tomorrow. Learn as if you were to live forever.”
--- On Fri, 22/6/12, Eleanor Dodson wrote:
From: Eleanor Dodson
Subject: Re: [ccp4bb] help regarding structure solution - high R values after MR
To: CCP4BB@JISCMAIL.AC.UK
Date: Friday, 22 June, 2012, 3:30 PM
I wonder if this could have happened here
I wonder if this could have happened here?
Some one in the lab has yet again been trapped by a "feature??" of REFMAC.
Say your MR solution is found to be in P21212 after you searched various
orthorhombic SFs,
but the input MTZ file has the space group still listed as P222 (i.e. the point
gr
Hi Sonali,
You could try wide-search MR:
https://portal.sbgrid.org/d/apps/wsmr/
Best of luck,
val
On 20 June 2012 19:13, sonali dhindwal wrote:
> Dear All,
>
> I am working on a protein for last so many years and for which i have got
> crystal now in a tray which i kept 1 years ago. It diffra
r sure.
>
> Regards
>
> --
> Sonali Dhindwal
>
> “Live as if you were to die tomorrow. Learn as if you were to live forever.”
>
> --- On Thu, 21/6/12, Mark J van Raaij wrote:
>
> From: Mark J van Raaij
> Subject: Re: [ccp4bb] help regarding structure solution
Raaij wrote:
From: Mark J van Raaij
Subject: Re: [ccp4bb] help regarding structure solution
To: "sonali dhindwal"
Date: Thursday, 21 June, 2012, 11:33 AM
you didn't answer the most important question - are you 100% sure the protein
in the crystal is not a contaminant?
Unfortunatel
trying all the things as
suggested.
Regards
--
Sonali Dhindwal
“Live as if you were to die tomorrow. Learn as if you were to live forever.”
--- On Thu, 21/6/12, Peter Hsu wrote:
From: Peter Hsu
Subject: Re: [ccp4bb] help regarding structure solution
To: CCP4BB@JISCMAIL.AC.UK
Date: Thursday
Hi Sonali,
Did you use MBP as your purification tag? That's around 45-50kDa if I remember
right.
If not, I've had a decent amount of luck using in situ proteolysis to get
crystals of degraded fragments. Try a limited proteolysis first overnight at 4C
at varying concentrations of trypsin, see w
- Original message
>Date: Wed, 20 Jun 2012 16:00:06 -0400
>From: CCP4 bulletin board (on behalf
of "R. M. Garavito" )
>Subject: Re: [ccp4bb] help regarding structure solution
>To: CCP4BB@JISCMAIL.AC.UK
>
> Dear Sonali,
> I think that first item on your
Dear Sonali
I would do the following things
1) Check your space group. Although rare it could be p2 or even p1
2) Run balbes server and check all space groups (in your case only p21 and p2)
If you want you can send data to me to see what might be going on
Regards
Garib
On 20 Jun 2012, at 19
Dear Sonali,
I think that first item on your possible to-do list is to verify that you have
indeed crystallized the protein you purified. We, too, got great crystals once
with protein X (100 kD) and noticed that 1) the lattice constants, space group
symmetry, and Matthew's coefficient were wit
Dear Sonali
have you run any diagnostics on your dataset e.g. via xtriage in PHENIX, or the
ccp4 programs to detect issues such as twinning and pseudotranslation.
You also did not provide any information regarding the data quality. Processing
your dataset via Xia2 from the ccp4 suite could also
Dear Sonali -
It seems very likely that your original protein (which did not
crystallize) was proteolytically degraded over the one year storage, and
you now have a fragment of the original protein which is capable of
crystallizing. You should analyze all of the homologous structures in
the
Sonali,
How did your MR search(es) fail?
1. Too many clashes? (allow more clashes or remove likely floppy bits
of the protein, e.g. N- and/or C-termini)
2. Could not place all molecules in the asymmetric unit? (Consider
searching for fewer molecules in asymmetric unit. A partial solution
On Wed, Jun 20, 2012 at 11:13 AM, sonali dhindwal <
sonali11dhind...@yahoo.co.in> wrote:
>
> I am working on a protein for last so many years and for which i have got
> crystal now in a tray which i kept 1 years ago. It diffracts well and
> resolution is 2.2A, which is good.
>
> I indexed in HKL20
Dear All,
I am working on a protein for last so many years and for which i have got
crystal now in a tray which i kept 1 years ago. It diffracts well and
resolution is 2.2A, which is good.
I indexed in HKL2000, mosflm and automar and it shows P21 space group in all
data reduction packages. But
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