Dear Clemens,
sounds like typical pathology of plate-like crystals, which often suffer
from slight growth defects and possibly deformation during
handling/freezing.
If the Se-Met crystals are indeed easy to obtain in large numbers you may
want to test as many of them as you can, because there can
On Thu, May 14, 2009 at 03:03:57PM -0400, Guangyu Zhu wrote:
> Zn and Se have similar f' and f''. Why Zn seems have much better phasing
> powder in practice? Is it just because Zn always binds tightly on protein
> but Se might have higher b-factor?
Also: Met sidechains often adopt alternate confor
Subject: [ccp4bb] Phasing at Low Resolution
To: CCP4BB@JISCMAIL.AC.UK
Dear all,
after the SeMet phasing discussion, what would be -in
general- the
best technique to phase low resolution data (<=4A) of large
complexes
(>=150 kDA) - in terms of
- derivatization compounds (is there som
Maybe I'm wrong. Myself solved structure with 1Zn/400aa. In Pete's case
1Zn/570 aa structure was solved at low resolution. I also heard some other
cases of 1Zn for > 400 aa. But for Se, I never heard 1se for > 300aa. Se
could be partially incorporated or have mixed oxidation state. This could
affec
Guangyu Zhu wrote:
> Zn and Se have similar f' and f''. Why Zn seems have much better phasing
> powder in practice? Is it just because Zn always binds tightly on protein
> but Se might have higher b-factor?
I don't have a better explanation than tighter binding for Zn, although
I suppose that it's
Dear Martin
You can either add the cluster as a powder, just dip the tip of a
needle in the powder and gently approach the drop with the needle, the
Ta6Br12 crystals will spray itself onto the drop. Then you just wait
for the crystal to turn green, I usually marked the position where the
Regarding question 1, see:
Acta Cryst. (2008). D64, 354-367
Towards a rational approach for heavy-atom derivative screening in
protein crystallography
J.
Agniswamy, M.
G. Joyce, C.
H. Hammer and P.
D. Sun
Cheers.
riya doreen wrote:
I have two questions regarding derivatization:
I have two questions regarding derivatization:
(i) Is there a pH dependence to making derivatives ? i.e. effectiveness of
getting derivatives at low vs high pH ?
(ii) Any thoughts on the effectiveness of Barium for phasing low resolution
structures (especially for magnesium binding proteins ) ???
Zn and Se have similar f' and f''. Why Zn seems have much better phasing
powder in practice? Is it just because Zn always binds tightly on protein
but Se might have higher b-factor?
Guangyu
On 5/14/09 2:31 PM, "Pete Meyer" wrote:
> You might find Structure 14, 973-982 Jun 2006 of interest.
>
Dear all
Now that tantalum clusters have been mentioned I have recently had
issues with the solubility of the Ta6Br12 cluster (obtained from Jena
Bioscience) in PEG-based crystallisation conditions at pH 8.0-8.5. Has
anybody also experienced this? Is there a trick to getting the compound to
di
You might find Structure 14, 973-982 Jun 2006 of interest.
Larger protein, Zn instead of Se (although only 8 sites), roughly
comparable to slightly lower resolution. This was mainly testing to
confirm that there was enough anomalous signal to phase off of, so the
model was essentially known; howe
--- Original message
>Date: Thu, 14 May 2009 09:35:28 +0200
>From: Clemens Grimm
>Subject: [ccp4bb] Phasing at Low Resolution
>To: CCP4BB@JISCMAIL.AC.UK
>
>Dear all,
>
>after the SeMet phasing discussion, what would be -in
general- the
>best technique to phas
OK, here's a concrete case:
A 150kDa protein complex, the plate-like crystals can be produced in
sufficient number; Se-Met derivatives available, total number of Met
around 20, subunits could be marked and combined individually.
Diffraction is highly anisotropic, in certain directions up to
Dear Clemens,
For the choice of derivatization compounds this might be helpfull:
Z. Dauter (2005). C. R. Chimie 8, 1808-1814.
Best Regards,
Georg
Clemens Grimm wrote:
Dear all,
after the SeMet phasing discussion, what would be -in general- the
best technique to phase low resolution data (<
Dear all,
after the SeMet phasing discussion, what would be -in general- the
best technique to phase low resolution data (<=4A) of large complexes
(>=150 kDA) - in terms of
- derivatization compounds (is there something like the 'golden
five' HA compounds for these cases),
- data colle
K
Sent: Friday, 9 May, 2008 4:05:38 PM
Subject: Re: [ccp4bb] phasing at low resolution
Hallo Sajid,
shelxe produces both .phs file. This can be displayed in coot as electron
density map. If you read in the .res file, it should show the 12 Se-sites.
They are good guiding points to start model building
Hallo Sajid,
shelxe produces both .phs file. This can be displayed in coot as electron
density map. If you read in the .res file, it should show the 12 Se-sites.
They are good guiding points to start model building. They should also
help you judge whether your solution is at all usable and cor
Hi All
I have a data set of Se-Met crystal 3.65A resolution collected at Inflection
and peak wavelength. Also I have a data set at same resolution in native form.
The protein size is 28000 dalton. I dont have any model for this protein. So I
started to find the heavy atom peak search to find out
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