Dear Sudipta, you are correct, your original scala.mtz has the wrong space group in it, resulting in very high Rfactors (and presumably bad electron density). In these cases, I usually reprocess (remerge) the data in the correct space group to get the statistics right (and gain probably a few extra h00 reflections that got rejected in P212121). If you use the same a, b and c axes as before, you do not need to rerun Phaser, otherwise you have to. If you have translational NCS, you have to live with it. The only way to get rid of it is to find another crystal with a different crystal packing.
Best, Herman Von: CCP4 bulletin board [mailto:[email protected]] Im Auftrag von Sudipta Bhattacharyya Gesendet: Dienstag, 15. Juli 2014 20:32 An: [email protected] Betreff: [ccp4bb] Translational NCS and molecular replacement. Dear Community, I have some doubts to clarify. In a way to solve a structure by Phaser-MR, I found phaser ended up with a potentially good MR solution (with good statistics, packing and electron density, and as we know the homolog structure so in a reasonable biological assembly also). However, the space group where phaser found the potential solution (P22121) is different what we got in pointless (P212121), and phaser also indicated the presence of translational NCS (NCS translation vector = 0.500, 0.494 0.391). Now when we try to refine the structure with its original scala.mtz file (which is indexed and sclaled in P212121) and phaser generated pdb file, the R/Rfree is very high (around 0.5) but when I tried refining with mtz file generated by phaser, it was reasonable, at least for first cycle of refinement (R/Rfree, 0.41/0.46). Now my question is, can I use the phaser generated mtz file instead of the original scala.mtz for further refinement? Or I have to reindex my original data into phaser suggested spacegroup and run the MR again? Translational NCS are generally associated with high R values, is there any way to get rid of that problem? Best regards, Sudipta.
