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CCP4BB  September 2009

CCP4BB September 2009

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Subject:

Rfactor got stuck with a data having alternate strong and weak reflections.

From:

Eleanor Dodson <[log in to unmask]>

Reply-To:

[log in to unmask]

Date:

Thu, 3 Sep 2009 09:33:35 +0100

Content-Type:

text/plain

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Parts/Attachments

text/plain (146 lines)

Yuan Cheng wrote:
> Eleanor Dodson wrote:
>> This phenonema doesnt necessarily mean you have lattice-tranlation 
>> defects - pseudo translations are quite common with perfectly good 
>> crystals.
>> Lattice translation defects usually imply your "crystal" has two or 
>> more layered different crystals in the beam.. It can be best detected 
>> by an analysis of the data statistics.
>>
>> Eleanor
>>
>>
>> Yuan Cheng wrote:
>>> Eleanor Dodson wrote:
>>>> You must have a pseudo translation vector of  ~ 0.02 0.5 0.0
>>>> That relates solution 1 and 2, and 3 and 4.
>>>>
>>>> That makes it hard to determine space group - there will be 
>>>> absences along 0k0 because of the translation so the space group 
>>>> could be P 2i 2 2i  or P2i 21 2i
>>>> But which ever SG it is thedata with k odd will be weak, and that 
>>>> means you will have a higher R factor.
>>>>
>>>>  Eleanor
>>>>
>>>>
>>>>
>>>>
>>>> Jerry McCully wrote:
>>>>> Dear all:
>>>>>
>>>>>           I am currently refining a structure solved by MAD and 
>>>>> somehow the R factor got stuck around 30% with 2.2 resolution.
>>>>>
>>>>>           There are four molecules in one ASU. Two had very good 
>>>>> density map and the other two were not equally good.
>>>>>
>>>>>           I tried using NCS during refinement but it did not help 
>>>>> much.
>>>>>
>>>>>          Then I checked my data. Actually I found that there are 
>>>>> alternate layers of strong and  weak reflections. THe crystal is 
>>>>> in a thin-plate shape with orthorombic space group.
>>>>>
>>>>>   Then I looked at my molecular replacement solution from Phaser 
>>>>> using my native data.
>>>>>
>>>>>           Actually phaser gave two sets of solutions, which showed 
>>>>> slightly different positions.
>>>>>
>>>>> You can also see that there is a translation inside the same set 
>>>>> of solution.
>>>>>
>>>>>
>>>>> SOLU SET  RFZ=12.8 TFZ=21.4 PAK=0 LLG=452 RFZ=10.7 TFZ=47.9 PAK=0 
>>>>> LLG=1693 RFZ=13.0 TFZ=47.6 PAK=0 LLG=2791 RFZ=10.7 TFZ=46.1 PAK=0 
>>>>> LLG=4045
>>>>> SOLU 6DIM ENSE ensemble1 EULER  184.052    0.185  175.770 FRAC 
>>>>> -0.49889 -0.00218 -0.00000
>>>>> SOLU 6DIM ENSE ensemble1 EULER  225.116    0.167  134.696 FRAC 
>>>>> -0.47056  0.49706  0.00051
>>>>> SOLU 6DIM ENSE ensemble1 EULER  359.333   31.677  180.633 FRAC  
>>>>> 0.75769 -0.71475 -0.14004
>>>>> SOLU 6DIM ENSE ensemble1 EULER  359.373   31.969  180.711 FRAC  
>>>>> 0.73074 -0.21423 -0.14108
>>>>> SOLU SET  RFZ=12.8 TFZ=21.4 PAK=0 LLG=452 RFZ=10.7 TFZ=47.9 PAK=0 
>>>>> LLG=1693 RFZ=13.0 TFZ=47.6 PAK=0 LLG=2791 RFZ=10.7 TFZ=47.3 PAK=0 
>>>>> LLG=4042
>>>>> SOLU 6DIM ENSE ensemble1 EULER  213.115    0.173  146.741 FRAC 
>>>>> -0.49931 -0.00269  0.00045
>>>>> SOLU 6DIM ENSE ensemble1 EULER  248.173    0.254  111.665 FRAC 
>>>>> -0.47091  0.49661  0.00101
>>>>> SOLU 6DIM ENSE ensemble1 EULER  359.399   31.602  180.578 FRAC  
>>>>> 0.75808 -0.71455 -0.13980
>>>>> SOLU 6DIM ENSE ensemble1 EULER  359.378   31.255  180.361 FRAC  
>>>>> 0.78370 -0.21555 -0.13830
>>>>>
>>>>>
>>>>>      I remember there is a discussion in CCP4bb about the same 
>>>>> topic with the focus of pseudo-symmetry or translational 
>>>>> pseudo-symmetry.             Can anybody give some troubleshooting 
>>>>> about my issue?
>>>>>
>>>>>      Thanks a lot and have a nice weekend,
>>>>>
>>>>> Jerry McCully
>>>>>
>>>>>
>>>>>
>>>>> _________________________________________________________________
>>>>> Windows Live: Keep your friends up to date with what you do online.
>>>>> http://windowslive.com/Campaign/SocialNetworking?ocid=PID23285::T:WLMTAGL:ON:WL:en-US:SI_SB_online:082009 
>>>>>
>>>>>   
>>> Hi Jerry,
>>>    I am having similar trouble with you. You might want to check out 
>>> this paper Acta Cryst.(2005) D61:67-74. It is about 
>>> lattice-tranlation defects and how to correct it. Hopefull it is 
>>> helpful!
>>>    Good Luck!
>>>
>>> Yuan
>>>
>>>
> Hi Eleanor,
>     Could you explain a little bit more about how to tell the 
> difference between pseudo-translational symmetry and lattice 
> translation defects? Thanks a lot!
>
> Yuan
>
>
Hmm - that is hard.. pseudo translation is relatively harmless - you 
have 2 or more molecules in the same orientation but in different 
positions in the unit cell, and the structure factors they generate will 
have some different properties.  For instance the 0k0 in your case will 
always have k=2n+1 weak because the translation is xt, 0.5,zt ( you can 
work that out from a SF equation if you like!)   And since the xt = 
0.02, ie is rather small, and zt = 0, at low resolution all the hkl with 
k=2n+1 will be weak.
use
hklview data.mtz and look at h0l then next level , next level etc and 
you should see this effect..
The only problem it gives in is determining the spacegroup. But phaser 
will usually sort that out as long as you let it test all SGs .

Lattice translation is effectively one form of twinning, you can 
visualise it as a set of crystals where that lattice are aligned in 2 
dimensions but there is slippage along the third. So each "reflection" 
is in fact the sum of two or more intensities and the twinning analyses 
should be valid. But as well you have the problem that some classes of 
reflections are very weak, in the same way as a pseudo translation 
affects the data.
And the twinning tests via moments, H test and Britten test are all 
distorted by the weak/strong pattern so really the only effective test 
is the L test, and that too can be badly distorted by anisotropy and 
other defects.

Apparently it is often possible to recognise a lattice defect by looking 
at the images, if you are good at that. Some classes of reflections will 
be very streaky ( where there is an overlap between the different 
crystal fragments) and others sharp. But once the data is integrated 
that information is lost.

Does that help?
Eleanor

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