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 <[log in to unmask]> 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 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
>>
>> 10.00 1023 173 204 84.8% 7.4%
>> 14.1% 1023 10.86 8.1% 99.5* -28 0.422 156
>> 6.00 4199 704 709 99.3% 11.1%
>> 15.1% 4199 10.43 12.1% 99.1* -25 0.515 640
>> 4.00 12401 2131 2137 99.7% 15.5%
>> 15.5% 12400 9.91 17.0% 97.7* -18 0.684 1893
>> 3.50 8429 1486 1486 100.0% 18.3%
>> 18.0% 8426 8.10 20.1% 96.4* -8 0.788 1259
>> 3.30 4630 842 842 100.0% 23.0%
>> 22.3% 4627 6.59 25.5% 94.5* -13 0.768 686
>> 3.10 6057 1121 1121 100.0% 28.3%
>> 26.3% 6053 5.50 31.4% 93.6* -3 0.829 882
>> 3.00 3527 664 664 100.0% 33.7%
>> 34.2% 3524 4.56 37.5% 86.8* 6 0.827 502
>> 2.90 3961 756 756 100.0% 48.4%
>> 49.5% 3956 3.24 53.8% 82.7* 2 0.784 549
>> 2.80 2140 699 862 81.1% 31.6%
>> 37.4% 2057 2.51 37.7% 87.0* 2 0.789 178
>> total 46367 8576 8781 97.7% 17.2%
>> 18.1% 46265 7.15 19.0% 98.2* -9 0.730 6745
>>
>>
>> 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
>
>
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