Hi ,
Please help me on this structure:
Data 1.8A: cell 84.892 84.892 172.580 90 90 90 with tetrahedral index
Space group: P43212 or P43, Final refinement Rfree indicates P43 is better
so most likely P43(also the systematic absence indicate P43 is it)
Matthew coeffient indicates: P43 3mol/a.u(2.58,52%) 2mol/a.u(3.87, 68%)
MR: Both Molerep and Phaser find out 2mol/au initially. Refinement reaches
Rfree 30% , R 27% finally. WE think, comparing with 1.8 resolution, The R
and Rfree are too high. Also considering the 1.8A resolution, there
should be 3 molecules in total. So we engaged into the effort to find out
the 3rd molecule.
Phased MR by MOLREP did find out the 3rd, so did
Phaser(fix two, find out the 3rd). Both solutions gave relatively poorer
statistics but packing is perfect. The 3rd molecule, solved by phased
MR of MOLREP and PHaser respectively, can not superpose showing
slightly different orientations, but position is similar.
Refinement indicates PHased MOLREP MR gives lower Rfree.
Using totally 3 molecule, When I restrain or constrain NCS during
refinement(used TLS),R free goes way up (R~30, Rfree > 36%). If I refine
without NCS,R factors slip right away to 27/30 but this strange thing
happens: two copies of the original solution refines very well -
low B factors,very good looking map. The 3rd copy, however, B factors
are high and the map is bad, no good density match with the model.And the
3rd molecule did no help to Rfree or R.
Story ends with my questions:
1,It seems the 3rd copy non-exist or globally disordered, under this
circumstance, can I say 'because of the 3rd molecule is globally
disordered so Rfree and R stay high (2mol/a.u with Rfree 30% R 27%, 1.8A
data)?
2,Anything I should worry about in the process finding out the 3rd?
3,Are there suggestions to further lower down Rfree (the reasonable Rfree
should be around 22%)?
THANKS
Yanming
