Hi Guohui,
Are you sure this is caused by disulfide bond formation? Do you have any
reducing agent in your buffer? 5 Cys residues in 30 amino acids looks very much
like a zinc finger to me. Is there any evidence for that? Are there any other
zinc binding residues, i.e. His in this region?
Good
Hi Everyone， Well,My Research Protein is easily Dimerzation caused by Disulfide bond for many Cys.And it leads to the SEC peak too wide about 5 mL. Then I Cut N-ter 30 Amino Acids in which 5 spaced Cys,but the SEC Peak is still wide and hard to Crystallize（as the protein is very pure and clean
Hi Ethan,In my understanding, indeed. Pretty much only 2nd domain solves the
structure. When I compare with isolated 2nd domain structure, which is ~half
MW, x-tal grown in different condition plus slightly higher res (2.4A), it's
the same! Only difference is domain1+2 is 3A with poor Wilson B
On Monday, 14 September 2020 22:22:34 PDT Rezaul Karim wrote:
> Hi Eleanor,Thanks for asking.
> Yes, 2nd domain refine alright with Rfree ~25%, inhibitor at the binding site
> and no major issues at all except that I don't see any trace of 1st domain
> and the protein from dissolved crystals are
Hi Eleanor,Thanks for asking.
Yes, 2nd domain refine alright with Rfree ~25%, inhibitor at the binding site
and no major issues at all except that I don't see any trace of 1st domain and
the protein from dissolved crystals are on SDS gel at right MW size = 1st+2nd
domain.I tried all other possib
Hi all,
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One more remark on the camera correction issue...
The camera correction does actually matter quite a bit, especially where it
concerns the movie alignments in the early phases of processing, as Tanaka
mentioned too. What I want to point out here is that the effect of the
camera correction needs t
Hello Abhik
In coot use: Calculate>Merge Molecules to append one structure to another.
Coot will change the chain labels for you, which might work out OK in this case.
Alternatively, I've done a lot of this in my time:
Make a copy of the reference PDB file
Open it in a simple text edit (emacs,
Hi,
How can I save two superposed protein structures in PDB format? Is there
any way I can do this in coot or pymol? There is only one chain in those
two PDB structures.
Thanks in advance,
Abhik
To unsubscribe from the CCP
Hi Randy,
> On 14 Sep 2020, at 18:52, Randy Read wrote:
>
> Thanks for pointing that out. I guess I hadn’t presumed to brand myself as
> an expert! I’ll have to find out now what else I’ve been missing...
Surely you should identify yourself as developer and have access to all the
options!
Hi Huw,
Thanks for pointing that out. I guess I hadn’t presumed to brand myself as an
expert! I’ll have to find out now what else I’ve been missing...
Randy
-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
Hi Luca,
as Eleanor mentioned, in the i2 interface there is in the option menu an
add water button. That will automatically run the coot find waters script
similar to the old interface. Paul did use some very sensible values to
look for blobs, which might be waters. These ones are used (basically
Just to follow up on this — if you’ve already tried searching for the
additional domain with the already placed ones fixed, and that didn’t work,
it’s possible that the missing domain is less well-ordered than the ones you’ve
already placed. So one thing you could try is increasing the relative
The videos from the CCP4 Study Weekend 2020 held in January are now available
to view on the CCP4 YouTube channel.
Regards
Karen McIntyre
CCP4 Project Administrator
Science and Technology Facilities Council
RCaH 1.22
Rutherford Appleton Laboratory
Harwell Campus
Didcot
OX11 0FA
karen.mcint...@s
Dear Andy,
I few thoughts from my side, but no solution I am afraid:
* Your twinning operator -h, -k, l is the standard alternative indexing for
P3x space group, which makes a lot of sense.
* P32 is a low symmetry space group, which makes MR easier, but this is
offset by the NCS.
*
Rezaul: You say
*But I only see the 2nd domain with exact same unit cell that I have solved
for 2nd domain's with same space group. *
I am afraid if that is so that you probably have only crystallised the 2nd
domain. Does that domain refine all right?
Eleanor
On Mon, 14 Sep 2020 at 09:02, Rezaul
To follow on from this thread:
To answer Jon, I did try to see if P6 subgroups were a possibility but can rule
this out for a few reasons (MR doesn't give solutions, merging stats not
suggestive of P6, the other dataset with the twin fraction that is
significantly further from 50:50); and the d
Eagerly following >I have a similar case. A 3A data with P3(1)21 from two
domains (80+% sequence identity) protein. No major twinning issue. But I only
see the 2nd domain with exact same unit cell that I have solved for 2nd
domain's with same space group. No proteolysis- crystals give protein b
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