Of Andrey
Nascimento
Sent: Thursday, March 28, 2013 12:41 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Strange density in solvent channel and high Rfree
Dear all,
As I said in the latest topic, I could not model the third molecule. But when I
superpose the two trimmers found in P1 MR solution
Dear Appu,
I am sorry, I do not have the script file. I ran it basically from default
parameters in CCP4 GUI. I just ran the sfcheck for 'check experimental data
only' and I got the twin law and twin fraction from the output (post script
file). So, I put these information on the detwin and ran it.
Dear Herman,
I would like to mention one more information, maybe I have forgotten. When
a process the data in P21212 and run the sfcheck it do not appear to have
twinning (even when a ran phenix Xtriage with older process data in
P21212). I will send direct to your e-mail the .pdf file with
Dear all,
As I said in the latest topic, I could not model the third molecule. But
when I superpose the two trimmers found in P1 MR solution (link below), I
get the first two molecules perfect aligned and the third molecule
inverted! (It is also possible to see the 2-fold axis and the third
Seems reasonable: P21 with beta=90 is pretty common, and it often ends
up twinned as well.
Most importantly, your R-factors support the hypothesis.
(Only keep in mind that R-factors are lower in twinned refinement - look
on Garib's webpage for the presentation where he describes that --
First - I dont think you have a 3rd molecule where you have put it - or at
least not one with full occupancy. Those maps are a clear indication that
something is wrong. What is the Matthews coefficient for the numbers in the
asymmetric unit?
Presumably your processing gave you a lattice which
Dear all,
I have tried the procedure recommended by Zbyszek, expanding data from a
higher symmetry and keeping the R-free set. But the map for third molecule
(new molecule placed) are still very bad, even when a tried to reprocess
data in P1 or P2 (P 1 21 1). The previous placed molecule (present
Subject: Re: [ccp4bb] Strange density in solvent channel and high Rfree
Maybe this thread still needs some more pedagogy/explanation for those newbies
and for biologist/ wanna-be crystallographers like me. My original reaction
was- if the true space group is P21 you wouldn't want to expand from
Dear Zbyszek,
I am concerned that the unmerged data would be bypassed and not preserved in
your recommendation. I also find it counter intuitive that the merged data
would then be unmerged into a lower symmetry and be better than the unmerged
data; there is I imagine some useful reference or
Dear all,
We have solved the problem. Data processing in P1 looks better (six
molecules in ASU), and Zanuda shows a P 1 21 1 symmetry (three molecules in
ASU), Rfactor/Rfree drops to 0.20978/0.25719 in the first round
of refinement (without put waters, ligands, etc.).
Indeed, there were one more
It is a clear-cut case of crystal packing disorder. The tell-tale sign is
that data can be merged in the higher-symmetry lattice, while the number
of molecules in the asymmetric unit (3 in P21) is not divisible by the
higher symmetry factor (2, by going from P21 to P21212).
From my experience,
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Zbyszek
Otwinowski [zbys...@work.swmed.edu]
Sent: Tuesday, March 19, 2013 9:37 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Strange density in solvent channel and high Rfree
It is a clear-cut case of crystal
Otwinowski [zbys...@work.swmed.edu]
Sent: Tuesday, March 19, 2013 9:37 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Strange density in solvent channel and high Rfree
It is a clear-cut case of crystal packing disorder. The tell-tale sign is
that data can be merged in the higher-symmetry lattice
A. Rice
[pr...@uchicago.edu]
Sent: Tuesday, March 19, 2013 10:34 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Strange density in solvent channel and high Rfree
Hi Zbyszek,
If the issue is perfect twinning, I agree - good point!
But you don't want to confuse people who simply have nearly
@JISCMAIL.AC.UK] On Behalf Of Phoebe A.
Rice
Sent: Tuesday, March 19, 2013 4:49 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Strange density in solvent channel and high Rfree
oops, I should have expanded my comments to include the sort of funky lattice
order-disorder Zbyszek so cleverly diagnosed
in lower symmetry (in contrast to cases with pseudo
symmetry).
My 2 cents,
Herman
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Phoebe A.
Rice
Sent: Tuesday, March 19, 2013 4:49 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Strange density
*Dear all,*
*I have collected a good quality dataset of a protein with 64% of solvent
in P 2 21 21 space group at 1.7A resolution with good statistical
parameters (values for last shell: Rmerge=0.202; I/Isig.=4.4; Complet.=93%
Redun.=2.4, the overall values are better than last shell). The
Check for translational NCS
And you are way too conservative with resolution. Even those holding
onto the Rmerge-dictated past would probably acquiesce to lower I/sig
cutoff. If you are using aimless, follow its recommendations based on
CC1/2, it's good for you.
Cheers,
Ed.
