Dear Iris,
just to add to Fred's posting: since XDS Version June 2, 2008 re-indexing is no
longer necessary if REFERENCE_DATA_SET is used - XDS then does the re-indexing
automatically in the CORRECT step. This makes it very easy to avoid the problem
of alternative indexing in space groups like P3x, P4x , P6x and others.
You should also inspect the top of XSCALE.LP. In case you forgot to use
REFERENCE_DATA_SET and the wrong setting was picked by chance, you probably see
some very small correlation coefficients (they should be 0.9, say). There may
also be a warning message to that effect.
HTH,
Kay
On Fri, 19 Oct 2012 13:45:48 +0200, vellieux frederic.velli...@ibs.fr wrote:
Well, the first thing I note is that P6(3) is a polar space group.
Hence what I would do myself is the following:
take your crystal 'number 1' (as a reference);
take the results of XDS for crystal number 2 (XDS_ASCII.HKL) and reindex it;
try to see which of the original XDS_ASCII or the reindexed XDS_ASCII
file gives you the lowest R-sym values, the one with the lowest Rsym's
has consistent indexing with your 'reference' crystal 1 - normally
somewhere in the XDS output (forgot where) there is a reindexing card
mentioned
repeat with crystal 3;
Then you know what is consistent w.r.t. crystal 1. So you take the 3
files that are appropriate and repeat the XSCALE scaling.
It may very well be that you do not have any twinning but that you have
not consistently indexed the 3 data sets. Unless you have already taken
care of consistent indexing but didn't say (write) it.
HTH,
Fred.
On 19/10/12 13:17, Iris Gawarzewski wrote:
Hello everybody,
I collected datasets with a resolution to 2.8A from 3 crystal grown
in the same condition. The space group seems to be P63. Statistic of
XSCALE.LP
SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE = -3.0 AS FUNCTION OF
RESOLUTION
RESOLUTION NUMBER OF REFLECTIONSCOMPLETENESS R-FACTOR
R-FACTOR COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano
LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed
expected Corr
10.001023 173 204 84.8% 7.4%
14.1% 1023 10.86 8.1%99.5* -280.422 156
6.004199 704 709 99.3% 11.1%
15.1% 4199 10.4312.1%99.1* -250.515 640
4.00 124012131 2137 99.7% 15.5%
15.5%124009.9117.0%97.7* -180.6841893
3.5084291486 1486 100.0% 18.3%
18.0% 84268.1020.1%96.4*-80.7881259
3.304630 842 842 100.0% 23.0%
22.3% 46276.5925.5%94.5* -130.768 686
3.1060571121 1121 100.0% 28.3%
26.3% 60535.5031.4%93.6*-30.829 882
3.003527 664 664 100.0% 33.7%
34.2% 35244.5637.5%86.8* 60.827 502
2.903961 756 756 100.0% 48.4%
49.5% 39563.2453.8%82.7* 20.784 549
2.802140 699 862 81.1% 31.6%
37.4% 20572.5137.7%87.0* 20.789 178
total 463678576 8781 97.7% 17.2%
18.1%462657.1519.0%98.2*-90.7306745
I tried Xtriage and got the following:
merohedral twin operator
twin law: h,-h-k,-l
Britton plot: 0.423
H-test: 0.439
Maximum Likelihood Method: 0.457
I have a model with the sequence of my protein and did Phaser_MR
(Z-score around 4... I know that this is quiet bad...). This solution
I refined with phenix.refinement using the twin law from Xtriage.
Rfree is around 0.44 best but the model looks weird...
Greetings,
Iris
___
Iris Gawarzewski
PhD student
Arbeitskreis Schmitt
Institut f�r Biochemie
Geb. 26.32.03.21
Heinrich-Heine-Universit�t D�sseldorf
Universit�tsstr. 1
40225 D�sseldorf
-Germany-
Tel: 0049-211-81-13577
--
Fred. Vellieux (B.Sc., Ph.D., hdr)
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494
