Hi Brent,
I forgot to mention the resolution and other statistics. Here they are (XDS
-unmerged data P2 below). Overall completeness is 93.4(85.2)% for 2.2A.
I do have some anisotropy in the b-direction. I have tried running phaser
with data scaled by the UCLA anisotropy server and obtained the same
results.
-Yarrow
SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION
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
6.40 4788 1487 1718 86.6% 2.7% 2.9%
4675 33.78 3.2% 99.8* 20* 0.895 873
4.60 8644 2667 2852 93.5% 3.0% 3.1%
8511 30.77 3.6% 99.8* 9 0.856 1461
3.78 10659 3301 3598 91.7% 3.0% 3.1%
10559 31.05 3.6% 99.8* 0 0.789 1747
3.28 12398 3874 4261 90.9% 3.7% 3.7%
12319 25.46 4.4% 99.7* -4 0.779 1981
2.94 14970 4587 4766 96.2% 4.8% 4.9%
14886 20.15 5.8% 99.7* -2 0.779 2476
2.69 16718 5129 5292 96.9% 6.7% 6.9%
16638 15.44 8.1% 99.4* -2 0.767 2681
2.49 17842 5536 5722 96.7% 9.3% 9.4%
17734 11.89 11.1% 98.9* -2 0.755 2779
2.33 19743 6017 6133 98.1% 12.0% 12.6%
19623 9.27 14.3% 98.4* -4 0.737 3132
2.20 16777 5566 6533 85.2% 17.4% 16.9%
16420 6.77 21.2% 96.8* -8 0.749 2334
total 122539 38164 40875 93.4% 5.3% 5.4%
121365 17.41 6.4% 99.7* -2 0.776 19464
NUMBER OF REFLECTIONS IN SELECTED SUBSET OF IMAGES 134095
NUMBER OF REJECTED MISFITS 11536
NUMBER OF SYSTEMATIC ABSENT REFLECTIONS 0
NUMBER OF ACCEPTED OBSERVATIONS 122559
NUMBER OF UNIQUE ACCEPTED REFLECTIONS 38170
On Thu, May 8, 2014 at 10:48 AM, Segelke, Brent W. <[email protected]>wrote:
> You didn’t report your resolution and completeness. Also, is there
> anisotropy in your data?
>
>
>
> Brent
>
>
>
> *From:* CCP4 bulletin board [mailto:[email protected]] *On Behalf Of
> *Yarrow
> Madrona
> *Sent:* Thursday, May 08, 2014 10:12 AM
> *To:* [email protected]
> *Subject:* [ccp4bb] stalled refinement after MR solution
>
>
>
> Hello CCP4 community,
>
>
>
> I am stumped and would love some help. I have a molecular replacement
> solution that has Rfree stuck around 40% while Rwork is aorund 30%. The
> model is actually the same enzyme with a similar inhibitor bound. Relevant
> information is below.
>
>
>
> -Yarrow
>
>
>
> I have solved a structure in a P21 spacegroup:
>
>
>
> 51.53 88.91 89.65, beta = 97.1.
>
>
>
> Processing stats (XDS) are very good with low Rmerge (~5% overall) and
> good completeness.
>
>
>
> I don't think twinning is an option with these unit cell dimensions. My
> data was highly aniosotropic. I ran the data through the UCLA anisotropic
> server to scale in the B- direction (
> http://services.mbi.ucla.edu/anisoscale/)
>
>
>
> I get a small (a little over 5) patterson peak suggesting there is not
> much t-NCS to worry about. However, the output structure does have 2 fold
> symmetry (see below) and as Dale Tronrud pointed out, there is always tNCS
> in a P21 space group with two monomers related by a 2-fold axis.
>
> I calculated the translation to be unit cell fractions of 0.36 0.35, 0.32.
>
>
>
> 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
>
>
>
> *Phaser stats:*
>
> * SOLU SET RFZ=20.3 TFZ=19.5 PAK=0 LLG=1314 RF++ TFZ=63.8 PAK=0 LLG=4745
> LLG=4947*
>
>
>
>
>