On Fri,
Wow, Usually on the default settings of adxv, I can see spots at this I/sig!
I suspect your data goes higher than 1.77.
Include more of the high resolution data. You very likely don't have the
correct space group.
F
On Mar 15, 2013, at 11:39 AM, Andrey Nascimento
of Andrey
Nascimento [andreynascime...@gmail.com]
Sent: Friday, March 15, 2013 1:39 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Strange density in solvent channel and high Rfree
Dear all,
I have collected a good quality dataset of a protein with 64% of solvent in P 2
21 21 space group at 1.7A
Hi Andrey,
I am taking a risky guess:
From your slide #2, it looks like a termini (unless this correspond to the
beginning or end of disordered a loop) of the protein chain(s) is (are)
extending toward(s) the solvent channel. Are the density features shown in
slides #3,4, and 5 extend from this
15, 2013 1:39 PM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] Strange density in solvent channel and high Rfree
*Dear all,*
*I have collected a good quality dataset of a protein with 64% of solvent in P
2 21 21 space group at 1.7A resolution
with good statistical parameters (values for last
@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Strange density in solvent channel and high Rfree
Dear all,
I have collected a good quality dataset of a protein with 64% of solvent in P 2
21 21 space group at 1.7A resolution with good statistical parameters (values
for last shell: Rmerge=0.202; I/Isig
could it be a PEG molecule?
Quoting Read, Jon:
Anyone see anything like this before? The data is 1.7Angstrom data with
good statistics. The picture shows the solid FoFc density contoured at 3
Sigma in light brown and -3 Sigma in purple. The density is odd as it
appears to be bound to a peptide
Hi,
These sorts of questions are always difficult, particularly in the
absence of any information about the protein or the contents of the
mother liquor. If the carbonyl you are talking about is the little
magenta dot visible through the hole in your blob, this could be a
metal atom with
--
*From: *Jon Read jon.r...@astrazeneca.com
*To: *CCP4BB@JISCMAIL.AC.UK
*Sent: *Wednesday, November 28, 2012 10:48:04 AM
*Subject: *[ccp4bb] Strange density
Anyone see anything like this before? The data is 1.7Angstrom data with
good statistics. The picture shows the solid
*To: *CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK
*Sent: *Wednesday, November 28, 2012 10:48:04 AM
*Subject: *[ccp4bb] Strange density
Anyone see anything like this before? The data is 1.7Angstrom data
with good statistics. The picture shows the solid FoFc density
contoured at 3
AM
*Subject: *[ccp4bb] Strange density
Anyone see anything like this before? The data is 1.7Angstrom data
with good statistics. The picture shows the solid FoFc density
contoured at 3 Sigma in light brown and -3 Sigma in purple. The
density is odd as it appears
From: Jon Read jon.r...@astrazeneca.com
To: CCP4BB@JISCMAIL.AC.UK
Sent: Wednesday, November 28, 2012 10:48:04 AM
Subject: [ccp4bb] Strange density
Anyone see anything like this before? The data is 1.7Angstrom data with good
statistics. The picture shows the solid FoFc
*From: *Jon Read jon.r...@astrazeneca.com
mailto:jon.r...@astrazeneca.com
*To: *CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK
*Sent: *Wednesday, November 28, 2012 10:48:04 AM
*Subject: *[ccp4bb] Strange density
How about chloride? I know, there are negative electrostatics, but I think
such is seen sometimes for halides. Or, is it possible that there is a side
chain flipped?
Jacob
On Tue, May 15, 2012 at 9:51 AM, RHYS GRINTER
r.grinte...@research.gla.ac.uk wrote:
Dear Community,
As I'm a relatively
Dear Community,
As I'm a relatively new to protein crystallography this might turn out to be an
obvious question, however.
I'm working on the structure of a enzyme requiring Ca2+ for activity and with
calcium coordinated in the active site by Asp and 2x backbone carbonyl groups,
in a crystal
Try refining with: Na, Ca or Water at that position and compare the
resulting maps. That should provide you with the information you need.
It could be a weakly bound sodium, or calcium ion. It could be that
calcium was not fully removed by EGTA treatment.
Kelly
On Tue, 2012-05-15 at 15:51 +0100, RHYS GRINTER wrote:
A colleague suggested that sulphate or phosphate could fit at these
distances, but these ions have not been added at any stage of the
crystallisation process.
