2QVO.xds: Difference between revisions

  *  21        tP          7.3      53.5  53.5  41.2  90.1  90.1  90.3    0  1  0  0  0  0 -1  0 -1  0  0  0

     39        mC        249.8    114.5  41.2  53.5  90.1  90.3  69.0    1 -2  0  0  1  0  0  0  0  0  1  0

  SPACE-GROUP        UNIT CELL CONSTANTS            UNIQUE  Rmeas  COMPARED  LATTICE-

   NUMBER      a      b      c  alpha beta gamma                            CHARACTER

After his comes the table that tells us the quality of our data:

       NOTE:      Friedel pairs are treated as different reflections.

   

     2.04        5134    1601      2347      68.2%    274.7%    291.2%    4913    0.40  325.5%  400.7%    1%  0.608    606

     total      91819  13782    14656      94.0%      5.7%      5.9%    91589  20.24    6.2%    15.0%    12%  0.897    6450

So the anomalous signal goes to about 3.3 A (which is where 30% would be, in the "Anomal Corr" column), and the useful resolution goes to 2.16 A, I'd say (pls note that this table treats Friedels separately; merging them increases I/sigma by another factor of 1.41).

We could now modify XDS.INP to have

  JOB=CORRECT  ! not XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT

  SPACE_GROUP_NUMBER=  77

and run xds again, to obtain the final CORRECT.LP and XDS_ASCII.HKL with the correct spacegroup, but the statistics in 75 and 77 are the same, for all practical purposes (the 8 reflections known to be extinct do not make much difference).

Following this, we create XDSCONV.INP with the lines

  SPACE_GROUP_NUMBER=  77  ! can leave out if CORRECT already ran in #77

  INPUT_FILE=XDS_ASCII.HKL

  OUTPUT_FILE=temp.hkl CCP4

===dataset 2===

==SHELXC/D/E structure solution==

<pre>

#!/bin/csh -f

shelxc j <<end

SAD  temp.hkl

SPAG P42

MAXM 2

end

This writes j.hkl, j_fa.hkl and j_fa.ins. However, we overwrite j_fa.ins now (these lines are just the ones that [[ccp4com:hkl2map|hkl2map]] would write):

<pre>

cat > j_fa.ins <<end

TITL j_fa.ins SAD in P42

LATT  -1

SYMM -Y, X, 1/2+Z

  shelxd j_fa

  shelxe.beta j j_fa -a -q -h -s0.55 -m20 -b  

  shelxe.beta j j_fa -a -q -h -s0.55 -m20 -b -i

Some important lines in the output: for dataset 1, I get

'''clearly indicating that the structure can be solved with each of the two datasets individually.'''

The safest way to optimize the data reduction is to look at external quality indicators. Internal R-factors, and even the correlation coefficient of the anomalous signal are of comparatively little value. A readily available external quality indicator is CC All/CC Weak as obtained by [[ccp4com:SHELX_C/D/E|SHELXD]].

[[Optimization]] does improve things as much as it often does: recycling of GXPARM.XDS to use as XPARM.XDS, and thus imposing the lattice symmetry in the geometry refinement in INTEGRATE. These findings my correspond to the fact that in P1 the angles do not refine to 90.0xx or 89.9xx degrees. In other words, the metric symmetry is not as well fulfilled as it should be. This results in fairly large deviations from the ideal P42 positions; the refinement of cell parameters in P1 partly compensates for this. I have however no idea why this deviation from metric symmetry could occur.  

==Limits==

With dataset 2, I tried to use 270 frames but could not solve the structure using the above SHELXC/D/E approach (not even with MAXIMUM_ERROR_OF_SPOT_POSITION=6.0). With 315 frames, it was possible.