Hi Lindsey,
I do agree with the others on improving your experimental strategy to enhance
the anomalous signal in your data, but did you try to solve the structure with
the data you already have? I have seen cases where there is only a pathetic
anomalous signal from fully Se-Met incorporated
Dear Xiao Lei,
You might want to consider UCSF Chimera for this task
https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchalign.html
Best,
Stefan
Pramod,
You already got good suggestions on how to handle DNA contamination in protein
preparations.
Let me point out briefly that you haven't demonstrated yet that your
contamination is DNA.
I had the same observation when purifying UvsX. A very persistent and strong
contamination in all
Correction,
I meant to say 0.5kb, not 500kb
sorry for that.
S.
Hi,
I doubt you have a TaBr cluster bound in your soaks.
You'd expect a strong anomalous signal from cluster compounds (that's what they
are made for) and you can easily get a low resolution anomalous signal from a
few dislocated HA in the solvent channels, especially if you don't counter
I have three brief questions (number two should be the easy one).
1. Where could an extra electron density of an (physically impossible)
additional molecule in an otherwise perfect map come from? (even in a wrong
solution in a {probably} too high space group?)
2. I would like to see how my data
back the resolution to preserve the weak reflections on
the original scale?
feeling a little lost here with all the pseudo symmetries ,
Stefan Gajewski
Jim,
This is coming from someone who just got enlightened a few weeks ago on
resolution cut-offs.
I am asked often: What value of CC1/2 should I cut my resolution at?
The KD paper mentioned that the CC(1/2) criterion loses its significance at ~9
according to student test.
I doubt that this
Hi Mahesh,
First of all, I risk going out on a limb here since I have no demonstrable
experience concerning your topic. I was trying to solve a non-merohedral
dataset for years, and I failed (like failure as defined in the dictionary).
That is hardly a reference, but I got to read a little on
Nat,
What do correct B-factors look like? What refinement strategy did you
use for them?
1) If I see strong positive density in the Fo-Fc map along the backbone of
two turns of an correctly placed alpha helix, therefore the B-factors are
too high in that region. The model after refinement
.
Thank you for your input,
Stefan Gajewski
Hey!
I was just wondering, do you know of any recent (~10y) publication that
presented a structure solution solely based on MIR? Without the use of any
anomalous signal of some sort?
When was the last time you saw a structure that was solved without the use
of anomalous signal or homology model?
Rubén,
the previous answer probably addresses your problem accurately.
However. If your protein of interest modifies DNA/RNA, it is quite common that
your pET constructs will mutate rapidly in E.coli. Lac operons tend to leak
quite a bit, which is not enough to detect the protein prior to
Jürgen,
Have you checked a simple selfrotation function in your currently favored
space group ?
Yes, both selfrotation function and patterson map do not look suspicious in
I422.
Do you have sufficient data collected to start out in P1 or C2 ? Then I
would start there and systematically
is the recommended protocol when dealing with many and very strongly
correlated NCS units, putative twinning and severe anisotropy all at the same
time?
Stefan Gajewski
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