Hi John,
What’s your buffer – it almost looks like MOPS? I’d look at your
crystallization conditions and/or make use of the check my blob site
(https://checkmyblob.bioreproducibility.org/server/) – highly recommended.
Best,
Eddie
Edward Snell Ph.D.
Professor, Materials Design and Innovatio
Looks like HEPES to me (or some other sulphonic acid buffer).
The flexibility in the ring could be why there's a gap?
Best wishes
Matthew.
From: CCP4 bulletin board on behalf of John Smith
Sent: 18 June 2025 13:52
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] U
dade Federal de São Carlos
>
> phone: +44 07861 273773
>
> * "A sorte acompanha uma mente bem treinada"*
> **
>
> --
> *De:* Pavel Afonine
> *Enviado:* domingo, 2 de março de 2025 22:10
> *
e bem treinada"
De: Pavel Afonine
Enviado: domingo, 2 de março de 2025 22:10
Para: Rafael Marques
Cc: CCP4BB@jiscmail.ac.uk
Assunto: Re: [ccp4bb] unknown density
Hi Rafael,
Regarding your question about hydroge
Hi Rafael,
Regarding your question about hydrogens: it's a good practice to include
them using the riding model towards the end of refinement, regardless of
resolution. Hydrogens make up about half of the model atoms, contribute to
the scattering, and about 85% of them have geometrically unambiguou
Hi Michael,
It looks like PEG to me too. Have you used a smaller PEG as cryoprotectant.
Such as PEG 200 or PEG400? Also, as an off topic thing, why are you refining
hydrogens at this resolution?
Best wishes
__
Rafael Marques da Silva
PhD
Dear Michael,
The maps are very nice indeed. Seen the tripod: something like sphingomyelin?
The 2 chains (left and right, eg. fatty acid and acyl chains) should be longer
but may be less resolved towards their ends. Did you have a try with DIMPLE
(CCP4)?
###
Dear Michael,
It appears to me like a PEG molecule with two alternative conformations at its
terminus and a bound water molecule?
Nice maps!
Tom Huxford.
==
Tom Huxford
Structural Biochemistry Laboratory
Department of Chemistry & Biochemistry
San Diego State University
(619) 594-16
Dear John
Ethanol would be my first guess,
Best wishes
__
Rafael Marques da Silva
PhD Student – Structural Biology
University of Leicester
Mestrando em Física Biomolecular
Universidade de São Paulo
Bacharel em Ciências Biológicas
Universi
Dear Mahmoud,
The first thing to do is to make a list of (a) all your protein buffer
components, (b) all your crystallisation conditions components, and (c) all the
cryo-protection chemicals, and try to consider all of those as possibilities,
but then again indeed it is most likely glycerol any
Dear Nick,
I like your idea and your comments on this substance. 1,2-hexandiol
supposed to be chiral but probably it is used as a racemic mixture in
cosmetics. There is even a crystal structure in the PDB (4EUS) and an
associated 3 letter code. I´ll give it a try because it seems to fit
nicel
Hi Peer,
Reminds me of a lipocalin structure I solved which co-purified fatty acid with
it. I could model fatty acids and we along with our collaborators used several
complementary biophysical methods followed by functional assays to identify the
ligand.
https://www.sciencedirect.com/science/art
Dear Peer,
This reminds me of my colleague Michael Rossmann's discovery of a Pocket
Factor which is a fatty acid-like molecule residing in a hydrophobic pocket
underneath the "canyon" in enteroviruses. See
https://link.springer.com/article/10.1007/s13238-014-0092-6. You likely
have an endogenous
Hi Peer,
If I understand you correctly you are saying that you do not know what
substance may be in the density; then perhaps you only need to extend by
an extra atom to create a new kind of symmetrical molecule that will fit
the density?
BW,
D
On 03/06/2021 11:55, SHEPARD William wrote:
Hi Peer,
Have you tried to model the hydroxyl O1 disordered at the carbonyl
position? Check the H-bonding pattern to the end groups, this might give
some clues.
