Dear all,
I am now trying to phase a structure in C2 using anomalous scattering at
5-6 A. It is hard to improve the derivative resolution at the moment.
Shelxd is able to locate 6 sites with a distinct CC and FOM. After density
modification in shelxe, the contrast of the two enantiomers is 0.59/0.
Hi all,
I have a 360 degree data set collect on home beam.
I used XDS to integrate the frames in P1.
I progressively merge the data from P1 to P2 or P1 to P3 in XDS and attach the
log below.
The cell looks like P3 and pointless suggest P6. But the Rmerge and Rmeas are
much higher than normal at
Hi all,
We run into an interesting space group problem. The same diffraction
image can be either indexed into space group C2, with a=145, b=44,
c=67, and beta=110.5; or space group P2 (should be P21 after
scaling), with a=67, b=44, c=136, and beta=96.8. Both are refined ok
during index. T
BTW, I forgot to mention that phenix.autosol also gave similar result.
On Mon, Mar 31, 2014 at 5:46 PM, Chen Zhao wrote:
> Dear all,
>
> I am now trying to phase a structure in C2 using anomalous scattering at
> 5-6 A. It is hard to improve the derivative resolution at the moment.
> Shelxd is a
Dear Chen,
how sure are you that your crystals contain the protein of interest? Repeatedly
washing harversted crystals in crystal stabilization solution followed by
SDS-PAGE coupled to appropriate staining protocols (e.g. Coomassie, Silver
staining) or western blotting can give a pretty conclus
Dear Savvas,
Thank you for your reply and your nice protocol. I am also worried of this
problem so I have already run my crystals on the gel for several times. The
result is so clean that you can hardly draw any other conclusions except
that the crystals are made up of the full-length molecule. Bu
additional info:
If I let xds go through, it will choose P6. actually pointless suggest P62/P64.
The thing is the Rmeas and Rmerge are significantly higher for P2/P3/P6 than
P1, especially the highest shell.
That indicates those higher symmetry ones are not the choice, it that right?
(Actually, th
Your symmetry is of family P6.
There is no dramatic difference between 7.8% and 9.3% of Rmerge
Go with pointless, wave reviewer nonsense.
BTW reviewer of what journal he is?
Dr Felix Frolow
Professor of Structural Biology and Biotechnology, Department of Molecular
Microbiology and Biotechnol
I thought there was a theoretical Rmeas number for I/sigma=2 that is around
50%? In my case, the Rmeas is much higher.
Before, we reported P62(4) and got rejected.
I'll just change a journal. Hopefully reviewer will not be too picky about
that.
Thanks to everyone!
It is definitely P6 or P3 with a twinning about the
unique axis. The differences in merging statistics between P2 P3 and P6 are
not very significant in my opinion.
On May 7, 2014, at 1:16 PM, wrote:
> additional info:
> If I let xds go through, it will choose P6. actually pointless suggest
Hello Rain Field,
I third Felix and Craig, there is nothing unusual about the statistics
table you present. The data look pretty good and I would assume
P6_something and integrate further than 3.1A.
Regards,
Tim
On 05/07/2014 08:16 PM, wrote:
> additional info:
> If I let xds go through, it wil
Hi,
please post the pointless table "Analysing rotational symmetry in lattice
group P 6/m m m". This gives a quite clear information about the
presence/absence of rotational symmetry axes.
Look at at the following example
Analysing rotational symmetry in lattice group P 6/m m m
--
Dear Junyu,
it looks to me like you encounter a classical monoclinic feature: one
can index monoclinic always in two ways
origin
|
V
A' -- A
\ /\
Take your c2 cell, go to niggli setting, double the c axis. apply
transform (-x+z,y-z,-z). now you end up with your P2 cell in the
niggli setting. you might have stromng pseudo translational symmetry
(or your unit cell is too big)
phenix.explore_metric_symmetry --unit_cell=145,44,67,90,110.5,90
What is the Rmerge in each case?
-James Holton
MAD Scientist
Junyu Xiao wrote:
Hi all,
We run into an interesting space group problem. The same diffraction
image can be either indexed into space group C2, with a=145, b=44,
c=67, and beta=110.5; or space group P2 (should be P21 after scaling)
Clemens is right of course. If you ignore the lattice centring in C2,
the cells are the same.
I was however under the impression that auto-indexing goes via the
primitive cell. Which makes the two solutions unique.
Ignoring the possible lattice translation in P2 will show up in a
Patterson functio
Dear all,
Thanks for all the advices. I am especially grateful to Dr. Clemens
Vonrhein, now I am clear about the relationship between this two
choices. Dr. Zwart raises another interesting point, which of course
is my major concern. C2 will have the advantage for phasing, since it
has a s
pseudo C2 centering in P21 will result in C2 systematic absenses being weak.
you can check this with e.g. dataman (parity check of even and odd
reflections of that type). and you will have that native patterson peak as
mentioned. this will make life bit more complicated of course since large
portio
. März 2014 23:46
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Space group problem?
Dear all,
I am now trying to phase a structure in C2 using anomalous scattering at 5-6 A.
It is hard to improve the derivative resolution at the moment. Shelxd is able
to locate 6 sites with a distinct CC and FOM
Betreff: Re: [ccp4bb] Space group problem
I thought there was a theoretical Rmeas number for I/sigma=2 that is around
50%? In my case, the Rmeas is much higher.
Before, we reported P62(4) and got rejected.
I'll just change a journal. Hopefully reviewer will not be too picky about
that.
T
rag von
Gesendet: Mittwoch, 7. Mai 2014 19:26
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Space group problem
Hi all,
I have a 360 degree data set collect on home beam.
I used XDS to integrate the frames in P1.
I progressively merge the data from P1 to P2 or P1 to P3 in XDS and attach the
log bel
>
>
> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von
> *Chen Zhao
> *Gesendet:* Montag, 31. März 2014 23:46
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [ccp4bb] Space group problem?
>
>
>
> Dear all,
>
> I am now trying to phase a structure
your unit
>> cell, or you find many more sites than you can explain, you should start
>> worrying about twinning. Even than the structure can probably be solved,
>> but then you need some real experts!
>>
>>
>>
>> My 2 cents,
>>
>> Herman
>>
>
looks ok except that the unit cell is rather crowded, I
>>> would go ahead and try to build the structure.
>>>
>>> However, if even a single protein molecule would not fit in your unit
>>> cell, or you find many more sites than you can explain, you should start
>
>>>> less? If everything looks ok except that the unit cell is rather crowded, I
>>>> would go ahead and try to build the structure.
>>>>
>>>> However, if even a single protein molecule would not fit in your unit
>>>> cell, or you
ular Biology
>University of Freiburg
>Stefan-Meier-Str. 17
>D-79104 Freiburg, Germany
>Tel: +49 (0) 761 203 52 77
>--
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>-Ursprüngliche Nachricht-----
>Von: CCP4 bulletin board [mailt
, assessment of the diffraction pattern etc.
Best,
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Nazia
Nasir Phd2009,ProteinCrystall.Lab
Gesendet: Dienstag, 1. April 2014 20:00
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] AW: [ccp4bb] Space group problem?
Dear Jurgen,
The
27 matches
Mail list logo
