In this tutorial, we will deal with the data from interferon gamma from Paralichthys olivaceus (POLI). This protein structure was solved at 2.3 Å and is available as PDB entry 6F1E. Detailed information can be found in the related scientific paper ¹⁾. Download the archive with the data containing:

• Structure model previously refined against data at 2.3 Å - poli67_edit12_2-3A_refmac1.pdb.
• Merged diffraction data up to 1.9 Å - poli67_1-9A.mtz
• Unmerged diffraction data up to 1.9 Å - poli67_XDS_ASCII_1-9A.HKL

Note that the structure model poli67_edit12_2-3A_refmac1.pdb was refined in REFMAC5 against work reflections only, i.e. this structure is not the same as the final deposited 6F1E structure that was refined against all the reflections. The X-ray weight was set to 0.06.

Let's have a look on the diffraction data. They exhibited severe anisotropy: According to the criterion of I/sigma(I) > 1.5 in the highest resolution shell, resolution cutoffs could estimated in the range from 2.26 to 2.71 Å. The following table shows merging statistics of poli67_XDS_ASCII_1-9A.HKL calculated with phenix.merging_statistics:

#shell d_max  d_min   #obs  #uniq   mult.  %comp       <I>  <I/sI>    r_mrg   r_meas    r_pim   cc1/2   cc_ano     cc* 
01     47.05   5.13  22367   1948   11.48  99.44     494.1    38.8    0.042    0.044    0.013   0.999  -0.214   0.9997
02      5.13   3.63  42232   3343   12.63  99.79     203.3    31.7    0.064    0.067    0.019   0.999  -0.163   0.9997
03      3.63   2.97  57138   4246   13.46  99.95      56.9    14.3    0.151    0.157    0.042   0.997  -0.166   0.9992
04      2.97   2.57  65007   5014   12.97  99.70      11.3     4.0    0.622    0.648    0.178   0.951  -0.025   0.9874
05      2.57   2.30  73887   5623   13.14  99.89       3.7     1.3    1.839    1.914    0.523   0.730  -0.014   0.9187
06      2.30   2.20  37405   2818   13.27  99.93       1.6     0.6    4.462    4.641    1.263   0.400   0.033   0.7559
07      2.20   2.10  45724   3363   13.60  99.91       0.9     0.3    7.623    7.920    2.129   0.196  -0.008   0.5725
08      2.10   2.00  49772   4021   12.38  98.51       0.3     0.1   16.989   17.721    4.963   0.027   0.008   0.2293
09      2.00   1.90  35920   4046    8.88  81.18       0.1     0.0   41.435   43.993   14.417  -0.132  -0.016   undefined

Now we are prepared to examine data at resolution higher than 2.3 Å. Despite poor merging statistics, there can be still a useful signal in the high-resolution data beyond that cutoff. Let's execute PAIREF in the minimalistic way - the required arguments are a structure model and merged diffraction data:

cctbx.python -m pairef --XYZIN poli67_edit12_2-3A_refmac1.pdb --HKLIN poli67_1-9A.mtz