Dear all,
I would like to get some information on proteins where there is
conformation/structural change between the crystal structure and solution
structure of the same protein. Do anybody came across such situations?
Thanks in advance..
cheers,
Vandu
The only thing you can do is to move the detector in and collect higher
resolution. Then you can determine what the I/sigI ratio is for each of your
resolution shells and manually set the resolution limit once you run
HKL2000. As far as the R/Rfree values go, you will need to manually set the
w
Thanks Pavel. Its not huge, but I need to process massive cases. Svergun's
envelope function or spherical harmonics expansion provides some concise
mask description, but just not sure whether ccp4 or other facilities can
generate it handy (from a pdb file to an atomic mask!)
Thanks again!
Hailian
Hi Hailiang,
I guess you can store the map in CCP4 map binary format or convert it into
corresponding Fourier map coefficients and store them in MTZ format (note:
in this case if you convert them back into a mask it will not be a binary
function anymore) - both shouldn't take a huge amount of spac
Hi All,
I am working with a methyltransferse protein and its later determined
crystal structure indicates its substrate SAM was bound during protein
expression or purification since no SAM was added during protein
crystallization. Now I want to obtain the apo form protein for further
characterizati
Hi,
As I understand, the general molecular mask generated by CCP4 (eg
sfall+mapmask) are binary mask file which needs lots of memory space. I
just wonder whether we can generate some small mask files represented by,
say, envelope function (F(sita,psi))
(http://journals.iucr.org/d/issues/2001/10/00
Hi Ethan,
You are absolutely right. As a matter of fact, I had initially
processed the data to 2.7A and it looked pretty decent with R symm
less than 10%. The maps looked good too.
The problem arose during second round of refinement. The Rfree got
stuck at around 29-30 while the Rfactor k
A Postdoctoral position is available immediately in the group of Dr. Svetla
Stoilova-McPhie (University of Texas Medical Branch (UTMB) at Galveston) to
study the structure and active conformations of membrane and
membrane-associated proteins:
http://www.utmb.edu/ncb/faculty/Stoilova-McPhieSvetl
On Friday, May 20, 2011 02:28:26 pm Mittal, Seema wrote:
> Hi All,
>
> I am currently working on a 3A resolution dataset. The scaled file shows the
> following statistics (scroll down to the end of this email). It is P212121
> space group with R merge of 8.8%.
Your data statistics look fine.
Hi All,
I am currently working on a 3A resolution dataset. The scaled file shows the
following statistics (scroll down to the end of this email). It is P212121
space group with R merge of 8.8%.
My question is : Is there a way to selectively use only the data with I/Sigma
value of 2 and more
Greetings fellow Crystallographers,
I'm working on a structure at 1.8-A resolution that contains an acetone
crosslink between 2 cysteines (crosslink was incorporated by adding
1,3-dichloroacetone). I figured that the easiest way to model this is to
mutate one of the cysteines to S-acetonylcysteine
I will refer you to the PymolWiki, it has all the answers you seek:
http://www.pymolwiki.org/index.php/Stereo_Figures
http://www.pymolwiki.org/index.php/Stereo_Ray
On Fri, May 20, 2011 at 2:51 PM, Matt Colins wrote:
> Dear all,
>
> We are preparing a submission to Nature Structural and Molecular
Dear all,
We are preparing a submission to Nature Structural and Molecular Biology, but
do
not know how to make a stereo image of electron densities as required by the
journal. We would appreciate it very much if you give us some detailed
protocols
on doing that.
Thanks!
Matt
You have one equation and two unknowns. You cannot solve for I(h1)
and I(h2) without some other source of information, i.e. another
equation.
As Ian said, you can't change the Wilson B by dividing the intensity
by two so there must be something wrong with your procedure. I can't
really fol
The true values of the components of the twin can't in general be
equal since they come from _different_ reflections that are unrelated
by the true crystal symmetry (they are only related by the
pseudo-symmetry of the twin).
Let's say:
Itwin(h1)=tf*I(h1)+(1-tf)*I(h2)
where I(h1) and I(h2) are th
Thanks Ian,
but your reply confused me a little.
I hope you can explain me where I was wrong.
I know that
I(twin)=tf*I(h1)+(1-tf)*I(h2)
I supposed that having tf=0.5 I could take the I(twin), dividing by 2 I
will get both I(h1) and I(h2), that are the two component (that are
equal in thi
No, simply applying a single overall scale factor to the intensities
can't possibly make any difference to the Wilson B since the fall-off
with resolution will remain unchanged. The Wilson plot is a plot of
ln(mean(I')/S) in shells of constant d* vs d*^2, where I' is I
corrected for symmetry and S
It might be SDS precipitation. Although 0.1% SDS is generally considered not
high enough to precipitate at 4 degree, it might interact with other
components in your solution to form even less soluble material.
Nian
On Fri, May 20, 2011 at 9:36 AM, WEI MIN wrote:
> Dear All
>
> I have a difficu
Hi Wei,
this milk is precipitated/microcrystals of SDS probably with some phosphate
since you are in PBS buffer.
I would have two suggestions.
1-Can't you find a better detergent than SDS for your membrane protein? Have
you run a detergent screen for this protein to find a milder and more
crystalli
Thanks Ian,
I tried to do this:
I took the file containing
hkl I and sigI
and generated a new file containing
hkl I/2 and sigI
because I know, from the refined structure that the twin fraction is
nearly 0.5. Now, using this new file the wilson plot give me a more
reliable estimated B factor.
The "milk" solution is a suspension of lots of micro-crystals which form
when temperature goes down. When you take the solution out, it worms up
and the crystals dissolve. If you take a look at them under high
magnification microscope in the cold room, chances are you'll see those
crystals. I canno
Dear All
I have a difficulty to crystallize my membrane protein(his tagged). I got
the salt crystals from many different screening conditions. The protein is
in PBS buffer and 130mM salt with 0.1% SDS. I store It in the 4 degree
although it forms the milk solution.
The solution is getting clear in
Kay Diederichs wrote:
Hi Joane,
since you're using NCS I'd like to add that this is indeed a good
strategy, but you should make sure that you should probably not restrain
the B-factors of the well-defined domain and the not-so-well-defined
domains to be equal - they do differ and the refinement
Dear All,
the recruitment service just changed the portal for applications.
If you are interested in this post please apply here:
http://www.esrf.fr/Jobs/english. Many apologies for the duplicate post,
cheers, Matt.
Dear CCP4 users,
We have an opening in the ESRF Structural Biology
Hi Joane,
since you're using NCS I'd like to add that this is indeed a good
strategy, but you should make sure that you should probably not restrain
the B-factors of the well-defined domain and the not-so-well-defined
domains to be equal - they do differ and the refinement should probably
not
Dear All,
I am working on enzyme which is expressed in Mycobacterium smegmatis. After
affinity chromatography and gel filtration, it is observed that enzyme stays
in dimeric form for 3hour approx. by the time it goes oligomeric form. i
want it to stay in dimeric form to get homogeneity of solution
Dear Joane,
we had a case, where we had five molecules in the assymmetric unit where
the biological functional unit was a homotrimer. So we had one
non-crystallographic trimer and two monomers, which were located along the
3-fold symmetry axis of space group I213. One of the monomers also showed
e
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