I vaguely remember a report about 2-3 years ago at the ACA meeting of
Your holo structure has a Ca++ and three water molecules that have not been
built into your low resolution apo map. These atoms are not expected to be
resolved at 3 A resolution, so I would expect them to appear as a large,
misshapened,
blob. Your screenshot only shows one contour level. It
-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of RHYS
GRINTER
Sent: Tuesday, May 15, 2012 9:51 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Strange Density
Dear Community,
As I'm a relatively new to protein crystallography this might turn out to be an
obvious question
On 07/04/2011 04:24 PM, ruheng wrote:
Dear all,
Recently we are working on an archaebacteria protein which was expressed and
purified from E.coli by conventional procedures. After we solved the
structure, we found that there is an extra density in one of the argninine as
shown in the
The distance to your modelled water seems to be in agreement with an
ionic interaction. What are the components of all buffers in the
crystallisation components ?
Fred.
ruheng wrote:
Dear all,
Recently we are working on an archaebacteria protein which was
expressed and purified from /E.coli
Looks like an anion, possibly sulfate or phosphate. What's in the
crystallization mix?
Roger Rowlett
On Jul 4, 2011 11:33 AM, ruheng rh_ibp2...@hotmail.com wrote:
Dear all,
Recently we are working on an archaebacteria protein which was expressed
and purified from E.coli by conventional
Mon. July 4th 2011
EBI
Good evening,
firstly, it could be something that came form the buffer/crystallisation
soup etc. What about phosphate?
Secondly, if you think it is a natural post-translation modification of
your specific protein this is gene/source depended. Check the uniprot
entry
Hi Ruheng,
Curious to know what was in the crystallization cocktail, cryoprotectant?
Did you collect the dataset at a synchrotron?
Shiva
2011/7/4 ruheng rh_ibp2...@hotmail.com
Dear all,
Recently we are working on an archaebacteria protein which was expressed
and purified from *E.coli *by
To: CCP4BB@JISCMAIL.AC.UK
Sent: Thursday, February 24, 2011 10:39:09 AM GMT -08:00 US/Canada Pacific
Subject: Re: [ccp4bb] strange density
I have heard hard and soft many times now about O's and N's--to
what property of those ligands does this metaphor refer?
JPK
On Thu, Feb 24, 2011 at 12:47 PM
To: CCP4BB@JISCMAIL.AC.UK
Sent: Thursday, February 24, 2011 10:39:09 AM GMT -08:00 US/Canada Pacific
Subject: Re: [ccp4bb] strange density
I have heard hard and soft many times now about O's and N's--to
what property of those ligands does this metaphor refer?
JPK
On Thu, Feb 24, 2011 at 12
the
security of our computer systems and checking Compliance with our Code of
Conduct and Policies.
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Alex Singer
Sent: 24 February 2011 00:35
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] strange density
Hi -- I
Dear Alex
I take it this density effect is in each of the four molecules?
I wonder if the crescent is a series termination effect, although relatively
rare in our field. If so what might have caused it? Do you have (radial) gaps
in your data set eg due to heavy ice rings?
Best wishes,
John
This looks suspiciously like a metal ion with 3
or more resolved water ligands. It's hard to tell from the
images provided, but it looks like the metal could be close to
octahedral, with 2 His and 3 water ligands well-defined. The
estimated metal-nitrogen bond
I'm voting with Roger this time.
If I were you I would model a nickel in there (unless you have a better
candidate)
if it is right, the distances to the His should be like seen in a SOD active
site.
Then you can model the bonds and waters. You may need partial occupancy on
the metal.
Reminds me
An additional information would be to calculate an anomalous difference
map: at typical synchrotron wavelenght of ~1 A, Ni would have ~2
electrons f'', whereas Cl would have only ~0.2 electrons f''. So, a
strong anomalous difference density peak would be more consistent with
Ni than with Cl.
Hi -- thank you for all your help. The majority opinion seems to be a
metal for the sphere (Ni from the Ni-affinity column, which (Joe
Patel, correct) was used during purification, but Zn and Fe were also
mentioned), and either water molecules, bis-tris or some other small
molecule
Dear Alex,
Sorry yes I was focussing on the crescent density, since I imagined
the metal atom assignment was secure. SInce Zn and Fe are now
mentioned you would need to consider a tuned Xray wavelength anomalous
experiment to be sure it is nickel, although the circumstatial
evidence looks
Alex,
I modeled in the bis-tris with the tertiary amine and and his
imidazole coordinating axially and the four oxygens coordinating in
the equatorial plane. However, it's hard for me to tell from your
images if there are two His coordinating? Either way, that crescent
shape could easily
I have heard hard and soft many times now about O's and N's--to
what property of those ligands does this metaphor refer?
JPK
On Thu, Feb 24, 2011 at 12:47 PM, Jeffrey D Brodin jbro...@ucsd.edu wrote:
Alex,
I modeled in the bis-tris with the tertiary amine and and his imidazole
coordinating
If I recall correctly this refers to the Pearson (?) hard/soft acid base
theory. It's been a long time since inorganic chemistry.
