Dear Petr Leiman :
It could be the result of series termination in anomolous map.(not sure)
The error in the position results in a shifted position in the 2Fo-Fc map.
As a check it is worthwhile to see an average of the two positions (three
coordinates)  results in a feature  consistent with Bijvoet Difference and
2Fo-Fc maps. But I do not know how this error affects just one site and
not others.
Best
Srinivasan Raghunathan
On Thu, 24 Apr 2014, Petr Leiman wrote:

Dear All,

We are looking for an explanation for a very strange observation.

Problem:
We have two fully independent data sets (two different crystals), in which the 
Bijvoet Difference Fourier map peak of one particular metal site is shifted by 
0.47 A from its position in the 2Fo-Fc map.

Relevant information:
The resolution of both data sets is 1.5-1.6 A.
The 2Fo-Fc and BDP maps are calculated using the same phases.
The metal ion is water hydrated and all the details are crystal clear in both 
2Fo-Fc maps.
The crystals are grown in the presence of Sr and the data sets are collected at 
the Sr K-edge.
There are many other Sr sites and all strong peaks in the BDF map overlap with 
2Fo-Fc map peaks perfectly. The Sr site in question is not the strongest, but 
it is well above the noise level of the BDF map.

Additional information:
The weird site is actually fully buried inside an internal cavity (it is 
surrounded by protein atoms from all sides), but a Sr atom is able to diffuse 
into this cavity somehow. All other Sr sites are on the surface of the protein.

Any thoughts about why a non-noise BDF map peak would not overlap with a 2Fo-Fc 
map peak are welcome!

Thank you very much,

Petr

------------------
Petr Leiman
EPFL
BSP 415
CH-1015 Lausanne
Switzerland
Office: +41 21 69 30 441
Mobile: +41 79 538 7647
Fax: +41 21 69 30 422


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