Re: [ccp4bb] R32 data

- Protein crystallography

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Protein-DNA complex prepartion for crystallization
From: Antony Oliver antony {- dot -} oliver {- at -} ICR {- dot -} AC {- dot -} UK
Date: 2008-10-02

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Subject: Re: SOme wquestions about refining.......
From: Kevin Cowtan cowtan {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-10-02

Subject: Re: R32 data
From: Peter Zwart PHZwart {- at -} LBL {- dot -} GOV
Date: 2008-10-02

Hi Josiah,

The primitive cell is what is important. The primitive cells for C2
and R32:H are the same as the P1 cell you report:

(using phenix.explore_metric_symmetry)

R32:H Niggli cell: (81.728198520053866, 81.728198520053866,
81.728198520053866, 84.166443879693517, 84.166443879693517,
84.166443879693517)
C2 Niggli cell: (81.537000000000006, 81.567520633215281,
81.567520633215281, 84.147871626167259, 84.163573178668059,
84.163573178668059)

Twinning, pseudo symmetry etc etc can all be possible, even if
intensity statistics indicate that things are fine.

P

2008/10/2 Josiah Obiero :
> Dear all,
>
> I have set of data (~2.7A). After indexing, HKL2000 suggests a
> rhombohedral space group or C centered monoclinic space group. I tried
> molecular replacement with R32 ( 109.55 109.55 155.28 90.00 90.00
> 120.00) and C2 (121.092 109.315 81.537 90.000 97.874
> 90.000) (both have good merging statistics), but did not get any
> solution. I also tried P1 ( 81.553 81.527 81.523 84.202
> 84.132 84.156) but did get any solution ( wt structure is known and
> the only difference with the wt structure is that the new structure is
> complexed with a smaller protein). I expect that there'll be some
> domain movement so searched for individual domains in phaser.
>
> The self rotation function in P1 showed both two fold and three fold
> peaks but they were both off the centre. The data does not appear to be
> twinned. I am curious to know if it is normal for cell dimensions to
> drastically vary from one space group to another. I am running out of
> ideas, could I be dealing with a wrong space group or pseudosymetry?
>
> Any suggestions would be appreciated.
>
> Thanks.
>
> Josiah.
>

--
-----------------------------------------------------------------
P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX: http://cctbx.sf.net
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CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Protein-DNA complex prepartion for crystallization
From: Antony Oliver antony {- dot -} oliver {- at -} ICR {- dot -} AC {- dot -} UK
Date: 2008-10-02

Next message:
Subject: Re: SOme wquestions about refining.......
From: Kevin Cowtan cowtan {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-10-02