Thank you Gert - very clear explanation..
Eleanor
On 16 July 2018 at 13:31, Gert Vriend wrote:
> Dear Eleanor,
>
> Salt bridges are a compromise between entropy and enthalpy. If, say, an
> Asp and an Arg side chain are a bit restricted in their freedom and the
> charges are close, enthalpy wins,
Dear Eleanor,
Salt bridges are a compromise between entropy and enthalpy. If, say, an
Asp and an Arg side chain are a bit restricted in their freedom and the
charges are close, enthalpy wins, and if they are very exposed, and not
close at all, entropy wins. The enthalpic gain upon protein fold
How do people decide on what is a salt bridge within a molecule and how to
count them for those Tables?
I have been looking at 2z2f - paper claims some score..-
But there are several residues in alternate conformation
with NZ A to OE1Aand NZ A to OE1B and NZ B to OE1B etc
Is that one salt
Thanks your suggestions! I tried Dials but couldn’t get any further. There just
too few spots like Artem suggested. I’ll follow Patrick’s advice to seed a new
screening with this crystal. This one was really tiny. I may get a bigger one.
Jan
> On Feb 17, 2018, at 2:43 PM, Harry Powell wrote:
>
Hi Jan
What happens if you use a program that can easily use spots from all images to
index, like DIALS or XDS? My recollection (which may be wrong) is that this is
not straigthforward in HKL3000.
> On 17 Feb 2018, at 19:32, Jan van Agthoven wrote:
>
> Dear all,
> At first I thought this was
@JISCMAIL.AC.UK] Im Auftrag von Mohamed
Noor
Gesendet: Freitag, 20. Januar 2017 11:45
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Salt bridge-hydrogen bonds
Dear all
Is it possible for two residues to form a salt bridge between them, and at the
same time**, each of them form a hydrogen bond with
Dear all
Is it possible for two residues to form a salt bridge between them, and at the
same time**, each of them form a hydrogen bond with another residue? In other
words:
Arg1 - Glu10 (salt bridge)
Arg1 - Tyr600 (H bond)
Glu10 - Thr590 (H bond)
** I understand proteins are not static stru
nell Email: esn...@hwi.buffalo.edu
Telepathy: 42.2 GHz
Heisenberg was probably here!
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bishop,
Catherine E.
Sent: Wednesday, July 16, 2014 10:56 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Salt!
I have been attempting to
Hi Catherine,
first of all, I'm sorry that you're feeling so frustrated.
In addition to the many sensible suggestions that you're surely going to
read here, I would like to point you to a paper I read a while ago in
Nature: "In situ proteolysis for protein crystallization and structure
determinat
Hi Catherine,
What buffer & salt do you have your protein in when you set up screens -
maybe this is leading to your salt crystal issues? How long does it take
for the salt crystals to appear?
Have you tried setting up trays at different temperatures? Microbatch
crystallisation under oil?
Failin
Hi Catherine,
If they are indeed salt crystals, have you tried preparing different
truncations of the gene encoding your target? I've seen a number of
successes in which, after a codon or two was added to the termini of the
gene being overexpressed, the target crystallized beautifully.
Best,
Chri
I have been attempting to obtain a protein crystal of my protein for just over
2 years at this point. We have attempted removing the tag, binding the protein
to its ligand, removing as much salt as possible (crashes at at too low a salt
concentration)--this lead us to try reverse vapor diffusio
Careina,
One thing to try if other ideas don't work or are too difficult, is
covalently (therefore unambiguously) labelling a little of your protein
with a fluorescent dye. If you add 20 nL of this to the drop *after the
crystals have grown*, protein crystals will light up, but salt crystals
will
Protein-DNA complex crystal with channels too small for the dye is *extremely*
unlikely, imho.
Original message
From: Ulrike Demmer
Date: 04/15/2013 8:48 AM (GMT-05:00)
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] salt or not?
Dear Careina,
altough your crystals
I may be biased, but the only way to really be sure is to shoot them.
If you see no spots at all, be sure to do a wide "oscillation" (rotation
during the exposure) shot as well. It is not unlikely for a salt
crystal to be oriented so that no relps are on the Ewald sphere, giving
no spots. B
Dear Careina,
altough your crystals does't take up the Izit dye it sounds promising. The
uptake of Izit depends on the solvent channels of the protein molecule -
sometimes the dye just can't enter the molecule.
Concerning the Calciumchloride - if the concentration is not too high and
without ot
Rhys
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Careina Edgooms
[careinaedgo...@yahoo.com]
Sent: 15 April 2013 11:18
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] salt or not?
Dear ccp4
I have been performing trials on a protein DNA complex for a while now and have
not see
rgreaves @astrazeneca.com <mailto:name.surn...@astrazeneca.com>
Please consider the environment before printing this e-mail
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Careina Edgooms
Sent: 15 April 2013 11:18
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] salt or not?
Dear
Dear ccp4
I have been performing trials on a protein DNA complex for a while now and have
not seen any crystals form. Today I checked an old plate (over a month old) and
I see 4 large crystals. *excitement* Three of them look tetragonal in shape
(like a pyramid) and one of them looks hexagonal.
In think most of the salt bridges I recall in structures are either in the core
of the protein or in interfaces (crystallin or complex interfaces with little
or no polar solvent around). Just like charge interactions, the lower
dielectric constant of the environment makes them stronger.
