[phenixbb] B-factor and phenix.refine+Occ+charge

[Haytham Wahba]

June 23, 2011, 9:30 AM

Dear all

dimer in AU
average B factor 21
resolution: 1.78

each subunit shows 2 Tin atoms in the active site

B factor for 2 tin in chain A 15 and 19

but 

B factor for other 2 tin in chain B 30 and 41

41 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))

and 30 of the other one near phoshate (occ: 0.70)

1- i tried to change the occupancy or refine the occupancy for tin trying to reduce B factor (41)
it works (reduced to 30) but it gives me a +ve peak

what could i do to solve this problem??

2- other trial to define charge for that tin
HETATM 3241 
 SN   SN C   3       6.543  -2.139 -14.821  0.25 41.55          SN4+
but it was the same result.

--- is this definetion for that charge is OK or it is not enough in PDB file

--- is this way is understandable by phenix.refine?
i mean does phenix differentiate in refinment between SN, SN2+ and SN4+??


N.B: protein soaked in DimethylTindiBromide

Haytham Wahba
Biochemistry
UdeM
Canada

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