Dear all,
Sorry for a non purely crystallographic question.
I am working on an enzyme which binds Fe2+ cations to catalyzes an
FeII-dependent hydroxylation reaction.
Because of fast oxidation in presence of the enzyme, it is very difficult to
soak Fe2+ ions into the crystals. We succeed only
On Tue, 30 Sep 2014 13:29:02 +0100, Phil Evans p...@mrc-lmb.cam.ac.uk wrote:
Be careful: the International Tables space group number may be ambiguous. For
example sg number 18 may refer to P 21 21 2 or its permuted settings P 21 2 21
or P 2 21 21, if you follow the proper IUCr convention that
Hi Tatiana,
Your problem is most reminiscent to the problem that Max Perutz faced when he
dealt with deoxy-haemoglobin crystals, but in those days only mounting in
capillaries was the way to bring the crystals to the beam, so he used
dithionite, just like you, but mounted the crystals in
I second that! The default should be symmetry based... cells stretch
and shrink, but symmetry is harder to change. (i.e. from crystal to
crystal.)
(I thought all CCP4 programs have supported this for ages.)
On 02/10/2014 10:25, Kay Diederichs wrote:
On Tue, 30 Sep 2014 13:29:02 +0100,
The strange thing is that small molecule crystallographers do not suffer
from this problem, because they don't use space group numbers! This is
just as well, because instead of just 8 combinations of primitive
orthorhombic space groups and settings, they have to consider 111 (if I
have
How does XDS decide on eg P 21 21 2 when say c b a? The initial indexing
may decide that the cell fits a primitive orthorhombic system, but I presume
that it will then have some convention, probably a b c, since the
identification of screws can only be done after integration, and even then
Hello everyone
I request you to please tell me the 3 letter code for p nitrophenyl
phosphate..
--
Regards
Faisal
School of Life Sciences
JNU
Hi, we shouldn't be using numbers at all (CCP4-style or otherwise, since
no-one else outside the MX community uses these). We should be using the
unique full Hermann-Mauguin symbol, since the 'standard setting' space
group number in IT obviously does not uniquely define the setting, and it's
the
Dear Tatania,
Without having the details, it is difficult to make specific comments, but here
are some suggestions:
Aerobic experiments: you claim that added Fe2+ immediately oxidizes when added
to a buffer containing 5 mM Fe2+. That means that the 5 mM Fe2+ in your buffer
was already
On 02/10/14 11:50, Faisal Tarique wrote:
I request you to please tell me the 3 letter code for p nitrophenyl
phosphate..
No. But here's how to find it yourself:
Go to rcsb.org
nitrophenyl phosphate - Search
Top hit in Chemical Name table.
or similarly File - Search Monomer Library in
I took the liberty of googling this for you. I trust that other search
engines will give the same answer. Try your favorite next time.
http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/complete/4NP
Andreas
On 02/10/2014 11:50, Faisal Tarique wrote:
Hello everyone
I request you
Thank you..i got it
On Thu, Oct 2, 2014 at 5:04 PM, Andreas Förster docandr...@gmail.com
wrote:
I took the liberty of googling this for you. I trust that other search
engines will give the same answer. Try your favorite next time.
When I google 3 letter code for p nitrophenyl phosphate the second site
listed is:
http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/complete/4NP
Which looks like it might contain the answer you seek.
HTH,
Dave
[image: David Briggs on about.me]
David Briggs
about.me/david_briggs
Hi Faisal
The 3letter code for p nitrophenyl phosphate would be 4NP
http://www.rcsb.org/pdb/explore/explore.do?structureId=1D1Q
On Thu, Oct 2, 2014 at 4:20 PM, Faisal Tarique faisaltari...@gmail.com
wrote:
Hello everyone
I request you to please tell me the 3 letter code for p nitrophenyl
Hi Faisal,
You can also look in LigandExpo http://ligand-expo.rcsb.org/index.html
If you don't find a result immediately, you can also search by formula, even
without hydrogens.
Cheers,
Robbie
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Dear Tatiana,
Having worked also worked on various Fe(II) dependent hydroxylases, may I
suggest trying some other less redox sensitive divalent cations? My old lab
routinely used to screen hydroxylases with (to my knowledge) Co and Mn,
which essentially inhibited enzymatic turnover, so they were
With the successful introduction of racemic crystallization to
macromolecular, a large number of possible space groups have been opened
up to this audience. You can find examples in the PDB of space groups P
-1 (i.e. P 1-bar), I -4 2 d, etc.
On 10/02/14 06:51, George Sheldrick wrote:
The
Yes, we ran into exactly that issue as well.
