Hi Tracy,
I think I know the PW for XrayDB. Let's talk tomorrow.
Jürgen
-
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4510
FAX: +1-206-685-7002
Web: http://faculty.washington.edu/jbosch
Dear All:
We have a crystl with P4222 sg.
All statistics look fine.
However, there is a system absense in l axis.
Any body have experiences on that?
Any suggestions would be high appreciated.
jaishin
A small molecule crystallography text would give you the formulation
for an ideal case.
A rough guide is that a B factor of 80 is equivalent to a mean vibration
about the coordinate of 1A
But for proteins the B factor becomes the collection bin for all sorts
of other errors - unrecognised
劉家欣(NTHU) wrote:
Dear All:
We have a crystl with P4222 sg.
All statistics look fine.
However, there is a system absense in l axis.
Any body have experiences on that?
Any suggestions would be high appreciated.
jaishin
can you give more details, eg all reflections along the particular
Dear All
the closing date for the study weekend registration is 15 December.
Details, registration at
http://www.cse.scitech.ac.uk/events/CCP4_2009/
Charles
One of the many facilities in pointless is to search for absences and provide a
list of likely spacegroup choices based on the results. It includes adjustments
for neighbouring spots to address one of Eleanor's concerns. NCS can cause
reflections to be systematically absent too.
The program
Dear Prof. Dodson:
Thank you for your kindly suggestions.
Actually, the sg we predicted was P4222. However, the systematic absence was
showed alone 00l in the log file(In below).
Is ant conflict on that?
Thanks again I appreciated.
Sincerely,
jaishin
Intensities of systematic absences
h
Will someone knowledgeable shed light on these issues at the ccp4
meeting next month?
Thanks
Andreas
Frank von Delft wrote:
Hi Manfred
thanks a lot for your comments, since they raise some interesting
points.
R_pim should give the precision of the averaged measurement,
hence the name.
Just to clarify what Eleanor is saying:
It was pointed out earlier (by James Holton, if I remember correctly?)
that only the vibration in the direction parallel to the diffraction
vector matters. If the mean-squared vibration in that direction is
1A^2, then the B-factor will be about
I hate scalepack for this - it only lists absences and not the other
axial reflections so you dont get a comparative scale..
SCALA is much more informative..
And it is always a bit dodgy basing the choice of space group on 3
absences alone,
However after that gripe, indeed all 3 have I 3SigI so
On Dec 10, 2008, at 17:02, Mischa Machius wrote:
On Dec 10, 2008, at 9:52 AM, Mark J. van Raaij wrote:
as a small variation on this, I would first finish the protein,
and then include ligands, working from larger to smaller (ATP =
citrate = glycerol = sulphates = waters). Sometimes several
Postdoctoral Research Position (Photosynthesis and Light Signalling)
School of Biological Sciences, Biosciences Building, Crown Street,University of
Liverpool, Liverpool L69 7ZB
Background
The aim of the research programme is to investigate the spectroscopic and
structural properties of a
Hi Tassos,
Am 11.12.2008 um 13:58 schrieb Anastassis Perrakis:
...
Having said these, I will shamelessly admit here (as I think I also
did in the latest Gordon conference?) that I have never found an
omit map to be *really* useful,
and it never told me something I could not see in the
Dear colleagues,
In my idea, the partilly recorded reflections from one unique reflection
are treated as individual
reflections and their intensities are added at a later stage. If no fully
recorded reflection, what should
happen? Recently, I am working on a set of data, in which there is
劉家欣(NTHU) wrote:
Dear Prof. Dodson:
Thank you for your kindly suggestions.
Actually, the sg we predicted was P4222. However, the systematic absence
was
showed alone 00l in the log file(In below).
Is ant conflict on that?
Thanks again I appreciated.
Sincerely,
jaishin
Jaishin, Are we understanding your original question? P4(2)22 of course has
systematic absences, [0 0 l] = 2n. Dave
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On
Behalf Of Eleanor Dodson
Sent: Thursday, December 11, 2008 7:28 AM
To: CCP4BB@JISCMAIL.AC.UK
In parallel with the discussion around this off-CCP4-topic, are they any
good examples of the opposite case, where the protein is a monomer in
solution (as evident from light scattering, MW determination through
centrifugation, EPR, etc.) but crystallizes as a dimer or higher multimer?
Bernie
Hi
What about the SFcheck omit map calculation in 'Map and Mask utilities' module
in CCP4?
R.Sreekanth
On Wed, 10 Dec 2008 Kathleen Frey wrote :
Hi Everyone,
Can anyone tell me a relatively easy way to generate an omit density map for
a ligand? I know that CNS can do this, but I was
the tandem KH domain of FMRP crystallized as a very convincing dimer
(valverde et al 2007), but is a monomer in solution, although it is
not the whole protein but just two domains of it.. anyway, i would
think these ar much more common than the other way around.
Tommi
Quoting Poul Nissen
On Thursday 11 December 2008, Santarsiero, Bernard D. wrote:
In parallel with the discussion around this off-CCP4-topic, are they any
good examples of the opposite case, where the protein is a monomer in
solution (as evident from light scattering, MW determination through
centrifugation, EPR,
Mass action is on the crystal's side.
Two recent examples of proteins that are dimers by standard
solution assays, but form weak/transient/co-factor-dependent
tetramers to function, and those tetramers are seen in the
crystal. (There is good solution data to back up the
relevance of the tetramer
There used to be a program called OMIT in CCP4. Seems to be still
supported.
