Subject: [ccp4bb] data collection
Hi All,
I wish to confirm that when we collect native dataset 0-360 for a protein
crystal (P1 space group) , the redundancy could very well be
>2 since many reciprocal points cross Ewald sphere twice, right ?
Thanks a lot.
John
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Hello John,
if you merge Friedel pairs, then yes, the multiplicity (the term used by
scala
and more accurate, if I understand correctly) may approach 4.
If you do not merge Friedel pairs, the multiplicity may approach 2 but
would not
be greater.
Tim
Any reciprocal lattice point (relp) not in the blind region will cross
the Ewald sphere twice. This is because it follows a closed circular
path that passes through a closed surface. Must be one "in" and one
"out". However, even in P1 there is always a Friedel mate, and that is
"symmetry equ
Hi All,
I wish to confirm that when we collect native dataset 0-360 for a
protein crystal (P1 space group) , the redundancy could very well be
>2 since many reciprocal points cross Ewald sphere twice, right ?
Thanks a lot.
John
On Sat, 26 Jun 2010, Sudhir Kumar wrote:
Hi ALL
I don't know if I'm asking the right question:
What are Remote, Inflection and peak values for X ray data collection?
Sorry if question is wrong or under-status.
I wouldn't say it's under-status, and it's certainly a "correct" question.
The answ
Dear Sudhir,
Fair enough to ask, but I think your question has understatus for the ccp4bb,
indeed - you will find information of basic matters of protein crystallography
in any text book on the subject - including also the nature of anomalous
scattering and how it is exploited by data collectio
Dear Sudhir,
these terms refer to a MAD (multi-wavlength anomalous dispersion) experiment,
where you collect a data set each at different wavelengths from one crystal.
The actual wavlengths depend on the atom type you want to exploit in order to
carry out phasing, and they are usually determined
Hi ALL
I don't know if I'm asking the right question:
What are Remote, Inflection and peak values for X ray data collection?
Sorry if question is wrong or under-status.
thanks in advance to all
--
best regards
Sudhir Kumar
Research Scholar
Structural Biology Laboratory
SLS, JNU,
New Delhi-110067
On Mar 15 2007, Yi Xue wrote:
So far, the native crystals diffracted best to 2.4A. The MAD data
diffracted to 2.6~2.7A. We attempted to use phenix.hyss to identify copper
atoms, and the program had hard time to identify the sites.
The protein: Cu ratio is around 1:1, which is decided by ICP-A
I personally have had problems solving structures with large copy #s in
the asymmetric unit despite a good model (my failure occurred at 14 in
the a/u in primitive orthorhombic) - at the time finding the first
monomer proved to be impossible. This was also a structure in which the
systematic a
There are no easy answers for difficult problems, but have a look at
A. Gonzalez, J. Synchrotron Rad. (2007). 14, 43-50
Hopefully some of the tips given there can help in your case.
On Thu, 15 Mar 2007, Yi Xue wrote:
YX > Thus, basically, the Cu anomallous signal is very weak, and the
YX >c
Hi
For your SAD / MAD data, firstly after merging can you see any peaks in the
anomolous difference patterson map - this is critical. You could try using
SOLVE / RESOLVE or SHARP / AUTOSHARP to identify sites and to calculate phases,
as you have a little bit more control over the process. You
So far, the native crystals diffracted best to 2.4A. The MAD data
diffracted to 2.6~2.7A. We attempted to use phenix.hyss to identify copper
atoms, and the program had hard time to identify the sites.
The protein: Cu ratio is around 1:1, which is decided by ICP-AES measurement
of the crystalliza
It would be useful to know how you tried to solve the structure by MR.
Just because there is a large number of chains in the ASU isn't a reason
that MR will fail. At times you need to find some of the chains, do some
rebuilding, and then use that amended model for a continued search.
Bernie Santar
Hi:
Is the resolution of the data sufficient to apply direct methods to find
only the copper atoms, then use the copper atom positions in an
old-fashioned
'heavy-atom' phasing method, combined with direct methods?
Incidentally, was the following publication of any relevance in your
effort
Dear all:
We already got nice crystals of a drug-protein complex, however, MR
failed due to the huge copies (>12) of protein molecules per asu. Protein
itself is a small one, only ~70 aa.
Later on, we collected MAD data of copper (copper : protein ~ 1: 1),
Rsym of the data was around ~9%
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