Cheers,
Bill
Le 03/06/21 12:50, « Peer Mittl » a écrit :
>I'm struggling with the electron density shown in the attachment. The
>
board on behalf of Jon
>> Cooper <488a26d62010-dmarc-requ...@jiscmail.ac.uk>
>> *Sent:* Monday, March 22, 2021 5:38:40 PM
>> *To:* CCP4BB@JISCMAIL.AC.UK
>> *Subject:* Re: [ccp4bb] unknown density
>>
>> Definitely water pentamer, no doubt at all ;-0
>
gt; *From:* CCP4 bulletin board on behalf of Jon
> Cooper <488a26d62010-dmarc-requ...@jiscmail.ac.uk>
> *Sent:* Monday, March 22, 2021 5:38:40 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] unknown density
>
> Definitely water pentamer, no doubt at all ;-0
> Cheers, J
Germany
Phone: +49 (0)30 94793-284
From: CCP4 bulletin board on behalf of Jon Cooper
<488a26d62010-dmarc-requ...@jiscmail.ac.uk>
Sent: Monday, March 22, 2021 5:38:40 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] unknown density
Definitely water pe
<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] unknown density
Hi
Please look at the pic attached. found similar pentagon water network.
On Mon, Mar 22, 2021 at 12:40 PM Jon Cooper
<488a26d62010-dmarc-requ...@jiscmail.ac.uk<mailto:488a26d62010-dmarc-requ...@jiscmail.
Definitely water pentamer, no doubt at all ;-0
Cheers, Jon.C.
Sent from ProtonMail mobile
Original Message
On 22 Mar 2021, 14:16, Mark J. van Raaij wrote:
> The ring looks too big to be imidazole or a nucleotide or a carbohydrate, so
> it’s probably mainly water molecules.
> P
The ring looks too big to be imidazole or a nucleotide or a carbohydrate, so
it’s probably mainly water molecules.
Perhaps partially replaced by PEG to explain the density between them (i.e.
water molecules in most copies of the protein and PEG in some other copies).
I’ve seen horse-shoe shaped
Could be 5 water molecules. Pentagons of water molecules are common in high
resolution structures. Add 5 waters and see if the inter-water distances are
appropriate for hydrogen bonding (2.5-3.2 A).
From: CCP4 bulletin board on behalf of Sam Tang
Date: Monday, March 22, 2021 at 9:00 AM
To: C
Hi Nick,
It sometimes helps tweaking the solvent mask settings. In Refmac the command
for the option is 'solvent optimise'. PDB-REDO uses this function as well.
Cheers,
Robbie
On 31 May 2019 10:53, Nicholas Keep wrote:
There is no blue (2fo-fc) density at least at the current contour level
in
There is no blue (2fo-fc) density at least at the current contour level
in your difference density. That probably indicates what you are seeing
is noise rather than a real feature.
I am also seeing more intense (above 7 sigma in some cases) positive
difference density without actual density i
Oops. I meant to say that Ca2+ usually has seven coordinating atoms.
Mg2+ usually has six. Sorry for the error.
-Daniel
On Wed, Mar 7, 2018 at 2:27 PM, Daniel M. Himmel, Ph. D. <
danielmhim...@gmail.com> wrote:
> Rajesh,
>
> Ca2+ usually is coordinated by five atoms, whereas Mg2+ usually is
>
I would not rely only on coordination numbers, since Ca2+ can be also
hepta-coordinated. You can look at the high resolution structures of
parvalbumin and nucleoside hydrolases. And, although not up to date, this site
is also useful http://mespeus.bch.ed.ac.uk/tanna/ . The anomalous map
sugges
Rajesh,
Ca2+ usually is coordinated by five atoms, whereas Mg2+ usually is
coordinated by six. I've seen that a lot in structures that I've
determined.
-Daniel
On Wed, Mar 7, 2018 at 2:14 PM, Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
> You just calculate a anom ma
You just calculate a anom map - it doesnt need you to dselect Ca or Mg or
anything else..
Judge the peak heights by the signal you get over any S sites in the model.
The relative signal you expect depends on your wavelength of course.
