B-factor and phenix.refine+Occ+charge
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
i mean does phenix differentiate in refinment between SN, SN2+ and SN4+?
In the phenix.refine log file look for this section:
============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 4 Type Number sf(0) Gaussians Zn2+ 1 27.88 1 O 20 7.97 2 N 12 6.97 2 C 33 5.97 2 sf(0) = scattering factor at diffraction angle 0. The "Type" is exact including charge. The label is one of the entries from Int Tab Vol C Tab. 6.1.1.4. For SN this is your list above (SN, SN2+, SN4+). Ralf
Hi, some typical things to try in this situation: - refine occupancy and B of Sn starting with different (reasonable) values; - make sure the input PDB file contains charge and phenix.refine did recognize it (check log file as Ralf suggested); - try refining anisotropic ADP for Sn only. - 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. Pavel. On 6/23/11 9:36 AM, Haytham Wahba wrote:
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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participants (3)
-
Haytham Wahba -
Pavel Afonine -
Ralf Grosse-Kunstleve