Jūrgen
..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Streetx-apple-data-detectors://4, W8708
On Thu, 2 Oct 2014 11:38:08 +0100, Phil Evans p...@mrc-lmb.cam.ac.uk wrote:
How does XDS decide on eg P 21 21 2 when say c b a? The initial indexing
may decide that the cell fits a primitive orthorhombic system, but I presume
that it will then have some convention, probably a b c, since the
Thank you every one..
On Thu, Oct 2, 2014 at 5:27 PM, Robbie Joosten robbie_joos...@hotmail.com
wrote:
Hi Faisal,
You can also look in LigandExpo http://ligand-expo.rcsb.org/index.html
If you don't find a result immediately, you can also search by formula,
even
without hydrogens.
On Thu, 2 Oct 2014 11:58:42 +0100, Ian Tickle ianj...@gmail.com wrote:
Hi, we shouldn't be using numbers at all (CCP4-style or otherwise, since
no-one else outside the MX community uses these). We should be using the
unique full Hermann-Mauguin symbol, since the 'standard setting' space
group
I'm still a bit confused about why there is a problem: why use SG numbers? P 2
21 21 (or indeed P22121) is clear and unambiguous. There is no need to use
the numbers (and certainly not the weird CCP4 numbers like 3018 which I was
trying to hide in Pointless
Phil
On 2 Oct 2014, at 15:04, Kay
Dear Sjors,
In 3D auto-refine routine, what does the flatten-solvent option does?
Specifically, i'd like to know is there a mask involved and if yes, what kind
of mask?
Thanks for this and for your explanations in Grenoble.
Isai
On 2 October 2014 13:51, Kay Diederichs kay.diederi...@uni-konstanz.de
wrote:
I don't see any sticking to initial indexing as worthwhile to worry
about, since in the first integration, P1 is often used anyway, and it is
quite normal (and easy) to re-index after the intensities become
Dear ccp4bb,
Another easy method to find and/or generate ligands is via the smiles code:
Wikipedia has smiles codes for many compounds:
http://en.wikipedia.org/wiki/Para-Nitrophenylphosphate
look up the smiles code:
smiles: C1=CC(=CC=C1[N+](=O)[O-])OP(=O)(O)O
You can now generate the cif file
Watch out with oils and oxygen. Oxygen is fairly soluble in oils. When we
worked on deoxyhemerythrin, we had to degas our sealing wax to keep things
anaerobic. If you heat wax, and then put it in a vacuum, it'll froth as all
the gases come out of the liguid. Then of course it hardens and
Hi Phil,
as far as I understand, you are stating a consensus (do not use
numbers, do use the Hermann-Mauguin-symbols), rather than a problem. The
problem seems that the artificial space group numbers 1018, etc.,
contained in symop.lib, do not follow the consensus and thus cause
irritation.
Best,
How can it be if you're not even sure what the correct space group is?
Ambiguities may arise in the presence of pseudosymmetry and/or packing
disorders. In some cases, you can determine crystal structure from the
same data in different space groups that do not have subgroup/supergroup
I would be grateful for any advice on how to obtain refmac information
equivalent in detail to the shelxl Disagreeable restraints before
cycle N listing. In the later stages of refining a set of related
structures, I have been alternating between shelxl and refmac. Typically
this relies on
Dear Alistair,
Erratic behaviour is often caused by the antibumping restraints because
they get switched off and on, and riding hydrogens and changes in the
occupancies can affect their action. This probably applies to both programs.
Any suggestions for improving the bulk solvent model in
On Thursday, 02 October, 2014 12:07:54 Alastair Fyfe wrote:
I would be grateful for any advice on how to obtain refmac information
equivalent in detail to the shelxl Disagreeable restraints before
cycle N listing.
This is controlled by the MONI keyword.
To get a full list on every cycle
On Thu, 2 Oct 2014 16:00:30 +0100, Ian Tickle ianj...@gmail.com wrote:
On 2 October 2014 13:51, Kay Diederichs kay.diederi...@uni-konstanz.de
wrote:
I don't see any sticking to initial indexing as worthwhile to worry
about, since in the first integration, P1 is often used anyway, and it is
Dear ccp4bb,
I am having an issue with low resolution shell when converting unmerged
data from Scalepack using Aimless.
My data has a resolution of 30- 2.6 angstroms as written in the .sca file.
However, when I convert it to mtz using Aimless the resolution changes
automatically to 91.46 - 2.6.
I would like to add that this happens only when the Ensure unique data and
add R free column flag is ON.
I tested this on both Linux and Mac Maverick systems.
Thanks again!
On Thu, Oct 2, 2014 at 8:15 PM, Alisa Glukhova alis...@umich.edu wrote:
Dear ccp4bb,
I am having an issue with low
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