Cheers, Roger Rowlett
On Feb 24, 2011 1:39 PM, Jacob Keller j-kell...@fsm.northwestern.edu
wrote:
I have heard hard and soft many times now about O's and N's--to
this is helpful,
Mike
- Original Message -
From: Jacob Keller j-kell...@fsm.northwestern.edu
To: CCP4BB@JISCMAIL.AC.UK
Sent: Thursday, February 24, 2011 10:39:09 AM GMT -08:00 US/Canada Pacific
Subject: Re: [ccp4bb] strange density
I have heard hard and soft many times now about O's and N's--to
what
Are you sure the sequence is right? It looks like tyrosine
Phil
On 24 Nov 2010, at 12:10, Vinson LIANG wrote:
Dear all,
I'm refining a structure and find some strange triangle density on the oxygen
of Ser and Thr at the C terminus. One picture of the strange density is
attached here.
look like tyrosines to me!
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia
c/Darwin 3, Campus Cantoblanco
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.researcherid.com/rid/B-3678-2009
On 24 Nov 2010, at 13:10, Vinson LIANG
Hi Vinson
Beyond the possibility for another type of residue as already suggested by Phil
and Mark, there is also the possibility of O-linked glycosylation of the serine
and threonine, if your protein undergoes such post-translational modification
and it has been expressed via an expression
glycosylation.
All the best,
Vinson
发件人： Savvas Savvides savvas.savvi...@ugent.be
收件人： Vinson LIANG lwg_conrad_1...@yahoo.com.cn
抄 送： CCP4BB@JISCMAIL.AC.UK
发送日期： 2010/11/24 (周三) 9:27:31 下午
主 题： Re: [ccp4bb] Strange density on Serine oxygen.
Hi Vinson
Beyond
Hi Vinson,
along these lines: did you check the molecular weight of your protein with
MS? This should help to answer if the molecular weight deviates from the
expected one.
Best wishes,
Linda
Savvas Savvides schrieb:
Hi Vinson
Beyond the possibility for another type of residue as already
...@yahoo.com.cn
抄 送： CCP4BB@JISCMAIL.AC.UK
发送日期： 2010/11/24 (周三) 9:27:31 下午
主 题： Re: [ccp4bb] Strange density on Serine oxygen.
Hi Vinson
Beyond the possibility for another type of residue as already suggested by
Phil and Mark, there is also the possibility of O-linked glycosylation
Phosphoserine ?
शेखर चिं मांडे
हैदराबाद
On Wed, Nov 24, 2010 at 5:40 PM, Vinson LIANG
lwg_conrad_1...@yahoo.com.cnwrote:
Dear all,
I'm refining a structure and find some strange triangle density on the
oxygen of Ser and Thr at the C terminus. One picture of the strange density
is attached
Subject: Re: [ccp4bb] Strange density on Serine oxygen.
Hi Vinson
is O-glycosylation possible at all given the origin of the protein and
the expression system used?
best
Savvas
On 24 Nov 2010, at 14:42
savvas.savvi...@ugent.be
收件人： Vinson LIANG lwg_conrad_1...@yahoo.com.cn
抄 送： CCP4BB@JISCMAIL.AC.UK
发送日期： 2010/11/24 (周三) 9:48:28 下午
主 题： Re: [ccp4bb] Strange density on Serine oxygen.
Hi Vinson
is O-glycosylation possible at all given the origin of the protein and the
expression system used?
best
Savvas
all you guys, so quick and helpful.
Best wishes,
Vinson
发件人： Linda Schuldt lschu...@mb.au.dk
收件人： CCP4BB@JISCMAIL.AC.UK
发送日期： 2010/11/24 (周三) 9:35:33 下午
主 题： Re: [ccp4bb] Strange density on Serine oxygen.
Hi Vinson,
along these lines: did you check
Hello My Friends,
I hope you are all enjoying the Sabbath on this first day of April.
I have recently been struggling to understand the meaning of my structure
and now I am looking for guidance. After a long period aimlessly wandering
through dense regions of ambiguity, I have of late been
Hey, dude, thanks for writing!
I could swear (so to speak) You sat next to me on an 11 hour airplane
flight not too long ago and tried to strike up a similar conversation. I
apologize for being too engrossed in the latest Dawkins book.
However, we encountered a similar structural riddle in need
Superb picture - thankyou - will add it to the lab gallery!
Eleanor
William Scott wrote:
Hey, dude, thanks for writing!
I could swear (so to speak) You sat next to me on an 11 hour airplane
flight not too long ago and tried to strike up a similar conversation. I
apologize for being too
:[EMAIL PROTECTED] On
Behalf Of Jesus Christiano
Sent: Monday, April 02, 2007 5:01 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Strange Density
Hello My Friends,
I hope you are all enjoying the Sabbath on this first day of
April
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