xxBMDA]
___
From: CCP4 bulletin board on behalf of zeyaul islam
Date: Monday, January 6, 2025 at 2:57 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Unidentified Density
You don't often get email from zeya1...@gmail.com. Learn why this is
important<
he density may be.
>> Have you considered that it might be a small peptide?
>> Best regards, tom
>>
>> ---
>>
>> From: CCP4 bulletin board on behalf of zeyaul islam
>>
>> Sent: Monday, January 6, 2025 6:55 PM
>
> *From:* CCP4 bulletin board on behalf of zeyaul
> islam
> *Sent:* Monday, January 6, 2025 6:55 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Unidentified Density
>
> You don't often get email from zeya1...@gmail.com. Learn why this is
> important <htt
From: CCP4 bulletin board on behalf of zeyaul islam
Sent: Monday, January 6, 2025 6:55 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Unidentified Density
You don't often get email from zeya1...@gmail.com. Learn why this is
important<https://aka.ms/LearnAboutSenderIdenti
david-lawson
Email: david.law...@jic.ac.uk<mailto:david.law...@jic.ac.uk>
From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>>
On Behalf Of zeyaul islam
Sent: 21 February 2023 11:13
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: [ccp4bb] Unidentified densi
...@jic.ac.uk<mailto:david.law...@jic.ac.uk>
From: CCP4 bulletin board On Behalf Of zeyaul islam
Sent: 21 February 2023 11:13
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Unidentified density
You don't often get email from zeya1...@gmail.com<mailto:zeya1...@gmail.com>.
Learn why this i
; Subject: [ccp4bb] Unidentified density
>
> Dear all
>
> We have solved the structure of nanobody at 1.25 angstrom. We observe some
> unidentified density near the serine. Please have a look at the figures.
> Protein
> was purified in PBS buffer (137 mM NaCl, 2.7 mM KCl, 8
Dear Shanti Pal,
did you use ethylene glycol as cryoprotectant? It may even be there in
small amounts in your PEG400 solution. As Nicholas and Tony have said, this
could be noise (or could be distorted due to noise) as it's on a 2-fold
axis. From those pictures, it looks to me like one molecule of
Dear Shanti
Looks like you’re looking down the symmetry axis - so this could simply be
‘noise’, or a superposition of two bound ligands on top of each other… what’s
your cryo-protectant?
With regards,
Tony.
- - - - - - - - - - - - - - - - - -
Dr Antony W Oliver
Senior Research Fellow
CR-UK DNA
Looks like you're on the twofold axis, which will make interpretation
challenging. Anything you put in may end up being too close to itself in
the neighboring AU. What happens if you put in a water and display the
symmetry?
On Mon, Jun 23, 2014 at 8:17 AM, Shanti Pal Gangwar
wrote:
> Dear All
bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Sudhir
Kumar
Sent: Wednesday, October 17, 2012 7:07 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] unidentified density
Dear all,
I have been working on the crystal structure of an enzyme in which I found the
unidentified density (see images in
Do you have matching 2Fo-Fc density? It is not obvious from the pictures.
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Sudhir
Kumar
Sent: Thursday, 18 October 2012 12:07 a.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] unidentified density
Dear all,
I have been working
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Vandna Kukshal
[vanx...@gmail.com]
Sent: Wednesday, October 17, 2012 12:38 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] unidentified density
I think it might be PEG. u should try to fit that.
On Wed, Oct 17, 2012 at 7:13 AM, R
ehalf Of Sudhir
> Kumar [sudhir.1...@gmail.com]
> Sent: 17 October 2012 12:07
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] unidentified density
>
> Dear all,
> I have been working on the crystal structure of an enzyme in which I found
> the unidentified density (see images in at
Is this density on an 2 fold axis?
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Sudhir Kumar
[sudhir.1...@gmail.com]
Sent: 17 October 2012 12:07
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] unidentified density
Dear all,
I have been
Thanks to the members for responding to my queries. I would like to
summarize the post as:
1.Improve the crystals to have a better dataset.
2. Poly A/G modelling to improve the density and then model the sequence.
3. use of secondary structure prediction tools and docking the sequence
accordingly.
On 02/10/2012 07:35 AM, intekhab alam wrote:
Hi all
I have a 3A dataset for a protein-protein complex. I have successfully
build the first protein and refined it to R/Rfree 24/28. I can see some
density for my second protein but the density is a bit noisy. I have
attached the coot image of the de
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hallo ,
first build a poly-ALA stretch. In coot or O this is conveniently
achieved using baton-build mode. This should improve the phases. Then
look at the side chains.Turbo-frodo has got somehting like a slider that
shows the sequence on screen
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Sudhir Kumar
Sent: Friday, February 10, 2012 7:06 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Unidentified density
Dear all,
I have a 2 A
hi sudhir,
i think in second snapshot you can fit MPD as its structure is
seems similar. .
On Fri, Feb 10, 2012 at 11:36 AM, Sudhir Kumar wrote:
> Dear all,
> I have a 2 A structure of an enzyme which show 12 molecules per
> asymmetric unit. While placing waters i found out some blobs wh
I have MES, Tris, maleic acid and small PEG in my solution. No
reducing agents and no cryo (and no salt or EDTA). Calcium seems to be
the best fit (assuming 100 percent occupancy) and also literature
suggests it. I tried Ni and Mn but they give negative density after
refinement.
Thank you
AM
Subject: [ccp4bb] Unidentified density.
Dear All,
I am refining structure of protein at 1.7A. It is enzyme with 3 histidine
residues in the active site, which are chelating metal (at the moment I
built in calcium but I do not know for sure, which metal is bound there).
I can see addition
Nevertheless, what do you have in mother liquor/protein buffer?
On Thu, 2010-08-12 at 17:24 +0200, wrote:
> Dear All,
>
> I am refining structure of protein at 1.7A. It is enzyme with 3
> histidine residues in the active site, which are chelating metal (at
> the moment I built in calcium but
Dear All,
I am refining structure of protein at 1.7A. It is enzyme with 3
histidine residues in the active site, which are chelating metal (at
the moment I built in calcium but I do not know for sure, which metal
is bound there). I can see additional density "on top" of metal, which
I can
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