There isnt much evidence for twinning that I can see. Moments sensible,
Ltest sensible for untwinned data, some distortion of the cumulative
intensity plot but that could be due to integration problems.
Comparing Rfree in P3 is only proper if you have kept the same FreeR set
as you assigned in P321.
So I think you probably should stay with P321.
Eleanor
Parthasarathy Sampathkumar wrote:
Dear All,
Back ground:
This is my first experience with a twined dataset. Crystals belong to a
small domain of 132 aa, out of which ~40 residues appears to be disordered
(~30 of those from C-terminal and C-term His6 tag).
Initial space group: P3 with unit cell dimensions: 62.507 62.507 55.117
90.00 90.00 120.00; Resolution 2.35Angs.
Pointless suggested P321 (space group # 150) as possibility. I determined
structure by MR with Phaser (1 molecule in ASU). After several model
building and refinement cycles R and Rfree got stuck at 24.0% and 31.6%
respectively.
Therefore, I considered P3 space group (now Two molecules in the ASU) with a
twin component. I was only able to add handful residues to the model already
refined in P321. My current R and Rfree factors are 21.0% and 29.1%,
respectively for Two molecules refined in P3 space group.
Questions:
1. H-test in cTruncate suggested a twin fraction of 0.43 for the twin
operator -h-k, k, -l. Where as Refmac5 with Amplitude based twin refinement
gave an initial value of 0.508 for the same operator. Why these values are
different between cTruncate and Refmac5 (is this because I asked Refmac5 do
amplitude Twin refinement instead of Intensity based)?
2. I noticed in Refmac5 log file that twin fractions changes for every cycle
of refinement. During my most recent Refmac5 run Initial estimate of 0.508
for -h-k, k, -l operator changed to 0.504 at the end of 20th cycle. The
corresponding values were 0.519 and 0.529, respectively, in a previous
round. Since twin estimates were based on measured Intensities (in turn
amplitudes) why would they change with refinement (am I missing something
here)?
3. When I repeated my final round of Refmac5 WithOut Twin Refinement my R
and R-free factors are 22.9% and 28.6%, respectively, which also appears to
be OK for 2.35 Angs. data (in fact, slightly better R-free). These values
are likely to improve little bit after completing the solvent model. So, is
this crystal really twinned?
I have attached log files of cTruncate and most recent Refmac5 run with Twin
refinement. Apologies for attachments (at least no image files).
Thank you all in advance for educating me.
-Partha
