Dear all,
I don't know how closely this relates to what James pointed at, but
regarding the aspect of NCS information usage in the heavy-atom
finding/refinement stage, I would like to mention two programs of my
knowledgethat are able to detect NCS in a set of putative heavy atom
sites froma
] Phasing with Many Monomers/AU
The problem of many monomers in the ASU is not restricted to
macromolecules. An interesting recent small molecule example is the
structure of L-tryptophan (http://dx.doi.org/10.1107/S0108768112033484)
which, amazingly, was not published until 2012. This is perhaps
The problem of many monomers in the ASU is not restricted to
macromolecules. An interesting recent small molecule example is the
structure of L-tryptophan (http://dx.doi.org/10.1107/S0108768112033484)
which, amazingly, was not published until 2012. This is perhaps in part
due to difficulty in
In my experience translational NCS also can a part when one has many molecules
in the a.u. If MR is an option, modern packages are rather good in dealing with
TNCS.
We used Molrep + Refmac at 3.x A (still unpublished) for a case with 18
complexes (36 monomers) in the a.u. and things weren't as
Is the monomer the biggest unit you have to search with? If there is a
dimer, tetramer, etc. that is conserved, you could try searching with that.
On 01/19/14 14:30, Chris Fage wrote:
Thank you all for your responses. I already have a few ideas about how
to approach the problem.
One of my
I agree. Searching with a larger unit is likely to be successful if you
have a good idea of the structure of that larger unit. We had an example
of a low homology (29% identity) MR situation with 8 subunits per ASU
with twinned data. Not solvable with monomers. Solvable with a dimer
search
What is the sequence identity of your best search model? Finding that many
copies in P1 with 3A data is a challenge but certainly not impossible if
there is a reasonably close (20-25% identity) search model available. I
would suggest spending some time on preparing a very good search model with
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Phasing with Many Monomers/AU
What is the sequence identity of your best search model? Finding that many
copies in P1 with 3A data is a challenge but certainly not impossible if
there is a reasonably close (20-25% identity) search model available. I
would
] On Behalf Of
Eugene Valkov
Sent: Monday, January 20, 2014 6:37 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Phasing with Many Monomers/AU
What is the sequence identity of your best search model? Finding that
many copies in P1 with 3A data is a challenge but certainly not
impossible
I am grateful for all of the suggestions. I think I have enough tricks to
try at this point, but I may check back with this group if things don't
work out.
Many thanks once again,
Chris
On Sat, Jan 18, 2014 at 11:14 AM, Chris Fage cdf...@gmail.com wrote:
Hello Everyone,
I am currently
Wasn't there this huge thread just 3 days ago on heavy atom soaking
On 19/01/2014 07:18, Felix Frolow wrote:
Francis, It can happened
We have (not yet published) P1 with 24 molecules. When we cut His-tag we get
P1 with 32 molecules.
In our case we believe it is dictated by very strong
Thank you all for your responses. I already have a few ideas about how to
approach the problem.
One of my concerns with so monomers per asymmetric unit at lower resolution
was the failure of MR software. Neither PHENIX nor Phaser MR have made
progress. I am fairly new to anomalous methods, having
Chris,
On Jan 19, 2014, at 11:30 AM, Chris Fage cdf...@gmail.com wrote:
Thank you all for your responses. I already have a few ideas about how to
approach the problem.
One of my concerns with so monomers per asymmetric unit at lower resolution
was the failure of MR software. Neither
Hello Everyone,
I am currently trying to phase a structure with an asymmetric unit
predicted to contain 20-24 monomers (space group P1). The native crystals,
while beautiful in appearance (see attached), only diffract to ~3.4-3.0
angstroms at best, and SeMet-derived crystals grow with poor
Hi Chris,
It would be nice to have a wee bit more information. Is 3.4-3.0 angstroms from
a home source
or synchrotron? What are the crystallization conditions for both the native
and SeMet crystals?
Did you see the SeMet crystals with the native crystals. Have you tried MMS
with the native
You sure about this space group? 24 monomers in P1 is unusual (at least to me)
F
On Jan 18, 2014, at 9:14 AM, Chris Fage cdf...@gmail.com wrote:
Hello Everyone,
I am currently trying to phase a structure with an asymmetric unit predicted
to contain 20-24 monomers (space group P1). The
Francis, It can happened
We have (not yet published) P1 with 24 molecules. When we cut His-tag we get
P1 with 32 molecules.
In our case we believe it is dictated by very strong interaction between two
monomers, and strong interaction between dimers with build a flattish tetramer.
Probably
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