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Hi,<br>
<br>
some typical things to try in this situation:<br>
<br>
- refine occupancy and B of Sn starting with different (reasonable)
values;<br>
- make sure the input PDB file contains charge and phenix.refine did
recognize it (check log file as Ralf suggested);<br>
- try refining anisotropic ADP for Sn only.<br>
- a somewhat higher ADP for Sn compared to surrounding atoms is not
too unexpected as it is an "isolated" atom (not covalently bonded to
other atoms), and therefore can be more mobile.<br>
<br>
Pavel.<br>
<br>
<br>
On 6/23/11 9:36 AM, Haytham Wahba wrote:
<blockquote cite="mid:940871.56101.qm@web113808.mail.gq1.yahoo.com"
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June 23, 2011, 9:30 AM<br>
<blockquote style="border-left: 2px solid rgb(16, 16,
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<td style="font: inherit;" valign="top">Dear all<br>
<br>
dimer in AU<br>
average B factor 21<br>
resolution: 1.78<br>
<br>
each subunit shows 2 Tin atoms in the active
site<br>
<br>
B factor for 2 tin in chain A 15 and 19<br>
<br>
but <br>
<br>
B factor for other 2 tin in chain B 30 and <span
style="font-weight: bold; color: rgb(255, 0,
0);">41</span><br>
<br>
<span style="font-weight: bold; color:
rgb(255, 0, 0);">41</span> for tin which is
between the 2 cysteine (photo attached) (occ:
0.25) this one which i am worry about
((because the average B factor for the
surrounding amino acid is 20))<br>
<br>
and 30 of the other one near phoshate (occ:
0.70)<br>
<br>
1- i tried to change the occupancy or refine
the occupancy for tin trying to reduce B
factor (41)<br>
it works (reduced to 30) but it gives me a +ve
peak<br>
<br>
what could i do to solve this problem??<br>
<br>
2- other trial to define charge for that tin<br>
HETATM 3241 SN SN C 3 6.543 -2.139
-14.821 0.25 41.55 <span
style="font-weight: bold;">SN4+</span><br>
but it was the same result.<br>
<br>
--- is this definetion for that charge is OK
or it is not enough in PDB file<br>
<br>
--- is this way is understandable by
phenix.refine?<br>
i mean does phenix differentiate in refinment
between SN, SN2+ and SN4+??<br>
<br>
<br>
N.B: protein soaked in DimethylTindiBromide<br>
<br>
Haytham Wahba<br>
Biochemistry<br>
UdeM<br>
Canada<br>
<br>
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