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 si
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 a
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 coul
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 (CCP4m
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:
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 i
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
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 environme
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,
Is
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
Hello!
I would be grateful for suggestions on cryoprotectants for crystals growing
in > 3M ammonium sulfate.
Thanks!
Brenda
Email Disclaimer: www.stjude.org/emaildisclaimer
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 Natar
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
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.)
Cheers
Dear Brenda
Check out malonate
http://www.ncbi.nlm.nih.gov/pubmed/14646118?
ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubm
ed_DefaultReportPanel.Pubmed_RVDocSum
Malonate: a versatile cryoprotectant and stabilizing solution for
salt-grown macromolecular crystals.
H
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 "M&M" section in Kyndt J. et al Biochemistry 2007
Jan 9;46(1):95-105 for a more detailed description of what we di
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 better)
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 b
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).
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
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.
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 haven
Did you make the plt file on the same platform? If not, try regenerating it
(I never managed to get byte-swapping to work).
Seems to work ok in 6.1.2 fink install (as does xloggraph
and xccpjiffy2idraw).
On Wed, Aug 12, 2009 at 10:49 AM, Brad Bennett wrote:
> Hi all-
> CCP4 distribution: 6.1.1
>
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:
http://xquartz.macosforge.org/tr
24 matches
Mail list logo
