Dear All,
I wanted to check some structure using the validate server
http://deposit.pdb.org/validate/
In the validation summary file I got a list of close contacts
based on crystal symmetry:
---------------------------------------------------------------------------------------------------
==> Close contacts in same asymmetric unit. Distances smaller than 2.2
Angstroms are considered as close contacts.
none
==> Close contacts based on crystal symmetry. Distances smaller than 2.2
Angstroms are considered as close contacts.
Chain Atom Res Seq Chain
Atom Res Seq Symm_Code Distance
-------------------------------------------------------------------------
A OD2 ASP 58
- A O PHE 70 ( 2, 5, 5, 5) Dist = 0.13
A CA PRO 18
- A N LEU 82 ( 2, 5, 5, 5) Dist = 0.13
A C THR 63
- A C GLU 73 ( 2, 5, 5, 5) Dist = 0.23
A OH TYR 190
- A C GLY 131 ( 2, 5, 5, 5) Dist = 0.24
A NE ARG 159
- B OE2 GLU 20 ( 2, 5, 5, 5) Dist = 0.24
A CE1 TYR 154
- A N SER 130 ( 2, 5, 5, 5) Dist = 0.27
B OG SER 130
- B CB LYS 111 ( 3, 5, 5, 5) Dist = 0.33
A N GLY 164
- A CG2 VAL 167 ( 2, 5, 5, 5) Dist = 0.34
B CG2 VAL 188
- A N GLY 184 ( 3, 5, 5, 5) Dist = 0.35
A C GLY 14
- A CG TYR 41 ( 3, 5, 5, 5) Dist = 0.35
A OE2 GLU 50
- A CG2 THR 147 ( 2, 5, 5, 5) Dist = 0.35
A C LEU 127
- A OG SER 182 ( 2, 5, 5, 5) Dist = 0.36
A CB VAL 118
- A O GLY 164 ( 3, 5, 5, 5) Dist = 0.37
A CG ASN 120
- A O SER 83 ( 2, 5, 5, 5) Dist = 0.39
-----------------------------------------------------------------------------
Actually, the list is really long, a lot of such contacts.
My question: why a crystal structure would have all these bad
contacts?? Does it indicate that the space group (R 3) used to solve
the structure was not right??
I'd love to hear the comments from people having experiences with
structures solved in R3 sg.
regards,
Ibrahim
Ibrahim M.Moustafa, Ph.D.
Pennsylvania State University
Biochemistry & Molecular Biology Dept.
201 Althouse Lab.
University Park, PA16802
Tel (814) 863 8703
Fax (814) 865 7927
