Re: [ccp4bb] Nearly perfect twinned data????

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

Previous message:
Subject: Re: Past CCP4 meeting on problem structures
From: "P {- dot -} J {- dot -} Briggs" p {- dot -} j {- dot -} briggs {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-09-27

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Subject: SHELXL - FMN parameterization problem
From: Jonathan Elegheert jonathan {- dot -} elegheert {- at -} UGENT {- dot -} BE
Date: 2007-09-27

Subject: Re: Nearly perfect twinned data????
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-09-27

1) You dont say whether there is a non crystallographic translation
vector - if that is so the twinning statistics can be misleading.
SFCHECK analyses this or you can just run a native patterson to 4A say
and see if there is an off-origin peak.

2) The twinning tests that use the correlation between possibly
"twinned" reflectons ( ie hkl and kh-l for tetragonal) always say your
data is twinned if the true symmetry IS 422 when hkl and kh-l are
symmetry equivalents.. (They should say - either twinned or with a
higher symmetry..)

3) I believe in the moments plotted in TRUNCATE providing there isnt a
non crystallographic translation vector..

Eleanor

Joe Smith wrote:
> Hi all,
>
> We have collected few X-ray data sets for a protein-RNA complex to
> resolutions of 3.2-3.5A. While processing the data using HKL2000, we
> have obtained following distortion index consistently:
>
> primitive cubic 19.16% 127.98 74.67 130.85 74.57 85.00 73.91
> 111.17 111.17 111.17
> 90.00 90.00 90.00
>
> I centred cubic 24.26% 132.28 189.90 127.98 120.33 85.97 120.47
> 150.05 150.05 150.05
> 90.00 90.00 90.00
>
> F centred cubic 22.17% 177.47 190.41 189.90 46.24 90.79 91.90
> 185.93 185.93 185.93
> 90.00 90.00 90.00
>
> primitive rhombohedral 16.32% 130.85 129.06 174.88 131.21 133.20 86.12
> 144.93 144.93 144.93
> 116.85 116.85 116.85
> 229.30 229.30 74.67
> 90.00 90.00 120.00
>
> primitive hexagonal 15.40% 130.85 127.98 74.67 106.09 74.57 95.00
> 129.41 129.41 74.67
> 90.00 90.00 120.00
>
> primitive tetragonal 9.40% 127.98 130.85 74.67 74.57 106.09 95.00
> 129.41 129.41 74.67
> 90.00 90.00 90.00
>
> I centred tetragonal 0.91% 177.47 174.88 74.67 90.21 88.59 91.47
> 176.18 176.18 74.67
> 90.00 90.00 90.00
>
> primitive orthorhombic 9.38% 74.67 127.98 130.85 85.00 105.43 106.09
> 74.67 127.98 130.85
> 90.00 90.00 90.00
>
> C centred orthorhombic 6.53% 74.67 245.95 130.85 89.44 105.43 89.13
> 74.67 245.95 130.85
> 90.00 90.00 90.00
>
> I centred orthorhombic 0.84% 74.67 174.88 177.47 88.53 91.41 90.21
> 74.67 174.88 177.47
> 90.00 90.00 90.00
>
> F centred orthorhombic 0.68% 74.67 245.95 252.32 89.16 88.86 89.13
> 74.67 245.95 252.32
> 90.00 90.00 90.00
>
> primitive monoclinic 6.52% 74.67 130.85 127.98 95.00 106.09 74.57
> 74.67 130.85 127.98
> 90.00 106.09 90.00
>
> C centred monoclinic 0.49% 74.67 245.95 130.85 89.44 105.43 89.13
> 74.67 245.95 130.85
> 90.00 105.43 90.00
>
> primitive triclinic 0.00% 74.67 127.98 130.85 85.00
> 74.57 73.91
>
>
> As you see, distortion index table indicates I centered tetragonal, I
> centered orthorhombic, F centered orthorhombic, C centered monoclinic
> and triclinic as possible Bravais lattices.
>
> Data processed in I centered tetragonal gives low Rmerge in all the
> possible space groups namely I4, I41, I422 and even I4122. Other
> space groups in lower symmetry lattices also gave low R merge values
> (around 6% in most of the cases).
>
> Since we have not been able to obtain a solution in any of the space
> group from I centered tetragonal to triclinic (I4, I4122, I222, C2 and
> even P1) using Se-SAD, we decided to check the data for any intrinsic
> problem such as twinning.
>
> Cumulative intensity distribution calculated using scalepack2mtz shows
> no sign of twinning. However, data processed in I4 shows nearly a
> perfect twin (twin fraction=0.489 with twin operator 100 0-10 00-1) in
> Yeates server whereas SFcheck indicates a twin fraction of 0.431 with
> twin operator –h,+k,-l. Data processed in I4122, I222, C2 and P1
> doesn't show any twinning due to absence of any twin laws for these
> space groups.
>
> Now my question is:
> - Are data showing low Rmerge value in I4122 due to nearly perfect
> twin in space group I4?
>
> - Why cumulative intensity distribution shows a normal pattern for
> the data where as Yeates server and SFcheck indicates nearly a perfect
> twin? Why Yeates server and SFCheck shows different twin fraction and
> twin operator?
>
> - Is it possible to detwin this data and use it for structure solution?
>
> Thank you for reading till this line and I am sorry for such a long
> mail. I hope I haven't made any mistake at any stage. I really need
> your valuable suggestions to solve this problem.
>
> Regards
> Joe
>
>
>
>

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

Next message:
Subject: SHELXL - FMN parameterization problem
From: Jonathan Elegheert jonathan {- dot -} elegheert {- at -} UGENT {- dot -} BE
Date: 2007-09-27