Dear Urmi,
My first question, did you collect a full data set at a synchrotron and
processed this data? I think your diffraction is not as bad as you think it is,
and you may get 3-3.5 Å data from it. I asume the crystal structure of the
antigen is known and even with 4.5 Å data you could run m
Use "random" microseeding to pick up new conditions, and work with those.
See http://www.douglas.co.uk/mms.htm and
http://www.douglas.co.uk/MMS_proc.htm for theory, references and practical
details
On 24 May 2013 03:20, Urmi Dhagat wrote:
> Hi,
>
> I am working on a protein antibody complex w
Rajiv, I don't quite get your idea. Once the crystals of the single
proteins have grown, you can't "soak" the other protein in, can you? Or do
you mean something else?
Umri, if you do get crystals of one of the components it's well worth
trying "cross-seeding" into the complex, again using rando
I think this is an advice not to follow.
Vaheh
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajiv K
Bedi
Sent: Friday, May 24, 2013 1:44 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Improve diffraction ...any ideas?
Dear Umri,
I
I think you can soak another protein into a protein crystal if it is small
enough to pass through water channels, I guess.
More info:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2483499/
Hello Scott
Setting up rMMS by hand works fine, but it's a bit slow and uses more
protein and (sometimes much more important!) more seed stock.
We recommend using a Hamilton syringe, preferably with a rounded needle, to
set up by hand. 1.0 protein + 0.7 reservoir solution + 0.3 seed stock
works
Thank you everybody for their nice suggestions..
On Thu, May 23, 2013 at 7:39 PM, Matthew BOWLER wrote:
> I keep sending mails by accident today - apologies for the spam. The last
> sentence of my should read:
>
> This could of course be due to too high a concentration of mother liquor
> but qu
Dear users,
I am using refmac 5.7.0029 for refining a structure (resolution 2.2 Ang)
bound to 2 ligands. After MR There is a very clear density of ligands but
after refinement, I get negative fofc map near one of the ligand upto 5
sigma. However its 2fofc map covers the whole ligand. Also for the
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Dear Kavya,
I assume that you carried out molecular replacement without the ligand
in the search model (otherwise you are probably looking at model
bias). In that case the ligand most likely has reduced occupancy. You
can either manually set all atoms
Sir,
I used model without ligand for MR. This happens
only for some atoms not for all. So should I reduce
the occupancy for all atoms? I did use occupancy refine
it showed different occupancy like 0.8, 0.6 for two
different atoms.
Thank you
Regards
Kavya
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> Ha
Sir,
I used model without ligand for MR. This happens
only for some atoms not for all. So should I reduce
the occupancy for all atoms? I did use occupancy refine
it showed different occupancy like 0.8, 0.6 for two
different atoms. I mean for the same ligand it shows
occupancy of 1 for one atom and
Dear colleagues,
I would like to draw your attention to a notification from the wwPDB partners
about "Deposition and Release of PDB Entries Containing Large Structures" -
see:
http://www.wwpdb.org/news/news_2013.html#22-May-2013
There are major changes afoot in the way large struct
Perhaps a silly question: will old entries with SPLIT records be superseded by
consolidated entries? And what about entries split for other reasons than size
(there are only a few of those, and they are old)?
Cheers,
Robbie
Van: Gerard DVD Kleywegt
Verzonden: 24
Kavya,
Does your ligand contain any heavier atom (S, P or other)? Is it possible that
your ligand binds in different orientations? So your atom X could actually be
atom Y?
Debasish
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Kavyashree Manj
Hi Kavya,
If I understand you correctly (from title and text), you meant your negative
FoFc was around your ligand, is that right? I wonder if this is a case in
which the ligand has an occupancy below 1, but was modeled as 1, so the
refinement program had to give it a high B factor to compensa
Sir,
It has two 'P's. This is the one which shows different occupancy
one of them 0.64 and another 1. I checked to confirm that it is
not P but water but it is too close to ligand to be water.
Thank you
Regards
Kavya
> Kavya,
> Does your ligand contain any heavier atom (S, P or other)? Is it po
Sir,
Yes it is around ligand. The average B-factor of one of the ligand is
36.78, of which one of the atom has
occupancy B factor
0.58 39.37
0.56 38.77
0.87 37.00
Three atoms are of same type.
The other ligand's overall Bfactor is 17.64.
occupancy B factor
1.0
Dear users,
I tried giving occupancy of 0.65 and 0.6 respectively for all
atoms of the two ligands and refined. Now after refinement,
the atoms of ligand does not have negative density but those
which did not have negative density previously appear positive.
So what do I need to do? under what cir
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