Hi everybody,
I collected a number of X-ray data sets from crystals originating from the same
cryst. drop. I solved the initial structure in P22121 space group by MR with
Phaser locating two molecules (data to ~ 2.1 Angstr.); refined R/Rfree:
0.213/0.244.
Processing of some of the other data s
Hmmm -
well the I212121 cell and the P21221 cells you give here have different
volumes, so they cant be just rearrangements of symmetry operators and
non-cryst translation.
Do you get other sets of cell dimensions for different processing?
Eleanor
On 13 October 2014 09:47, Florian Schmitzberger
Hi Florian,
Not sure if this is helpful or not but I have a particular protein that seems
to be either P22121 (with 2 molecules) or I222 (with one molecule).
Not from the same drop but crystallised in similar conditions but with
different small molecules bound.
In many cases the crystals can
It might help to look at the images and predictions. You a have serial vs
integral extinctions
(i.e. conditions limiting reflections are:)
P 2 21 21 (Standard: P 21 21 2, btw)
0K0 : K=2N only
00L : L=2N only
I222
HKL : H+K+L=2N only
Alternatively you could process unmerged data wit
Yes, having different crystal forms in the same crystallization conditions is,
while clearly uncommon, not unheard of. I had a case once where at least four
different crystal forms were observed in crystals harvested from identically
prepared drops. It may be that there is some major set of con
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Hi Florian,
When your pseudo-translation (native Patterson peak) is close to (0.5,0.5,0.5)
even in p22121 you will have have most of reflections with
h+k+l=2n+1
measured as weak. In your lower resolution datasets 2.6 and 3.0 A non-weak
reflections can be lost in noise and your group assignment
Hi Bernhard et al
>
> The lattice metric is the same for both SGs (did not understand Eleanor’s
> remark)
>> Hmmm -
>> well the I212121 cell and the P21221 cells you give here have different
>> volumes, so they cant be just rearrangemen
I think Eleanor was looking at the cell axis in particular a and b they are off
by almost 10%, hence unlikely to be identical, unless I missed something there.
Jürgen
..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecul
Hi Florian,
a couple of things come to my mind:
a) you have to be careful in your use of XDS; if you specify space group number
18 it will use "P 21 21 2" as space group, whereas you seem to use the ordering
ahttp://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/IDXREF.LP ) to find
whether
Hi everybody,
Thank you for your comments!
The data sets that index in I222 tend to have shorter a and b axes. I have data
sets in I222 with a=95.31 b=106 c=125.9 though (still need to look at these in
detail). These axes are relatively close to those in the original P22121, which
I processed
Stephen,
Robbie advice is 100% correct. Be careful about the naming of the sulphur
atoms (is S1 opposite S4 or next to it). I recall that the distributed CCP4
dictionaries have different atom naming than the PDB chemical components
dictionary. If this is the problem is that the naming is differen
> As I understand, P22121 should be fine to process (and deposit in the
PDB); and there is no need to reindex to HM convention P21212.
No need to, but trivial and then in conformance with the ITC. If we have a
standard listing in ITC, why not use it? Having different symbols/settings
for the
Yes, I missed the second set of cell constants and assumed Florian is
talking about ambiguity in the same data set.
Thx BR
From: Harry Powell [mailto:ha...@mrc-lmb.cam.ac.uk]
Sent: Montag, 13. Oktober 2014 12:14
To: b...@hofkristallamt.org
Cc: Harry Powell; CCP4BB@JISCMAIL.AC.UK
Subject: R
Dear Matthew, Robbie Hans and Oliver,
Thanks for the advice, it seems that it is simply the geometry definitions in
the dictionaries distributed with CCP4 6.4 are different to those calculated
from the atomic coordinates. For example, the chiral volume definitions in the
for the 4Fe4S cluster
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Deat CCP4ers,
In relation to this topic, I'd like to mention that SF4 has replaced FS4
as the Fe4S4 monomer in the CCP4 monomer library.
However, the dictionary values for bond lengths and angles are not
correct, and this is especially noticeable when the dictionary is used
in a high-resolution r
Hello,
I am wondering if anyone has experience or advice for my current situation:
I have a native dataset of a ~50kD protein complex at 2.4angstroms. One of the
members of the complex (~10kD) was able to be found easily by molecular
replacement. The space group was determined as P65. I was abl
Hi Gabriel,
what you want to do is called MRSAD - use the partial MR model to find the
sites, combine the phase information, and complete the model. There are hits
with the keyword MRSAD if you search on phenix-online.org
HTH,
Kay
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I’ve had success with MRSAD as Kay suggests. One option is to try putting
everything into Auto-Rickshaw. It can run multiple cycles of MRSAD,
auto-building a model for improved molecular replacement, finding new heavy
atom sites and repeating.
There is a paper on this available: http://dx.
I appreciate all of your responses and I will give your recommendations a try!
Thanks,
Gabriel
On Oct 13, 2014, at 1:50 PM, Kay Diederichs
wrote:
> Hi Gabriel,
>
> what you want to do is called MRSAD - use the partial MR model to find the
> sites, combine the phase information, and complet
Dear all (dear developers),
on a recent discussion on the phenixbb, Nat figured out that sftools
calculates the R-factor incorrectly as
"200*Sum|col1-col2|/sum(col1+col2)"
instead of
"100*Sum|col1-col2|/sum(col1)"
May I suggest to either correct this or not call it Rfactor in order to
avoid fu
Hi,
Since my crystallization condition contains PEG, I am trying to use PEG as
one of my cryo for testing. For example, one crystallization condition is
0.2M Na2PO4, 20%PEG3350. I want to make 0.2M Na2PO4 and 40% PEG3350 as
cryoprotectant. When I added 200ul salt from 1M stock, and 800ul PEG from
Hi Mayer and Jason,
Thanks for your quick reply! I read from Hampton that for PEG smaller than
5K, directly increasing its concentration is a way of making cryo. But
you're right, glycerol or PEG400 will be a good way and might be easier.
I'll try that first.
Thanks a lot!
Best,
Xiao
2014-10-13
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Hi Xiao,
what you run into here is a aqueous two phase system, phosphate and PEG tend to
form that, see wikipedia entry.
35% PEG 3350 is not a bad cryo, the combination with phosphate is just
unfortunate. Any chance you can replace with a different salt or buffer? I
don't know if adding small P
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