Eleanor
On 7 March 2018 at 19:09, Rajesh Kumar wrote:
> Hi I
Hi Ivan,
https://csgid.org/csgid/metal_sites/
suggest that Mg++ is the correct metal. Ca++ is not acceptable.
I am going to validate it by calculating anomalous peak for Ca++ too.
Thank you
Rajesh
On Wed, Mar 7, 2018 at 1:06 PM, Ivan Shabalin <
iva...@iwonka.med.virginia.edu> wrote:
> Hi, Raj
Hi, Rajesh,
It does look like Ca to me. It has around 2.4 A distances to waters and
quite many electrons (18), which correspond to rather wide and high
density peak in the middle.
Mg has distances at 2.07, and 10 electrons (should be a smaller peak).
Na has 2.41 distances to waters, 10 elect
Hi Rajesh,
It might be water molecules present at the symmetry axis, one more water
molecule at the centre (exactly at the axis, with occupancy of 0.5). If you
put three water molecule you probably may find the other three
symmetry-mates water molecules in opposite sides. OR One water molecule at
Hi Rajesh,
You may find this database is also useful while refining your model
http://mespeus.bch.ed.ac.uk/MESPEUS_10/
and for calcium
http://mespeus.bch.ed.ac.uk/MESPEUS_10/_5.jsp
Abhik
On Tue, Mar 6, 2018 at 10:59 PM, Patrick Loll wrote:
> Calcium likes to form octahedral complexes with w
Calcium likes to form octahedral complexes with water (or other
oxygen-containing) ligands. This looks like a classic example.
After you model and refine this, you’ll want to check water-metal distances, to
make sure they are appropriate for calcium. There is a nice literature on such
things,
You could try to put CA (as you have CA in your crystallisation condition) and
waters for coordinating atoms. If after refinement distances are around 2.3-2.4
(if I remember correctly) and B values of atoms (CA and waters) are consistent,
i.e. similar to each other then CA is good interpretation
Hi Rajesh,
Can you please let everyone know the buffer/reagents involved throughout the
process.
Also, how strong is the density? In other words, until what contour level you
see it in the Fo-Fc map?
Anyways, looking at the shape, it looks well coordinated - could be cacodylate?
Or water, am
Hi Hussain,
Crystallization condition is 200 mM CaCl2 and 20% PEG 3350.
I some what realized that it could be Ca++ with coordinated waters. But I
really wanted to have
second opinion from our group.
Thank you every one.
-Rajesh
On Tue, Mar 6, 2018 at 5:37 PM, Hussain Gps wrote:
> Hi Raje
Mg2+(H20)6 ?
> On 6 Mar 2018, at 22:19, Rajesh Kumar wrote:
>
> Dear All,
>
> Have you had experience with this kind of density? I am wandering what this
> could be?
>
> Thank you very much for the help.
>
> -Rajesh
>
>
>
>
It looks like 6 coordinated metal atom with coordinated (possibly) with waters.
The simplest case could be NA. You could use anomalous difference map to see if
there is any anomalous signal there.
Regards
Garib
On 6 Mar 2018, at 22:19, Rajesh Kumar wrote:
> Dear All,
>
> Have you had experi
Dear all,
Thank you very much for help!
The problem was solved very easy (thanks Dominik A. Herbs). I just used another
program for refinement (Refmac5 instead Phenix.refine) and this "noisy" density
almost disappeared.
http://www.4sync.com/photo/--e2gHrG/Density-Refmac5.html
Thanks a lot for
Dear Pavel,
you should also always consider your cryoprotectant molecules, so let's say
if you used PEG for cryoprotection, there's a very high probability you may
see it in your structure. It's very hard to say from the snapshots, but
for the patch of density depicted in fig.2 I would try PEG (of
Dear Pavel,
Is this density located on a symmetry axis?
There is quite often a lot of "noise" around these regions - and it may not, in
fact, be possible to model this satisfactorily.
Tony.
