Hi ,
I am co-crystallizing a protein with compound and would like to know how much
of compound to add to protein solution to start with. I know that the protein
binds compound in a 1 to 1 ratio but also noticed that the compound
precipitates out of solution when DMSO is diluted off. Where shoul
Hi all,
I want to add 2 new ligands (that do not exist in PDB) to my structure. I
generated the ligands from PRODRG. The problem is that both of the ligands
have the same name DRG. After renaming the ligands in both PDB and CIF
files, I always get this error message "CIF dictionary does not contai
You might to consider that PEG 3350 has phosphate contamination, so playing
around with small amounts of phosphate (or removing it) might be worthwhile.
Cheers, tom
From: Regina Kettering [mailto:reginaketter...@yahoo.com]
Sent: Thursday, August 25, 2011 04:46 AM
To: CCP4BB@JISCMAIL.AC.UK
Subjec
Is there anything that consistently matters in crystallography? ;-)
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von Delft
[frank.vonde...@sgc.ox.ac.uk]
Sent: Wednesday, August 24, 2011 5:21 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re:
And now, does anybody know of /systematic/ data indicating how
consistently all this matters?
phx
On 24/08/2011 21:45, Prince, D Bryan wrote:
For those of us truly controlling types :), I used to make the PEG
solutions and filter them over a Bio-Rad resin that filtered out all the
junk ad
For those of us truly controlling types :), I used to make the PEG
solutions and filter them over a Bio-Rad resin that filtered out all the
junk added to stabilize the PEG solution. Then, of course I had to
freeze all my PEG solutions in aliquots, or wrap them in foil and store
at 4C in the dark. T
!Hola!
About 6 years ago I noted a couple of structures I was interested in were
removed from the pdb. I saw in a recent email discussion that it is possible
to access obsolete entries, however unfortunately I do not have the pdb code
of the structure I am interested in - and neither does the
PEG is a polymer and it can be made by anionic or cationic polymerization.
Whichever you use, you go "the other way" to terminate the reaction at an
appropriate time (so you have the molecular weight you want). So when you start
with an acid, you terminate with a base and vice versa. If you te
Commercial polyethylene glycol is contaminated with polymers that have aldehyde
groups at the ends. Other impurities include some amount of internal epoxide
linkages. The aldehyde groups can be additionally oxidized to carboxylic
acids. I would assume that oxidation to terminal carboxylic aci
PEGs have small amounts of anti-oxidants added to them by the manufacturer.
I think different manufacturers may use different compounds.
And you might imagine that PEGs themselves with their -OH groups go from
alcohol to adelhyde to carboxylate.
-Original Message-
From: CCP4 bulletin boa
A while ago I measured the pH's of old and new PEGs and found them
very different, and internally attributed all "old vs new PEG issues"
to pH. Upon reflection, this seems too simplistic. Are there other
known mechanisms of crystallization capacities of PEGs of various
ages?
Jacob Keller
Something else to try would be the Protic Ionic Liquid kit from Hampton.
I recently had crystals of a protein that would only grow as laminated
stacks of plates. Optimizing the conditions and using an additive screen
didn't improve crystal morphology. I tried the PIL kit from Hampton and
was able t
Thanks for the protocole and advice! I'll put my spherulites on gel. It will
make things clear.
Jan
2011/8/24 Regina Kettering
> Something to consider is the quality of the PEG 3350. We have found that
> different qualities of PEG 3350 can give different results, depending on the
> type and am
Something to consider is the quality of the PEG 3350. We have found that
different qualities of PEG 3350 can give different results, depending on the
type and amount of contaminants. What used to be the Fluka PEG 3350 is now the
pharm grade of PEG 3350 (aka Miralax). We use high quality PEG 3
You should check these "spherulites" on SDS-PAGE gel to make sure that these
contain your protein. Then you can start thinking about optimization.
On Wed, Aug 24, 2011 at 2:05 PM, Jan van Agthoven wrote:
> Dear all,
>
> I recently obtained some spherulites while trying to crystallize my
> protei
Dear Jan
I would recommend running the following protocol on your spherulites. Just
pretend that they are crystals :)
This was posted some time ago on the ccp4bb.
best regards
Savvas
> On Tue, Nov 2, 2010 at 9:15 AM, Kenneth Verstraete <
> kenneth.verstra...@ugent.be> wrote:
>
> > Hi Ivan,
> >
>
Dear all,
I recently obtained some spherulites while trying to crystallize my protein.
