Dear colleagues,
A symposium/exhibition celebrating 100 years of crystallography in the
International Year of Crystallography 2014 (www. iycr2014.org) will be
held in Innsbruck (Austria) on8-9 September 2014. It aims to feature
contributions from scientists having built the technical advances
Dear all,
I am trying to reproduce some protein crystals. The protein I am getting
after cutting the his tag is very pure. I am using the reported protein
concentration. The cofactor and EDTA needs to be added externally. The
condition has calcium acetate, peg 4k and sodium acetate buffer.
Hi,
you changed something, and although it seems very small a change, this
can make a difference between crystals and non-crystals. And removing
the His-Tag is not a small change, since it influences the net charge.
The first thing to try is micro and macro-seeding. If they don't work,
you may
Dear Colleagues,
we are pleased to announce the CCP4 structure solution school at the Photon
Factory, Tsukuba. All details can be found at
http://www.ccp4.ac.uk/schools/Japan-2014
Title:
CCP4 school: From data processing to structure refinement and beyond
Dates: November 4 to 8, 2014
Site:
Hmmm…not enough information but I am wondering about the EDTA plus Ca
business….the Ca++ ions are forming a strong chelate with the EDTA, so
depending on your molar ratios either the free Ca ions would be consumed by
EDTA or the EDTA by Ca …(?) – any variance
in ratio here might prove
You may unleash a deluge of anecdotes and horror stories, but this is quite
common. I have experienced this many times, and you just need to step back and
ask yourself what is being done differently:
1. Are all materials used in the preparation of the protein the same
(suppliers, sources,
Hi Alisa,
almost the right syntax. The last one is a list, i.e. it should read:
copy_residue_range_from_ncs_master_to_chains(0, C, 377, 402,[B])
... and make sure you have the mast chain set to C.
... and there was a similar discussion earlier:
'oil separation and light ppt' is not necesserily an indicator that
something is wrong with your crystallization condition. Actually,
there are quite a few proteins that only crystallize in conditions
with oil/water-like phase separation. Some crystals even appear WITHIN
the oily drops
Dear Katherine,
Thanks for pointing this out! As far as I can tell the community has not
reached a consensus on dealing with disordered side chains. I’m afraid it
simply didn’t occur to us, when we were writing the validation task force
report, that one approach would be favoured over the
Hi Robert,
Thanks for your interest in AMPLE and reporting this bug. There is a
small bug that has come about as a result of the latest MRBUMP update
last week that causes this problem. We're preparing a fix for it which
should be in the next ccp4 update towards the end of this week or early
There is some disagreement on terms used to deposit data. We need a definition
and an algorithm
for each definition.
Unique Reflections
My definition is all the possible reflections out to the high resolution
reported not related by symmetry.
Where can I find this? The .mtz contains a list
Dear all,
I have 3 short questions about PEG solutions:
Does anyone know the best way to store crystallization screening blocks that
contain PEG 3350?
Is it a good idea to freeze the PEG solutions at -80°C and thaw them before use?
Would the freeze-thaw process considerably alter the PEG chain
My preference is to use the term 'observed' for reflections whose
intensities have been integrated, and the term 'informative' for those
that satisfy some statistical criteria of being useful for structure
determination.
Programs like Truncate have hidden criteria of rejecting some observed
Hi Jerome,
-I have heard that PEG solutions can become unstable in light. We usually
store our block in the fridge, where photons are scant anyway. For any
stocks that I prepare, I wrap the tube/bottle in aluminum foil. I'm not
sure about freezing them.
-Some labs (not ours) evidently prepare
I don't think storage matters. I doubt Hampton stores their PEG stock
solutions at -80 before they ship out to customers.
I've solved tons of structures leaving my PEGS and PEG screens at RT in the
light.
Nick
On Mon, Jul 14, 2014 at 12:32 PM, Chris Fage cdf...@gmail.com wrote:
Hi Jerome,
Hi Alisa,
This is how I would do this.
1. In COOT got to Extensions -- Modelling -- Copy Fragment. In the dialog box
that opens change Atom selection to //C/350-402 then hit OK.
2. To move the newly created fragment into position in B, go to Calculate --
LSQ Superpose. Change Reference
Jerome,
Does anyone know the best way to store crystallization
screening blocks that contain PEG 3350?
I would recommend storing them in a fridge or a clean coldroom (mold-free).
Lower temperature and low light does help.
Is it a good idea to freeze the PEG solutions
at -80°C and thaw
I also used to store my PEG solutions in light, and my stocks do sit
out on the bench. I can't say for sure whether light or temperature
make a difference, but I like to heed what seem like superstitions in
crystallography to eliminate variables. We purchase our screens from
Qiagen, who suggests
Michael, Chris and Nick,
Thank you so much for your help.
-Jerome
Jerome Nwachukwu
jnwac...@scripps.edumailto:jnwac...@scripps.edu
On Jul 14, 2014, at 1:48 PM, R. M. Garavito
rmgarav...@gmail.commailto:rmgarav...@gmail.com wrote:
Jerome,
Does anyone know the best way to store
I have a pdb file for a non-protein having C 1 2/c symmetry. PyMol can't
recognize the spacegroup. Can someone recommend software that can apply the
crystallographic symmetry to give the full structure?
Richard Gillilan
MacCHESS
Cornell University
Dear Richard,
Coot shouldn't have an issue with non-Sohnke space groups. I used it to
build a structure in P-1.
If you want to edit the molecule, you could also try ShelXle, available
at http://ewald.ac.chemie.uni-goettingen.de/shelx/eingabe.php.
Best,
Tim
On 07/14/2014 10:26 PM, Richard
Thanks to all who responded so quickly! Coot worked.
Richard
On Jul 14, 2014, at 4:33 PM, Tim Gruene wrote:
Dear Richard,
Coot shouldn't have an issue with non-Sohnke space groups. I used it to
build a structure in P-1.
If you want to edit the molecule, you could also try ShelXle,
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Jealott's Hill, Bracknell, Berkshire, UK
We are seeking a highly talented and motivated crystallization scientist
who is enthusiastic about working on a wide variety of biological systems.
The successful candidate will have a strong background in structural
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As an emerging method, serial crystallography with bright micro-focused X-ray
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