Re: [ccp4bb] Histogram matching in DM - question

Dear Ed, The question of dealing appropriately with density modification in the presence of heavy atoms has been discussed in the paper on SHARP 2.0 (see Acta D59, 2023-2030, published in 2003) and the solution described in that paper has been available in all versions of SHARP/autoSHARP

[ccp4bb] Postdoctral Position Available

Dear All, The Frontier Research Center for Applied Atomic Sciences of Ibaraki Univ. (Ibaraki, Japan) invites a highly motivated young scientist in the field of neutron/x-ray protein crystallography or biochemistry to join our research team. The Postdoctoral Research Fellow candidate will work on

[ccp4bb] Identification of the hydrophobic residues on the dimer interface

Hi, everybody I have a crystal structure as homodimer, from which residues in the dimer interface need to be identified. Using PISA on the EBI website, residues involved in forming hydrogen bonds, salt bridges, disulfide bonds and covalent bonds could be identified. But hydrophobic interaction

Re: [ccp4bb] Identification of the hydrophobic residues on the dimer interface

Hi Hunter, 1. how to find those hydrophobic residues PISA will also tell you this - you just need to look at the hydrophobic residues which are highlighted and have a buried surface area (BSA) value in the PISA output. You can take these residues and plot them in your favourite pdb viewer

Re: [ccp4bb] Histogram matching in DM - question

And to add another small item: the SOLOMON interface in SHARP allows adjustment of the mean density depending on protein, DNA or RNA content. See http://www.globalphasing.com/sharp/manual/denmod2.html#MeanDensity Cheers Clemens On Wed, Aug 19, 2009 at 09:26:34AM +0100, Gerard Bricogne wrote:

Re: [ccp4bb] Identification of the hydrophobic residues on the dimer interface

Hello, PISA gives you quite a lot of information on hydrophobic interactions, down to atomic level (subject to interpretation). In the list of interfaces, PISA gives just the sum hydrophobic effect for each interface. If you click on interface number, it will take you to further details for the

[ccp4bb] cyseteine modification

Dear Sir, Is there any other oxidation states of cysteine other than cysteine sulphinic acid and cysteine sulphonic acid. In my protein, the cysteine molecule is definitely overoxidized but the electron density is not corresponding to the sulphinic or the sulphonic acid. The positive density

Re: [ccp4bb] cyseteine modification

Dear Debajyoti There is also the sulfenic acid species (-S-OH) which is actually the first oxidized form of sulfhydryls on the way to sulfonic acid. However sulfenic acids are very susceptible to further oxidation to sulfinic and sulphonic acids, and therefore need a protective chemical

Re: [ccp4bb] cyseteine modification

You can also have a look at Active site structural features for chemically modified forms of rhodanese. Gliubich F, Gazerro M, Zanotti G, Delbono S, Bombieri G, Berni R. J Biol Chem. 1996 Aug 30;271(35):21054-61. Best Roberto On 19 Aug 2009, at 15:41, Debajyoti Dutta wrote: Dear Sir,

[ccp4bb] Bucanneer and molecular replacement

I have been trying to get my head around using bucanneer for molecular replacement. I am not sure that I have understood the specify a heavy atom or MR model and what this does or the model to be extended options. I am not sure of the difference between the two, and bucanneer will only run on

[ccp4bb] Cryoprotection in 3M ammonium sulfate

Hello! I would be grateful for suggestions on cryoprotectants for crystals growing in 3M ammonium sulfate. Thanks! Brenda Email Disclaimer: www.stjude.org/emaildisclaimer

Re: [ccp4bb] Unknown density

The density looks an awful lot like a polyatomic anion (sulfate, phosphate, etc.). It's hard to tell from the fixed images, but it appears to be tetrahedral. Is there any chance a polyatomic anion could be in the crystallization solution? Perhaps from the protein stock solution? Sampath

Re: [ccp4bb] Cryoprotection in 3M ammonium sulfate

Hi Brenda, You can try sugars like glucose, trehalose and sucrose for high AS contents. It has been succesfully used in really hard cases such at protein RNA crystals grown in AS. see Acta Cryst (2002) D58 1664-1669 Garber et al. HTH Pascal Egea

Re: [ccp4bb] Cryoprotection in 3M ammonium sulfate

Soluble possibilities include glucose, ethylene glycol, DMSO, glycerol (15-30%). You may not need much cryoprotectant at all at these salt concentrations. PEGs are not very soluble in high ammonium sulfate solutions. (I think PEG-400 can go up to only 4% or so at 2 M ammonium sulfate.)

Re: [ccp4bb] Cryoprotection in 3M ammonium sulfate

Dear Brenda Check out malonate http://www.ncbi.nlm.nih.gov/pubmed/14646118? ordinalpos=2itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubm ed_DefaultReportPanel.Pubmed_RVDocSum Malonate: a versatile cryoprotectant and stabilizing solution for salt-grown macromolecular crystals.

Re: [ccp4bb] Cryoprotection in 3M ammonium sulfate

Hi Brenda Try 3M ammonium sulfate itself! We have tried that with great succes by cryo-cooling xtals grown at 3.2M AS straight out of their crystallization drops. You can consult the MM section in Kyndt J. et al Biochemistry 2007 Jan 9;46(1):95-105 for a more detailed description of what we did.

Re: [ccp4bb] Cryoprotection in 3M ammonium sulfate

Dear Brenda, I'd suggest using a mixture of 75% Paratone-N oil with 25% light, white mineral oil. Mix the two thoroughly with a positive displacement pipette then add a small amount next to the mother liquor (ML) drop. Remove a crystal from the ML using a matched cryo loop (the smaller the

Re: [ccp4bb] Cryoprotection in 3M ammonium sulfate

Or saturated LiSO4 works too. Should work in this case. -Tom Tom J. Brett, PhD Assistant Professor of Medicine Division of Pulmonary and Critical Care Washington University School of Medicine Campus Box 8052, 660 S. Euclid Saint Louis, MO 63110 From: CCP4

Re: [ccp4bb] Cryoprotection in 3M ammonium sulfate

I second that one. Ammonium sulfate is one of my favorite cryos. I recommend making up a saturated solution of ammonium sulfate, as it is actually a very good cryo all by itself, and then dilute it by adding the rest of the stuff in your condition (buffers, etc. and a little bit of water).

[ccp4bb] strange pattersons

Hi All Im receiving some strange patterns in my pattersons. Space group is C222 with no confidence (due to resolution) of systematic absences to transform to C2221. Thanks! FR pattersonmap.pdf Description: Adobe PDF document - Francis Reyes

Re: [ccp4bb] Histogram matching in DM - question

Hi Peter, You can specify in DM the mean density of the protein region in the SOLC keyword. However I am not sure this will affect the density distribution used for histogram matching. All the best, Adam.

Re: [ccp4bb] strange pattersons

Hi Francis, The space group will not influence the Patterson, as both C222 and C2221 will become Pmmm in Patterson space. (Aside: You can change the packing pattern from one into the other by shifting the origin by x+0.5, I think, equivalent to adding 0.5 to the x-coordinate. However, you

Re: [ccp4bb] hardware stereo in Coot on Mac

Dear David: I don't know if anyone answered this, but I think for #1 you need to issue the command defaults write com.apple.x11 enable_stereo -bool true For #2, I think the latest X11 from here works ok, but I don't actually have a way to check it: