I will try this but I performed molecular replacment with the same structure that has a simillar size ligand (Orthorhombic unit cell instead of monoclinic with different lengths and angles). I would be surprised if the changes were this large without any visible fo-fc density showing up.
On Thursday, April 17, 2014, Paul Adams <pdadams@lbl.gov> wrote:
Given the resolution you might want to try auto(re)building or morphing to see if there are any unexpected structural changes which explain the high R-factor.
On Apr 17, 2014, at 6:05 PM, Yarrow Madrona <amadrona@UCI.EDU> wrote:
> There is no significant peaks for translational NCS. I also didn't see anything in the patterson map.
>
> However, the Multivariate Z score L-test gives 6.218. Also the observed Centric reflections are more intense than they should be but I don't suspect twinning in a monoclinic space group.
>
> -Yarrow
>
>
> On Thu, Apr 17, 2014 at 4:37 PM, Paul Adams <pdadams@lbl.gov> wrote:
>
> What does triage say about translation NCS?
>
>
> On Thu, Apr 17, 2014 at 4:25 PM, Yarrow Madrona <amadrona@uci.edu> wrote:
> Hello,
>
> I using the latest stable build of phenx.refine (1.8.4) I recently collected data, processed and obtained an MR solution using phaser. I am stuck trying to refine with an Rfree sitting at 40%
>
> I really want to know if the high Rfree is due to poor data quality or if non-crystallographic symmetry involving a near perfect two fold rotation between the two molecules in the ASU could somehow impede refinement. Stats and other information is below. Thank you for any help you can give.
>
> -Yarrow
>
>
> Visually, the quality of the data is marginal at best (streaky/ice rings in many frames) despite good processing stats from XDS. Processing with mosflm or HKL2000 managed to index but failed pretty bad in integration and scaling.
>
> Phaser gave high TFZ scores for 2 molecules in the asu (see below).
>
> Density for a cholesterol like ligand shows up even though not present in the search model.
>
> MolRep Self rotation shows rotational symmetry.
> https://www.dropbox.com/s/2zsajl5o091k50r/CYP142A2-032814_21_rf%20copy.pdf
>
> The 2 molecules in the ASU are related by almost a 2 fold rotation:
>
> Rotation matrix for chain A to chain B:
>
> new_ncs_group
> rota_matrix 1.0000 0.0000 0.0000
> rota_matrix 0.0000 1.0000 0.0000
> rota_matrix 0.0000 0.0000 1.0000
> tran_orth 0.0000 0.0000 0.0000
>
> center_orth 15.2016 0.5245 33.7070
>
> rota_matrix -0.9860 -0.1636 -0.0309
> rota_matrix -0.1659 0.9511 0.2605
> rota_matrix -0.0132 0.2620 -0.9650
> tran_orth 34.3310 -24.0033 107.0457
>
> center_orth 15.7607 7.2426 77.7512
>
> RMSD, B onto A = 0.0007 after phaser
> RMSD, B onto A = 0.347 after one round of refinement in phenix
>
>
> Refinement using aniostropically corrected data (ucla web server: Services.mbi.ucla.edu/anisoscale) did not improve the Rfree in refinement.
>
>
> Statistics are listed below:
>
> UNIT CELL: 51.487 88.923 89.592 90 97.15 90 P21
>
> RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR R-FACTOR COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano
> LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr
>
> 5.99 8280 1927 2087 92.3% 3.1% 3.3% 8246 35.09 3.5% 99.8* 20* 0.909 1296
> 4.30 14606 3401 3487 97.5% 3.3% 3.5% 14580 33.37 3.8% 99.9* 11* 0.843 2273
> 3.53 17961 4244 4445 95.5% 3.8% 3.9% 17944 31.11 Building 80, Room 247
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