---
Dr Antony W Oliver
Senior Research Fellow
CR-UK DNA Repair Enzymes Group
Genome Damage and Stabili
> Juergen
> *Sent:* Wednesday, 18 May 2011 14:06
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] unknown density
>
>
>
> I take the lysine back, just realized wrong color coding it's an oxygen and
> not a nitrogen closer to the extra density :-)
>
> Jürge
Bosch,
Juergen
Sent: Wednesday, 18 May 2011 14:06
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] unknown density
I take the lysine back, just realized wrong color coding it's an oxygen and not
a nitrogen closer to the extra density :-)
Jürgen
On May 18, 2011, at 2:03 PM, Bosch, Juergen wrote:
I take the lysine back, just realized wrong color coding it's an oxygen and not
a nitrogen closer to the extra density :-)
Jürgen
On May 18, 2011, at 2:03 PM, Bosch, Juergen wrote:
But that's a lysine, so maybe a PTM ? Acetylated perhaps ?
Jürgen
On May 18, 2011, at 1:56 PM, Shiva Bhowmik wrot
But that's a lysine, so maybe a PTM ? Acetylated perhaps ?
Jürgen
On May 18, 2011, at 1:56 PM, Shiva Bhowmik wrote:
Hi Cedric,
I presume you collected the datset at a synchrtron source. It could be free
radical generated due to X-ray radiation has modified the glutamate residues. I
have seen
Hi Cedric,
I presume you collected the datset at a synchrtron source. It could be free
radical generated due to X-ray radiation has modified the glutamate
residues. I have seen this happening for Ser residues.
Cheers,
Shiva
On Wed, May 18, 2011 at 9:08 AM, cedric bauvois wrote:
> Hi, everyone
Oct 2010 17:21:31 +0200
> From: herman.schreu...@sanofi-aventis.com
> Subject: Re: [ccp4bb] unknown density
> To: CCP4BB@JISCMAIL.AC.UK
>
> Hi Priscalla and Flip,
>
> I did not bother to find out what format the maps had, I just loaded
> them in coot with no problems. I fi
and not PEG.
Good luck!
Herman
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Priscila Oliveira de Giuseppe
Sent: Friday, October 01, 2010 4:39 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] unknown density
Hi Flip,
Following your suggestion
...@formulatrix.com]
Sent: Friday, October 01, 2010 9:18 AM
To: Priscila Oliveira de Giuseppe
Subject: Re: [ccp4bb] unknown density
Hi Priscilla,
I don't think a lot of people will take the trouble to find out for
themselves which format your map files have... Its better to send screen
shots, better still t
Hi,
I did a little bit of "modeling" in your density (starting from a
nicotinamide ring, the positioned nicotinamide is enclosed). The middle
part looks suspiciously like a 6 membered ring. Could it be a molecule
in a half-chair conformation? There is only the blob that is
perpendicular to th
8:01 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] unknown density
I think there is at least one more option here (relevant at least in some rare
cases):
Identifying what that something is likely to be can be significant and may
advance your career
Of course it is important to present sup
I think there is at least one more option here (relevant at least in some
rare cases):
Identifying what that something is likely to be can be significant and may
advance your career
Of course it is important to present supporting or otherwise evidence for
the interpretation. As already discussed,
Mark J. van Raaij wrote:
> as it appears to bear near the guanidine group of an arginine, I would
> suggest it is a partially occupied and disordered sulphate and/or
> phosphate.
> whether this is practically modellable is another matter, a sulphate at
> occ. 0.5 is an option, or putting a water wi
I agree with many others: this is quite possibly sulfate or phosphate.
If collected at 1.54A the anomalous map should help identify the
presence of sulfur. Sulfate or phosphate may be present at lower than
full occupancy. I would refine everything else you reasonably know in
the model (includin
General remark if I may
Putting nothing in:
no significant effect on model and life in general
Putting something potentially wrong and misleading in:
could be detrimental to your career
BR
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Katja
Schleider
Sent: W
On Wed, 2010-02-03 at 18:26 +0100, Mark J. van Raaij wrote:
> as it appears to bear near the guanidine group of an arginine, I would
> suggest it is a partially occupied and disordered sulphate and/or
> phosphate.
If it's a sulphate, a look at the anomalous map should show something.