Carlos
On 10/19/2012 10:37 PM, Acoot Brett wrote:
Will you please explain to me why the protein salt bridge can still
exist in the high salt concentration as used in the crystallization
condition?
You are saying it as if there is some fundamental law of nature that
says that salt bridges cannot be
Dear All,
A lot of 3-D crystal structures highlight the salt bridges in the structure,
although some structures of them are got at high salt concentrations.
Will you please explain to me why the protein salt bridge can still exist in
the high salt concentration as used in the crystallization
Sorry Jay,
They are for sure phosphate crystals.
They always looked like that.
psp
On Sun, May 29, 2011 at 5:18 PM, Jayashankar wrote:
> Dear Friends ,
>
> I need to know whether phosphate can form hexagon shaped crystals.
> In one particular condition i have 4 different pattern , 3 seems to me a
Best,
>> Herman
>>
>> --
>> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of
>> *Jayashankar
>> *Sent:* Sunday, May 29, 2011 11:18 PM
>> *To:* CCP4BB@JISCMAIL.AC.UK
>> *Subject:* [ccp4bb] salt or pr
s!
>
> Best,
> Herman
>
> --
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *
> Jayashankar
> *Sent:* Sunday, May 29, 2011 11:18 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] salt or protein...
>
> Dear Friends ,
>
> I need to kn
PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] salt or protein...
Dear Friends ,
I need to know whether phosphate can form hexagon shaped
crystals.
In one particular condition i have 4 different pattern , 3 seems
to me as salt
Dear Jayashankar,
I had several instances where salt crystals of
the same component takes different morphologies. So it is very possible, as it
appears that the hexagonal forms are also those of the salt components in the
precipitant/buffer. You can confirm the s
Definitely small molecule crystals. You might want to push the
detector closer and use better cryo solution for further confirmation.
Nian
On Tue, Dec 7, 2010 at 8:14 AM, xiuwen zhang wrote:
> Dear Colleagues,
>
> Currently we got several very tiny crystals. After exposuring a cluster
> of c
I agree - looks like small molecular diffraction.
Try increasing delta-phi to catch more of the lattice to confirm - I
often do a 5º image or two with the detector pushed as close as
possible to check for salt diffraction when screening.
The lack of low res (~15-20Å) spots around the beamstop is
Looks like diffraction off of tiny small-molecule crystals to me.
Artem
On Tue, Dec 7, 2010 at 8:14 AM, xiuwen zhang wrote:
> Dear Colleagues,
>
> Currently we got several very tiny crystals. After exposuring a cluster
> of crystals one hour in home source, we could find some weak diffracti
Dear All:
I am sorry that I did not know the policy.
And thanks a lot for the kind reminder.
Jerry
CC: CCP4BB@JISCMAIL.AC.UK
From: [EMAIL PROTECTED]
Subject: Re: [ccp4bb] FW: [ccp4bb] salt sensitive complex
Date: Thu, 31 Jan 2008 09:37:01 +0100
To: [EMAIL PROTECTED]
Dear all
Dear all -Sorry to intervene on a 'book keeping' issue, but indeed over the last few months an increasing number of people (Jerry is not the first, so Jerry please do not take it personally) attach pictures etc. I think in a bb standard practice dictates to only use text - if illustrations are need
Hi Jerry,
I believe that if you make your cuvette and sample buffers exactly the same,
you would really cut down on noise, and get an accurate reading. Did you do
that, or is it possible?
Jacob
***
Jacob Pearson Keller
Northwestern University
Medical Sci
Dear All:
Firstly I would like to thank many folks here for giving me great ideas
several days ago.
The following are some updates for this question.
I did ITC experiments again using 25mMTris(pH8), 60mM NaCl(low salt
condition).
But things still turn out to be a littl
Hi Jerry,
to summarise your problem, using (close to) physiological buffer, SPR
and ITC give you different results, you get different results in
different salt strengths and to add to your misery, the proteins
precipitate at low salt concentrations when mixed to together.
Ok.
Given the above, yo
Dear Jerry,
Are there some better ways that I can validate the binding affinity?
I think it is possible to calculate the interacting energies by
APBS... once you have the complex structure this is! Would be
interesting to compare the values of the constants you get from ITC
and SPR with
Dear All:
Recently I am pursuing the crystallziation of a complex formd by two
individual proteins and I met several interesting problems though they are
kind of off-topic.
Any suggestions for these problems will be highly appreciated.
BIAcore showed about submicro
Hi Sreeram,
assuming you have plenty of those crystals, why don't you loop a few
pass them through a drop of your reservoir for washing and load them on
a SDS gel ?
Juergen
Sreeram Mahesh wrote:
Hi All!
I have been trying to screen for my protein crystals, from the
crystals grown
Multiple overlapping salt lattices can sometimes look like protein
diffraction, as long as you're looking in only two dimensions. However, if
you can find the dominant rings, you should be able to discriminate since
the c-spacing of salt would nearly always be pretty small. Consider powder
patterns
Hi All!
I have been trying to screen for my protein crystals, from the
crystals grown in 0.5 M Ammonium Sulphate, 1.0M Lithium Sulphate
Monohydrate in 0.1 M TriSodium Citrate Buffer dihydrate Buffer at pH 5.6.
Two different kinds of crystals observed: rod shaped and thin platy
ones. Whe
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