I believe I used it years ago but I vaguely remember problems with
some space groups (might be wrong though...)
Regards,
Roberto
On 11 Dec 2008, at 16:20, rajan sreekanth wrote:
Hi
What about the SFcheck omit
Here we are dealing with two different state of chemistry,
solid state and solution state, If one of the minima in solid state
resembles
the biological state minimum, then there is a possiblw way to clearly
define
the biology and its significant interaction of that particular 'mer' of a
protein,
There are a number of examples of nuclear receptor heterodimers, where
crystallization of the individual partner, such as PPAR or LXR, crystallizes
as a homodimer, even though these species do not exist in solution. There
are also many examples of dimers showing one molecule per asymmetric unit,
Hi.
Non-crystallographic symmetry (NCS) doesn't apply to the entire crystal, so how
can it give rise to systematic absences? I know it can give rise to
systematically weak classes of reflections, but they aren't entirely absent.
Ron
On Thu, 11 Dec 2008, Winter, G (Graeme) wrote:
One of
Hi Bernie,
We had a case recently which was a dimer in the crystal (with 2
Ca binding sites in the symmetric dimer interface) but anSEC gave
monomer under standard conditions ( 20mM Tris, 200mM NaCl,
0.5mM TCEP at pH7.5, Temperature at 8C ).
The crystals had 0.2 M Ca Acetate. We had a
Yes, oops, silly me!
-Original Message-
From: Ronald E Stenkamp [mailto:[EMAIL PROTECTED]
Sent: Thursday, December 11, 2008 12:24 PM
To: Borhani, David
Subject: Re: [ccp4bb] About system absence in P4222?
Hi.
Maybe you made a typo in your message? In P4(2)22, the 0 0 l
On Thu, Dec 11, 2008 at 8:09 AM, Santarsiero, Bernard D. b...@uic.eduwrote:
In parallel with the discussion around this off-CCP4-topic, are they any
good examples of the opposite case, where the protein is a monomer in
solution (as evident from light scattering, MW determination through
Does anyone have any experience with an
"incufridge" for storing protein crystallization trays? (e.g.,
http://www.sigmaaldrich.com/catalog/ProductDetail.do?N4=Z708623|SIGMAN5=Product%20No.|BRAND_KEYF=SPEC).
I thought maybe these would be better than an empty lab cabinet or a
cold room that we
Yes, slight overkill.
But I would be concerned about vibrations. Also, would use cabinets in a
coldroom to shield the trays/drops from turbulence created by fans. A
colleague recently told me about excessive nucleation observed when a
plate was left in the coldroom on a bench as opposed to being
Santarsiero, Bernard D. wrote:
In parallel with the discussion around this off-CCP4-topic, are they any
good examples of the opposite case, where the protein is a monomer in
solution (as evident from light scattering, MW determination through
centrifugation, EPR, etc.) but crystallizes as a
...and in absence of TM domains and the 2D restriction of the membrane
they will probably not dimerize as free domains in solution now
suddenly gained the freedom of 3D diffusion
On 11/12/2008, at 19.03, Nathaniel Echols wrote:
On Thu, Dec 11, 2008 at 8:09 AM, Santarsiero, Bernard D.
There was a detailed and useful discussion of this on this list back
around Dec 1, 2003. If you search in the archives for I on sig I
you will find it.
Best
Richard
On Dec 10, 2008, at 5:14 PM, ANDY DODDS wrote:
Hi,
does anyone have a definition of I Sigma I please. Any definitions
I wanted to comment on a couple of things that came up during this
discussion.
1. We use crystallography because it enables us to get structural
information. But we have to be aware that most of the time a crystal will
not be an exact reflection of the biological environment, which is usually
I recently had a case, unpublished right now, where the NMR structure
of the monomer was determined and all other biochemical evidence
showed a monomer as the active form. The resulting crystal structure
turned out to be a domain swapped dimer. The group I did the work for
are still
On the question of solution structure vs crystal structure, another
comment worth considering is this:
The crystalline state of a protein can in some cases (eg a large enzyme
with small substrates) be more similar to physiological conditions than
a dilute solution.
If crowding effects are
My summary can be found at
http://wserv1.dl.ac.uk/list-archive-public/ccp4bb/2003-10/msg00431.html
Anthony
Anthony DuffTelephone: 02 9717 3493 Mob: 043 189 1076
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Richard Gillilan
Sent: Friday,
INFO REFCARD
Note: This message may contain confidential information. If this Email/Fax has
been sent to you by mistake, please notify the sender and delete it
immediately. Thank you.
Dear all,
I have recently installed Coot version 0.5 on Fedora 9. However, when I
tried to open a mtz file, the following error occurs.
CCP4 library signal library_file:Bad mode (Error)
raised in ccp4_file_readchar
Any advices? Thanks!
since its a same coot problem,
i have one more,
i am using mac 10.5 leopord osx the thing is, i dont get any pop upped
table even after i do a translate and do a real space refinement .
is it a bug or is it a problem in setups of other supportive libraries
S.Jayashankar
Research Student
I would strongly argue against protein crystals (in most cases) being
solid state. Most of the surface of a molecule is actually solvated and
protein crystals as they are miss some of the typical properties of
solid state. Although in some cases oligomerization occuring upon
protein
Woops!, yes Randy, I should have written B = 8*pi^2*u^2, not
8*pi*u^2 in my original response.
Incidentally, the A factor of a Lorentzian-distributed atom is 2*pi*w
where w is the full-width at half-maximum (FWHM) of the histogram of
displacements.
It is important to remember also that the
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