of 9 when dealing with metal cations in solution. By and large, metal hydroxides precipitate at alkaline pH. HTH Pr. Nadir T. Mrabet Cellular & Molecular Biochemistry INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 V

Re: [ccp4bb] Na/K Phosphate

The reason for the odd K/Na combination is solubility - mixed phosphate is more soluble than either of the individual ones. I try to avoid high phosphate conditions as the Plague. It's great for molecular biology but horrible for crystallization because phosphate + a variety of other ions = lovely

Re: [ccp4bb] Phasing at Low Resolution

OK, here's a concrete case: A 150kDa protein complex, the plate-like crystals can be produced in sufficient number; Se-Met derivatives available, total number of Met around 20, subunits could be marked and combined individually. Diffraction is highly anisotropic, in certain directions up to

Re: [ccp4bb] Phasing at Low Resolution

Dear Clemens, For the choice of derivatization compounds this might be helpfull: Z. Dauter (2005). C. R. Chimie 8, 1808-1814. Best Regards, Georg Clemens Grimm wrote: Dear all, after the SeMet phasing discussion, what would be -in general- the best technique to phase low resolution data (<

Re: [ccp4bb] Na/K Phosphate

Hi, pure sodium phosphate or pure potassium phosphate are not as soluble as the mix of both. Especially if you crystallize at temperatures below 20°C you will get a lot of salt crystals. I used 2.5 M or 2.0 M stocks of Na2HPO4 and KH2PO4 (or the other way round, i.e.NaH2PO4 and KH22PO4) and ad

[ccp4bb] Phasing at Low Resolution

Dear all, after the SeMet phasing discussion, what would be -in general- the best technique to phase low resolution data (<=4A) of large complexes (>=150 kDA) - in terms of - derivatization compounds (is there something like the 'golden five' HA compounds for these cases), - data colle

[ccp4bb] Na/K Phosphate

Dear all, Quite a few crystallisation conditions in the screens feature 'sodium/potassium phosphate'. I'm curious to know why such a Na/K mix is there. As the pH is mostly determined by the (H2PO4)- to (HPO4)2- ratio, is there such a need to have both cations? If so, is the Na to K ratio important

[ccp4bb] Senior Scientific Programmer Opening

There is a "Senior Scientific Programmer" Post available to work with the wwPDB at the EMBL-EBI site in Cambridge UK. One of the primary tasks of the post-holder is to implement the validation recommendations of the wwPDB validation task force (see http://www.wwpdb.org/workshop/2008/index.html)