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

Wed Oct 21 06:33:02 PDT 2015

Hi Shun,

This sounds pretty challenging.  For a crystal with lattice-translocation disorder the amplitudes are basically all modified by a modulation factor depending on the translocation and the fraction of the crystal involved.  Jimin Wang and colleagues used a simple fitting procedure to identify these parameters for both isomorphous and anomalous data (Wang, J., Kamtekar, S., Berman, A. J. & Steitz, T. A. (2005). Acta Cryst. D61, 67–74).  It has also been used more recently (for example see https://www.sciencemag.org/content/suppl/2008/02/21/319.5866.1083.DC1/Tanaka-SOM.pdf).  It is possible that this could help in your case.

Note that for 4.3 A data where anomalous signal is very weak after about 6 A it is not so surprising that automate model-building would fail.  You might want to try and find a distantly related structure from the PDB and try to fit domains into your map to evaluate it.  You could then use morphing or mr_rosetta to try and improve the model.

All the best
Tom T

________________________________________
From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Shun Liu [sliu.xtal at gmail.com]
Sent: Tuesday, October 20, 2015 10:35 PM
To: phenixbb at phenix-online.org
Subject: [phenixbb] Tantalum anomalous signal of a low-resolution SAD   dataset with lattice-translocation disorder

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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