Hello,
What about the enantiomorphic space groups (the 4(3) screw axes instead
of the 4(1) screw axes) ? These cannot be distinguised on the basis of
structure factor amplitudes (unless you have an anomalous scatterer) nor
on the basis of the specific extinctions (both screw axes extinguish th
Yuri,
I would try to preserve as much of the crystal to use it to seed. I
have first hand knowledge of at least three projects that had a
haphazardly grown crystal being crucial as a seeding source for the
completion of the project.
So, option I) (and option safe, and what I would do if there
Thanks a lot!
Dingwei
At 2012-11-30 17:32:50,"George Sheldrick" wrote:
That is a list of the strongest Patterson peaks, the ones marked with '*' are
used
as translation search vectors to kick-start the heavy atom location. x,y,z are
the
crystal coordinates of the peaks, height is the peak
I collected on 20% and 25% PEG4000 the trick though was small crystals (<100µm
longest dimension) so the liquid can freeze (is that the right word,
considering the 80+ thread we recently had) fast by plunging the mounted
crystal into liquid nitrogen. A faint ice ring was still visible but didn't
I would try your motherl liquor augmented with 10 per cent PEG 400 hoping for
the best. Better yet mount your crystal inside a capillary like old times &
measure room temp data. At least you have something for sure. Finally I have
heard (never did it) that if you do not have air on top of you
Suggestion: What does your plunge of a loopful of the buffer (no crystal) into
liquid nitrogen tell you?
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Yuri Pompeu
[yuri.pom...@ufl.edu]
Sent: Friday, November 30, 2012 7:22 PM
To: CCP4BB@JI
Dear Yuri,
I tried parathone oil once, and I can tell, that you need to be experienced in
using it, so if you have some other crystals, you should get practice with them
first.
As for your crystal: shoot upon the matrix solvent first, and you will know is
there are ice-rings or not . If yes, I
Dear Yuri,
I am a big fan of paratone oil (or similar oils) for freezing the "holy"
crystal. The only drawback is that after you have frozen it in the oil its
a little bit hard to recover the crystal if you want to seed from it, as
its somewhat sticky...
Best of luck!
Marc
Dr. Marc Kvansakul
Dear community,
I have what seems to be a pretty decent single crystal that grew from a screen
set up 2 weeks ago.
I am trying to reproduce it but so far I have not succeeded. I am however
afraid the crystal that did form will start to deteriorate. So this brings me
to dilemma, I feel like I sho
Hi, Dear CCP4 group,
I recently collect one dataset and indexed as P4 space group. When I try to do
MR with a tetramer as input, I found the solution file suggested P41.
SOLU SET RFZ=5.2 TFZ=10.3 PAK=0 LLG=239 LLG=366 TFZ==20.9
SOLU SPAC P 41
SOLU 6DIM ENSE ensemble1 EULER 50.265 0.217 219.800
Yes, that's the one I remember!
Thanks
Richard
On Nov 30, 2012, at 7:01 PM, Prince, D Bryan wrote:
Are you referring to the I3C magic phasing triangle by any chance? Beck, et al
Acta Cryst D 61(?) (2008) is the reference I think.
Good luck!
Bryan
Confide
Are you referring to the I3C magic phasing triangle by any chance? Beck,
et al Acta Cryst D 61(?) (2008) is the reference I think.
Good luck!
Bryan
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Richard Gillilan
Sent: Friday, November 30, 2012 5:21 PM
To: CCP4BB@JISCMA
Hi Sarathy,
What does the density modified electron density map after phasing from either
autoSHARP or Phenix? Can the auto building programs build protein chains
into this map?
Cheers,
Scott
On Nov 30, 2012, at 5:27 PM, Sarathy Karunan Partha
mailto:sarathyus...@gmail.com>>
wrote:
Dear all
Dear all,
Here is the XSCALE.LP output after scaling for the izit dye stained
crystak. Sorry for attaching the .INP file.
Sarathy
On Fri, Nov 30, 2012 at 4:19 PM, Sarathy Karunan Partha <
sarathyus...@gmail.com> wrote:
> Dear all,
>
>
>
> We did some Izit dye staining to test our crystal (salt
We've found that high PEG concentration seems to compete with dye binding, so
I'm not surprised your didn't see good uptake.
I doubt the anomalous signal is from the dye ... if you calculate the molar dye
concentration you would need to have significant occupancy in the lattice,
you'll probably
Hi Sarathy,
Are you sure your anomalous scatterers are not the Ca in the
crystallisation buffer? These would also bind to the acidic residues in
your protein, and Ca has a greater f'' (~2.5e compared to less than 1.5e
for S) at the wavelength you used.
Just another possibility - unless you alread
Dear all,
We did some Izit dye staining to test our crystal (salt or protein) and we
observed that the crystal didn’t take up the dye well. But, showed nice
protein diffraction (home source KCr 2.2909 A) and we collected a dataset
(360 frames, 1o osc, 5 min exposure) on this dye stained crystal.
Maybe low-spin, ferric cytochrome? 420 would be the soret peak
and 520 the alpha+beta peaks which are very broad in the
oxidized form. Add a little dithionite or ascorbate and see if
the soret peak shifts to longer wavelength and the alpha peak
sharpens up at 550-560 nm
Grishin, Andrey wrote:
D
Hi Andrey,
Are you sure it's not PLP? To me that looks like you have confounding
aggregation, and PLP in two forms, perhaps only partly incorporated when
considering your protein absorbance. Check out the spectra in the paper:
Turning pyridoxal-5'-phosphate-dependent enzymes into thermostable bin
Dear CCP4bb users,
this problem was already discussed many times here and I've read these
discussions before writing. I have a pale yellow protein. The spectrum contains
peaks at 320 and 420. Before we proceed to ICP-OES and wavelength scans at the
synchrotron, may be some of you had a similar
On Tue, 2012-11-27 at 21:46 -0800, William G. Scott wrote:
> Are Mg++ ions ever observed to chelate primary amines?
MESPEUS reports, for example, 13 structure where magnesium is
coordinated by a lysine. 7 with arginines and a bunch of asn/gln side
chains as well. It does not prove, of course, th
On 30/11/12 10:05, Almudena Ponce Salvatierra wrote:
I would like to know if it is possible to use either the "real space
refine zone" or the "regularize zone" tools just between two atoms in
a cofactor molecule.
Do you mean by that that you don't want the other atoms to move?
Yes, you can
Dear colleagues,
applications are invited for a joint international PhD position between the
University of Freiburg (Germany) and
Diamond Light Source (UK). Could you please bring this to the attention of
interested candidates.
Best regards,
Ralf
---
PhD position available
Structural and fu
Dear all,
I would like to know if it is possible to use either the "real space refine
zone" or the "regularize zone" tools just between two atoms in a cofactor
molecule. It works perfectly between two atoms when I use it on the
protein, but it doesn't when I try to modellate the cofactor. Instead
That is a list of the strongest Patterson peaks, the ones marked with
'*' are used
as translation search vectors to kick-start the heavy atom location.
x,y,z are the
crystal coordinates of the peaks, height is the peak height, mult
indicates how the
peaks have coalesced because they are on speci
Dear all,
When I used shelxc/d/e to locate the Se atoms in a protein, I found an output
file "shelxc_fa.lst".
Does anyone can tell me the meaning of the indicates in shelxc_fa.lst (red
word):
Thanks a lot!
Ding wei
shelxc_fa.lst:
Patterson (* indicates vector selected for search)
X Y
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