Hi Robert,
In addition to the great suggestions you already have received, maybe you
should also consider SIMBAD or similar programs? The behavior you are
describing is typical of, albeit not exclusive to, having crystallized a
contaminant protein.
Good luck!
Nukri
On Thu, Jun 18, 2020, 08:01 Rob
: CCP4 bulletin board On Behalf Of Robert S Phillips
Sent: Thursday, June 18, 2020 9:01 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Molecular replacement problem
EXTERNAL EMAIL – Use caution with any links or file attachments.
I've been pulling out my hair with this for a few months now. I
; about.me/david_briggs
> --
> *From:* CCP4 bulletin board on behalf of Robert S
> Phillips
> *Sent:* 18 June 2020 14:00
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Molecular replacement problem
>
> I've been pulling out my hair with
I managed to solve a structure by MR at 2.4 A with a 27% identity model.
Like you, I had to use a dimer search model to make any headway. To get
usable maps and an initial model, I used Chainsaw to truncate the search
model, Phaser (MR), Parrot (DM) with NCS averaging, then auto building with
Bucca
f Robert S
Phillips
Sent: 18 June 2020 14:00
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Molecular replacement problem
I've been pulling out my hair with this for a few months now. I have data sets
to 2.6 A for a new enzyme in the aminotransferase superfamily. Unfortunately,
the closest st
I've been pulling out my hair with this for a few months now. I have data sets
to 2.6 A for a new enzyme in the aminotransferase superfamily. Unfortunately,
the closest structure is only 25% identity. MR with PHASER using the monomer
was a complete failure. Since the minimum structure of enz
Umm - this is tricky.
First of all you need to reindex the C2221 data into the P21 cell - do you
know the operator?
then expand that data set to spacegroup P21. There is a cad option to do
this..
Then add that FreeR to the re-processed P21 data.
Eleanor
On 24 March 2013 14:37, Appu kumar wrote:
Sorry for the misconception. Yes i am expanding the space group from merged
mtz file. Actually i have enough number of images collected. when i
indexed, integrate, and scale the data in either C2221 or P 21, it fetches
the overall 98% completeness. But when i am trying to reindex the data
from C2
Dear Appu,
You want to be sure you have good reason to drop the space group from
C222(1) to P2(1). There may be many reasons why your Rfree may not drop
following refinement, especially if you only have one domain in your
protein located and just in case there are more molecules to locate in the
M
Hello,
Here we deal with symmetry and the unique part of reciprocal space (the
reciprocal space "asymmetric unit" so to speak).
C222(1) has eight asymmetric units (international tables, space group 20);
P2(1) only has two. Assuming that Friedel's law does apply, then the
minimum rotation ran
I run the phenix.xtriage to evaluate the twining but it suggest no twining.
When i reindex from C2221 to P21, the completeness of data reduced from 95
% to 35% whereas the map is very good and Rwork and Rfree are 26/31 for 2.2
resolution. I do not understand why the completeness of data reduced so
Thank you for the quick reply. After molecular replacement , i have done
only few cycle of refinement in refmac. I have not done any solvent
modification or NCS averaging. I have initially indexed the data in C2221
but Rfree was not decreasing so i reindexed the data in data in P121 space
group ke
Dear Appu,
I am not sure that I have a complete sense of the issue at hand since some
of the information needed to think your issue through is missing in your
email. For example, to what high resolution cut-off were the data measured?
What resolution limits were used for the MR search? How do the
Dear members,
I am doing a molecular replacement of a
transcription factor whose ligand binding structure(24000 Da) is available
in PDB but not for the DNA binding(13000 Da). When i am searching for the
two copies from ligand binding domain as a template model, i am getti
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