[phenixbb] B-factor and phenix.refine+Occ+charge
Haytham Wahba
haytham_wahba at yahoo.com
Thu Jun 23 09:36:01 PDT 2011
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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