Hi Jerry,
to summarise your problem, using (close to) physiological buffer, SPR
and ITC give you different results, you get different results in
different salt strengths and to add to your misery, the proteins
precipitate at low salt concentrations when mixed to together.
Ok.
Given the above, yo
Hi Joe,
I've known most salt crystals in Phosphate - and I think most people
are weary of phosphate.
Also, Calcium Sulphate is a fairly common one, esp if your buffers are
titrated with sulphuric acid. Fluoride Ions are also prone to form
salt crystals with transition metal ions.
HTH,
Dave
On
Dear Bill
William Scott wrote
Aqua simply behaves by slightly different rules. Although I am a
slobbering OS X fan, this lack of customizability to me, as well as
a lack
of focus-follows-mouse, it a negative.
To get focus-follows-mouse in Aqua, type the following in your
Terminal windo
Joe,
As David said many different types of salt crystals can grow in the
presence of phosphate, even when the concentrations of PO4 or many
divalent cations are VERY low (10s of micromolar or less). Struvite
is common (NH4MgPO4) when ammonium sulfate is the precipitant, mM
magnesium is
Hard to say without more information.
Have you refined the B factors for these residues? Most building
software gives some arbitrary b value, which must then be refined. (In
fact after any rebuilding activity you need to do a few cycles of
refinement before looking at the maps again)
Eleanor
Hi, All
Could any tell me how CCP4 handle free R flag? I know It is important to
select the same** FreeR reflections if I move to next step of refinement.
But everytime I start from fresh, the freeR Flag remains unchanged. The
Rwork and Rfree of my models are fine (20.7% and 22.9%). I thought Rfr
Yes, thanks, that does it for the Terminal.app, but not for any of the
rest. It would be great to have such a feature globally.
mb1pja wrote:
> Dear Bill
>
> William Scott wrote
>
>> Aqua simply behaves by slightly different rules. Although I am a
>> slobbering OS X fan, this lack of customizabi
Hi ccp4ers,
Sorry for this out-topic question:
Recently we have a membrane protein expressed, after solubilized with
detergent and purified from IMAC, the protein looks beautiful in SEC.
However, it completely precipitates after the 2-3 days storage in 4
degree. We supplement 2 mM DTT in the n
Sorry that I didn't explain the situation clearly. I used only one
output.sca file from HLK2000. I ran the scalepack2mtz (in CCP4i, data
reduction, import merged data) several times, on both linux Fedora and
window XP, the same computer though.
For the next step refinement, I mean add H2O, ion, li
Hi Lei,
Try this:
50-100 mM Arginine in your buffers. Or Glutamic Acid. Or both.
--
Lisa A. Nagy, Ph.D.
University of Alabama-Birmingham
[EMAIL PROTECTED]
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Zheng, Lei
Sent: Wednesday, January 23, 2008 10:51 AM
To
Zheng Zhou wrote:
Hi, All
Could any tell me how CCP4 handle free R flag? I know It is important
to select the same** FreeR reflections if I move to next step of
refinement. But everytime I start from fresh, the freeR Flag remains
unchanged. The Rwork and Rfree of my models are fine ( 20.7% a
Hi Eleanor,
Thank you for your information. I did do the B factor refinement in CCP4i and
at the first several rounds of refinement, there was no such difference map but
in the almost final run of refinement (including TLS and restrained), it
appeared. The B-factors (about 40) are similar to n
Hi James,
I did check teh B-factors and they are similar to the flanking regions (about
40). The difference density appeared at the later stage of refinement (TLS and
restrained in CCP4i).
What do you think and how to do it?
Best,
Sun Tang
James Irving <[EMAIL PROTECTED]> wrote: Hi Sun,
I
FREEFLAG (the program which is used to generate the test set)
description says when describing the keyword SEED:
By default, for a given job on a given machine, the random number
generator produces the same list of "random" free-R flags each time the
job is run. Since you would generally only
Thank you all for fast replying. The reason that I am trying to use a
different set of FreeR flag from the very beginning of the refinement is
that for some data set, my colleague's CNS refinement gave converged Rfree
and R work, 3% difference. However both my CNS and CCP4 refinement gave a
differe
Dear All,
I have a probably quite controversial question for the crystallographic
community (and there may be a strong personal bias too...).
Our group would like to select 4 meetings this year that would really be
focused towards our line of work (protein crystallography in
collaboration wit
GPCR Structural Biology Postdoctoral Position Openings
We have several openings for postdoctoral fellows in the area of GPCR
structural biology in the Kuhn-Stevens Laboratory at The Scripps Research
Institute. With the recent structure determination of the human beta2
adrenergic receptor (Che
17 matches
Mail list logo
