Dear Randy,
Thanks very much for your detailed explanation and helpful advice. I have
run the phaser job just as you have said. This is the result.
The resolution of this dataset is 2.45A.
=
I added the three commands to phaser
Are your unit cell and SG correct? I think you maybe should reindex to get a
cell volume 25% of this one, and maybe SG P21
That patterson peak is enormous..
Eleanor
On 1 Aug 2012, at 08:45, Qixu Cai wrote:
> Dear Randy,
>
> Thanks very much for your detailed explanation and helpful advice. I hav
Dear Eleanor,
The cell dimensions of the dataset with tNCS are 63.995 75.459 128.860
90.00 90.00 90.00 in P 2 21 21 space group.
But for the other dataset without tNCS of the same protein, the cell
dimensions are 64.203 65.319 76.443 90.00 90.00 90.00 in C 2 2 21.
So the cell volume
Dear colleagues,
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Allosteric Regulation of Cell Signalling in Madrid, on 17-19 September 2012.
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Dear All:
I collected 5 data sets from one crystal and would like to process them
together.
Here is how I did:
In HKL2000, load the all data sets. "Index" each set. When I try
"Intergrate", the program automatically go through the whole data sets
there, and do not go through.
I then process dat
Hi All,
I'm currently working of a protein with a ferredoxin protein with
anIron-Sulphur cluster. I was harvesting some crystals the other day and a
piece of my scalpel blade broke off and ended up in the well solution. I Sealed
the well without noticing, the shard of iron oxidised and the crys
The data sets were collected from the same crystal by "scan" collecting 40
frames from each section. The space group of this crystal is P2.
My guess that I may have to index and integrate each set indivadually, and
then scale them together.
Thanks
Uma
On Wed, Aug 1, 2012 at 9:01 AM, Machius, Mi
Take a look at http://en.wikipedia.org/wiki/Great_Oxygenation_Event
This might suggest you may have used up the available oxygen.
If you would like to try growing your crystals in an oxygen-free
environment, we (in Leicester) have a glove box with a Douglas Instruments
Oryx 4 robot. I know its n
Hi
I'd process (i.e. index, refine, integrate) each data set
individually, check that (at least) they all have the same crystal
system, then combine the datasets using Pointless. Then scale with
Aimless.
Of course, I'd use Mosflm/Pointless/Aimless rather than HKL, but
that's another que
Hi,
To me this looks like a simple redox displacement reaction which has
nothing to do with oxygen. E.g. if one puts a piece of iron in a
coppersulfate solution, the more noble copper ions take electrons from
the less noble iron and will come out of solution as a metal, while the
less noble iron
Note that neither Aimless nor Scala will do a particularly good job at scaling
data from Denzo or Scalepack, since the output files from Scalepack are missing
essential geometrical information. They work well with data from Mosflm or XDS
(or Saint) (although AFAIK the XDS & Saint scaling program
Please correct me if I am wrong:
The HKL is not good to combine multiple data sets, even they are come from
the same crystal?
With HKL, I also tried this way:
Index, integrate each data set individually, they all have the same space
group.
Then scale them together.
Still, the graph from scale o
Hi Umu,
apart from the other suggestions: you could also give autoPROC
(www.globalphasing.com and proc-deve...@globalphasing.com) a try -
which should deal with such a scenario automatically ... if the image
headers are correct ;-)
Please let us know, if you want more details off-list ...
Cheers
Hi
I don't think Phil or I are saying that HKL is not a good tool to use
in this case - but
(*) I develop Mosflm, so I have a certain bias.
(*) As far as Pointless and Aimless are concerned, to get the best
out of them you need to have some geometrical information that the
authors of HKL
Dear All:
I try to use Phaser to solve the structure by Molecular Replacement.
The data set is collected @180 degree. I process the data using HKL, and
have resonable good score: rejection (0.05), Linear R-factor (0.038),
completeness (98.3), resolution (50-1.5).
I then use Phaser to do MR. The
On Wed, Aug 1, 2012 at 11:27 AM, Uma Ratu wrote:
> The protein is in tetramer form. I define this by using the residue number
> (1332) which is 4 x monomer.
>
> After run, Phaser only gave 9 partial solutions, and no solution with all
> components. The resulted PDB contains only dimer form of the
Hi CCP4BBers,
I have a protein crystallized with 0.2mM Mg acetate and PEG 8000 or 0.1mM
cacodylate, pH 6.5, 0.2 Mg acetate, PEG 3350. Both of the conditions gave
triangle pyramid like crystals. I brought the crystals to synchrotron using 30%
PEG 400 as cryoprotactant, the resolution was only be
Have you tried different cryoprotectants? Can make a huge difference. Also,
have you shot an xtal at room temp - to see what the intrinsic diffraction
limit is? Additive screens? If all else fails you may well need to explore a
different expression construct.
Tony.
Sent from my iPhone
On 1
I notice one thing with my data sets.
The unit cells is slightly different from each other. For example, one has
a/b/c @ 79/126/83. The other has a/b/c @ 84/127/90. Although they are
collected from the same crystal.
Is this the reason that I can't index both with same parameter in HKL? And
subseq
Hi Uma,
I've used HKL2000 to combine datasets from different crystals, so it's
definitely possible to do so (although depending on the data volume it
may be better to deal with scalepack directly).
There are two things that you don't mention about your data - the
(approximate) resolution, an
> The unit cells is slightly different from each other. For example,
one has
> a/b/c @ 79/126/83. The other has a/b/c @ 84/127/90.
Although they are
> collected from the same crystal.
This is very substantial difference and with unit cell expanding by ~20%
one would expect scaling problems. Try
You might be killing crystals with the cryosolvent. Try soaking the
crystals briefly in well solution + 25-30% glucose or sucrose prior to
flash cooling. You can also try other cryoprotectants: glycerol, EG, etc.
You can also try sequential brief soaks in gradually increasing
cryoprotectant concent
Hi,
Thanks for the kindly answers from everyone. I actually haven't tried different
cryoprotectants. I might will give a try next time. I usually only use mother
liquor+30% PEG400. It is noticeable that it has some "patterns (cracks (?))" on
the crystal. However, it didn't form icy rings or etc
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