Hello Veronica, There are 2 aspects to your enquiry:
1- The different number of ligands in your structure could be easily sorted out by a longer soak. You don’t have to stick with 1 minute soak. A day or longer (I’ve heard of a case in which the soak went on for 30 days), would fill up as many sites as can take your ligand. Of course, the soak would have to be neutral to the crystal, i.e. won’t cause any damage. 2- C222 and C2221 are interchangeable if you shift the origin by 0.25in the x direction. You can try reindexing the mtz file to call the space group C222 and solve the structure again, and you will see all structures match up. Or you can simply shift the solution in C2221 by ¼ in X, and you get the same stats, identical. I have done this in the past. But there is one thing you need to do first: You need to permute the C2221 axes so that they are 217.4 354.3 147.0. But this will change the hand, because it isn’t a cyclic permutation. It is like looking down the b-axis with one version or up the b-axis with the other. There is a switch in REINDEX to allow to do that. The b-axis is some 9A longer, but apart from that there will not be much difference. The two cells are the same, effectively. Note that the rogue cell is longer than the other in all 3 dimensions, around 1 or 2 A in x and z, but 9 in y. If you look in the image processing log file, you will see the distance has refined to a slightly different value for this data set, provided you have used the same system for recording the diffraction patterns. The rogue cell could still have a hidden surprise. 3- A proviso for this game of reindexing and origin shift to work, is that the shift should be done in the z-direction, depending on how your molecules pack in the cell. Symmetry and pseudo-symmetry are fascinating games. I hope this gives you a different perspective. Good Luck. Pierre ******************************************************* Dr Pierre Rizkallah, Senior Lecturer Structural Biology Institute of Infection & Immunology, Sir Geraint Evans Building, School of Medicine, Heath Campus, Cardiff, CF14 4XN email: rizkall...@cardiff.ac.uk<mailto:rizkall...@cardiff.ac.uk> phone: +44 29 2074 2248 http://www.cardiff.ac.uk/people/view/126690-rizkallah-pierre From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Veronica Fiorentino Sent: 26 October 2016 13:32 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] ligand binding and crystal form Hello all, I just solved a NCS-tetrameric (biological assembly is just a dimer) crystal structures with ligand soak (same plate - same conditions). No density for ligand is observed in the first map. In the 2nd, I have 1 ligand bound. In the 3rd, I have 2 ligands bound. Is there any reason for this 'random' behaviour? In addition, I observed just one crystal out of 20 gave a different unit cell. Pointless confirms to me "Best Solution: space group C 2 2 2". REFMAC refinement shows R/Rfree ~ 20/25 % Cell from mtz : 216.5 345.8 145.2 90.0 90.0 90.0 Space group from mtz: number - 21; name - C 2 2 2 All other datasets have: Cell from mtz : 147.0 354.3 217.4 90.0 90.0 90.0 Space group from mtz: number - 20; name - C 2 2 21 I tried re-processing/refining the C2221 dataset in C222 but R/Rfree stays ~45%. Can I also consider the C2221 dataset as a 'different crystal form'? Am I safe? Thank you all, Veronica