The spherulites are manually reproducible, but changing pH, protein
concentration, and salt concentration does not result in crystal formation.
Microseeding with crushed spherulites isn't a solution either as it
Hi Francis,
Once I had asked Pavel Afonine the same questions and these were his
suggestions but most of these can be implemented in phenix...
I guess there is no general/unified procedure to do this, and in most of
cases the tools and outcomes vary case by case.
Some general points:
- Removing p
James,
After indexing the images with LABELIT it is possible to write out an
XPARM.XDS file that defines the unit cell, orientation, and beam parameters.
For example, index an image first:
labelit.index lysozyme_001.img --index_only
This gives several possible Bravais lattice solutions...e.g. t
Dear Tim
At the moment there is no option to stop refmac prematurely. I can add if it is
necessary. I can only give my experience.
After molecular replacement before running ARP/wARP or buccaneer I usually run
60-100 cycles of refinement with jelly body with sigma set to 0.01.
Then automatic mo
I agree with Herman, and would like to add to his list of
explanations why density may not be observed. It is possible
that the compound binding to your protein simply doesn't contain
those bits without density. I have known cases where the
compound in the vial does not match the label on the
Hi Tim
The answer is a definite NO, the goal of refinement is to maximise the
likelihood from the working set and the restraints. It is definitely not to
optimise Rfree or LLfree. The correct value of the latter is whatever you
get at convergence of refinement, i.e. at maximum of the likelihood,
Hello all,
this might not be the appropriate place, but I was wondering if anyone
knows of a database with protein experimental pKa values, with
possibility to search for Cysteines and .pdb structures.
"PINT: Protein-protein Interactions Thermodynamic Database" seems to be down.
The question aro
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Hash: SHA1
Dear all,
especially at the beginning of model building and/or at low resolution
both Rfree and "-LL free" as reported in the refmac logfile show a
minimum at a some cycle before rising again.
I am certainly not the only one tempted to first run refm
HI,
I've recently seen two examples where the description of a screen in a local
database was different to the current one on the manufacturer's web site. This
happened in two different labs, using different software, and with different
screen manufacturers.
This could potentially lead to an o
Tongqing
Thank you for highlighting an issue with a recent release of the
PDBePisa service. The option to return the atom detail as well as the
residue detail within the PISA service was accidentally missed from the
production service during a major update of features. I am sorry that
this
--
RESEARCH ASSOCIATE: A Multidisciplinary Approach to Protein Function and
Exploitation
--
Department of Physics/Strathclyde Ins
On Tue, 2011-08-23 at 15:01 -0400, Ed Pozharski wrote:
> On Tue, 2011-08-23 at 12:36 -0600, Francis E Reyes wrote:
> > Seems to be a quiet day on the BB
>
> So you need an earthquake :)
>
> This is similar, imho, to the issue of disordered side chains:
>
> https://docs.google.com/spreadsheet/gfo
Hi,
I apologise for the empty message. If you take the cell dimensions that you got
in LABELIT into XDS it should work. I guess you couldn't get XDS to index from
fresh, is that correct?
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 8
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
From: CCP4 bulletin board [CCP4BB@JIS
Dear all,
I'm able to index my images in LABELIT. Is it possible to use that
indexing solution in XDS?
James
Dear All
I may not have understood but if I run PDBe PISA
and go Interface>Details
then I get a table of the form eg for H-bonds
Hydrogen bonds
1 A:GLN 213[ NE2] 3.52A:SER 3[ O ]
2 A:ASN 112[ ND2] 2.77A:SER 3[ O ]
3 A:GLN 213[ NE2] 2.
Dear ccp4bb,
About 6 years ago I noted a couple of structures I was interested in were
removed from the pdb. I saw in a recent email discussion that it is possible to
access obsolete entries, however unfortunately I do not have the pdb code of
the structure I am interested in - and neither does
Coot:
Extension -> Modelling -> Residues with Missing Atoms...
Or watch out for the blue bars in the rotamer validation graph in Coot.
B
Dear all,
Does anyone know a program that will check a PDB file for missing
atoms and output a list of the corresponding residues?
Many thanks in advanc
Dear Francis,
Although I am a member of the "never truncate a disordered side chain"
camp, I think for ligands it is quite a different story.
For me a random disordered lysine on the protein surface is completely
uninteresting, except if one wants to examine the electrostatic surface.
A non-expe
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