--
Hi Katja,
What I personally do in such a situation is to start to fill the density
by water oxygen atoms, refine a bit (the position plus the isotropic
temperature factors) and then compute a new map. Usually it has cleared
up somewhat, thus allowing you to find out what it really is. This is
as it appears to bear near the guanidine group of an arginine, I would
suggest it is a partially occupied and disordered sulphate and/or
phosphate.
whether this is practically modellable is another matter, a sulphate
at occ. 0.5 is an option, or putting a water with a remark in the pdb
that
How about a 3-fold disordered metal ion?
Mark
On 19 Aug 2009, at 17:07, Sampath Natarajan wrote:
Dear All,
Currently I'm modeling one structure with 2.6A data. I could find an
unknown density which I located in the interface between the three
similar subunits. This density shows very st
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
Dear Bert,
Your density reminded me a little bit of the paper by Pearson et al.
Biochemistry 39:8575-8584(2000) which describes the water structure in the
catalytic center of urease. I just went back to it and it looks like Figure
3 in that paper may hint some similarities to your case, in that you
Hi,
Did you check for the 2N,2O coordination. Does your protein has copper
ion as cofactor, whats the pH of the buffer.
And if pH below 6 we can partially eliminate the speculation of copper ion.
S.Jayashankar
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germ
Theoretically, citric acid can decompose into beta-ketoglutaric acid, and
the latter may decarboxylate into malonic acid...
Not sure if this happens in aqueous solutions, but if your citrate had
malonate contamination and your enzyme prefers malonate to anything else -
that's where it may have com
It could be purine or pyrimidine ring stacked between the Phe an Tyr. check pdb
3etr or 3eub of xanthine oxidase binding purine substrates between two Phe at
the active site.
Hongnan Cao
UCR
Date: Tue, 10 Feb 2009 00:23:54 -0500From: lvmengx...@gmail.comsubject:
[ccp4bb] unknown density fo
Hi Mengxiao,
The density sure reminds me of a nucleotide.
Note the pi-pi stacking of the planar part
between Tyr and Phe, and in the third stereo
picture you attached, projections at what could
be the 2 and 6 positions remind me of Guanine...
plus there are Arg, Lys, etc. pointing toward
Hi,
If you could send in stereo mode of the density you want to get suggestion,
it will be convenient for the well trained eyes.
S.Jayashankar
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germany.
On Tue, Feb 10, 2009 at 3:16 PM, wrote:
> Hi,
>
> It could be a
Hi,
It could be all sorts of things, but the one that for some reason is stuck
in my mind is isopentenyl phosphate (phosphate, not pyrophosphate!). Of
course w/o seeing the density in 3D this is just a guess.
Artem
> Dear All,
>
> When I was refining my structure, I found some unmodeled blobs, s
Dear Mengxia,
the lower part could well be a sulfate ion. For the upper part, it is
difficult to guess from a static picture. Unfortunately, at the
resolution you have there are no programs which can build an unknown
small molecule from scratch according to the density. You have to guess,
fit it an
Dear Mengxiao,
From my experience I would say that the two e. densities (blob1 and blob2)
are present the same molecule.
What that might be is more difficult to answer.
Based in the concentration you gave us and the electron density volume I
would say that is more likely to be ammonium sulphate
Remember that since it is on a special position (2-fold?), you may not
be looking at a single object, but an overlay from two or more
positions.
The anomalous map is very useful; the mystery molecule must have an
anomalous scatterer. It would be even more helpful if you had mentioned
the wavelengt
ide (CH3)2-N-C(=O)-CH3
And so forth.
Artem
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Wu,
Mousheng
Sent: Thursday, July 26, 2007 6:35 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] unknown density in structure
There are four molecu
There are four molecules in the asymmetric unit. And this density is
present in every molecules.
-Original Message-
From: ANA MARIA MISIC [mailto:[EMAIL PROTECTED]
Sent: Thursday, July 26, 2007 5:24 PM
To: Wu, Mousheng
Subject: Re: [ccp4bb] unknown density in structure
Hi Mousheng
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