Dear Rui,
If your search model is itself a homodimer, you expect to find 2
equivalent solution
And indeed in your case:
50.3 + 128.6 = 178.3 (= aboput 180)
0.2 + 179.8 = 180
219.8 - 38.7 = 181.1 (= about 180)
indicating that both solutions are crystallographically equivalent.
What does worry me is the apparent special position that you obtain for
the translation solution. Are you sure you do not have a higher symmetry
or cetered space group?
Remy Loris
Vrije Universiteit Brussel and VIB
On 07/11/12 17:39, rui wrote:
Hi, Dear group,
I recently collected a dataset about 2.5 A and integrated with P4.
When I tried phaser I got a sol file looks like this, is this real
solution? Is LLG high enough?
SOLU SET RFZ=5.2 TFZ=10.3 PAK=0 LLG=239 LLG=366 TFZ==20.9
SOLU SPAC P 41
SOLU 6DIM ENSE ensemble1 EULER 50.265 0.217 219.800 FRAC 0.50029
0.49916 -0.00408 BFAC -0.04000
SOLU ENSE ensemble1 VRMS 0.639
SOLU SET RFZ=5.2 TFZ=10.0 PAK=0 LLG=239 TFZ==11.2 LLG=365
SOLU SPAC P 41
SOLU 6DIM ENSE ensemble1 EULER 128.607 179.813 38.677 FRAC 0.49991
0.49905 -0.00208 BFAC -0.06264
SOLU ENSE ensemble1 VRMS 0.642
Looks like there are two solutions,but in the output pdb file, I only
see one solution (homo-tetramer). So I took this output pdb and run
first round of refinement with Refmac, somehow, the structure fall
apart if I use restraint refinement( lots of atoms are not connected
any more ). If I use rigid body refinement, it's ok and Rfree is 52%.
Does that mean the solution might not be correct? What's the
acceptable Rfree for the initial refinement? Thanks a lot.
Rui
