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

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 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 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

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

-- -- Paul Scherrer Institut Dr. Tim Gruene - persoenlich - OFLC/102 CH-5232 Villigen PSI phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A