[phenixbb] [ccp4bb] Tantalum anomalous signal of a low-resolution SAD dataset with lattice-translocation disorder

Christian Roth christianroth034 at gmail.com
Wed Oct 21 14:32:50 PDT 2015


Hi,

difficult to say why it doesn't work. Generally as mentioned already 
automatic model buildíng will most likely fail at this resolution. 
However why do you think your sites are wrong? Ta-cluster are  regular 
compounds and the sites should fit with the geometry of the cluster at 
least.
Anyway, molecular replacement using anomalous differences and the 
cluster as search model might work in that case as well, if direct 
experimental phasing fails.

Cheers

Christian


Am 21.10.2015 um 05:19 schrieb Shun Liu:
> Dear CCP4 colleagues,
>
> We are working on a Ta6Br14 cluster-SAD dataset (4.3 angstroms) with lattice-translocation disorder (with a total Rmerge of 0.16). Both SHELXC and Xtriage gave the similar positive result about the anomalous signal (See below).
>
> -------------------------------------------------------------------------------------------------
>   Resl.   Inf.  9.58  7.61  6.65  6.04  5.61  5.27  5.01  4.79  4.61  4.45  4.31
>   N(data)    1427  1410  1410  1409  1385  1452  1367  1399  1367  1395  1385
>   <I/sig>    76.3  52.1  26.7  13.7   8.7   6.1   5.1   5.0   3.9   2.7   1.8
>   %Complete  98.8  99.9 100.0  99.9 100.0 100.0 100.0  99.9  99.7  99.6  95.8
>   <d"/sig>  11.67  9.67  6.12  3.73  2.50  1.59  1.21  0.99  0.84  0.79  0.68
> ------------------------------------------------------------------------------------------------
> unused:         - 49.7669 [   0/29  ]
> bin  1: 49.7669 -  9.2629 [3086/3100]  0.8212
> bin  2:  9.2629 -  7.3599 [3031/3031]  0.7689
> bin  3:  7.3599 -  6.4318 [3073/3073]  0.5380
> bin  4:  6.4318 -  5.8447 [3071/3075]  0.2933
> bin  5:  5.8447 -  5.4263 [3054/3054]  0.1230
> bin  6:  5.4263 -  5.1067 [3070/3071]  0.0363
> bin  7:  5.1067 -  4.8512 [3038/3039]  0.0126
> bin  8:  4.8512 -  4.6402 [3028/3048]  0.0074
> bin  9:  4.6402 -  4.4617 [2955/3037]  0.0021
> bin 10:  4.4617 -  4.3078 [2730/3059]  0.0000
> unused:  4.3078 -         [   0/0   ]
> --------------------------------------------------------------------------------------------------
> The Tantalum sites and the initial map seem ambiguous, with which automatic model-building failed.
> I am wondering whether the lattice-translocation disorder of the dataset impacts the reliability of the anomalous signal, tantalum sites and the initial map. If it does, how can we decrease its impact? If it doesn't, is it possible to find the accurate Ta sites and generate an interpretable map suitable for model-building with this dataset? (After all, it has been reported that Ta sites can be found at 6A resolution.)
>
> Any suggestion and comment will be highly appreciated!
>
> Best,
> Shun
>

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