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

[Tim Gruene]

Dear Shun,

finding the substructure is often the wider bottleneck than extending its 
phases and generating a decent map. And with 4.3A, autobuilding is quite 
certain to fail, I am afraid.

Did you compare solutions for the substructure from different programs, e.g. 
hyss, shelxd, sharp? If they coincide, at least you know that it is worth 
continuing with the solution and running density modification.

(I cannot comment on the impact of lattice translocation disorder).

Best,
Tim

On Tuesday, October 20, 2015 09:35:31 PM Shun Liu wrote:
> Dear Phenix 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   ]
> ----------------------------------------------------------------------------
> ---------------------- However, the tantalum sites we found 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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-- 
--
Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
OFLC/102
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A

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