Dear Monica, here are some comments from my side: -one can ask the bulletin board, or just decrease the occupancy during refinement and see what happens. If the statistics get better: keep it, if they get worse: reject the result. -I think it is not a question of correct or incorrect structures. You have two structures: one with a short soak and low ligand concentration, and one with a longer soak and higher ligand concentration, but with 88% complete data. I would refine both structures independently and in both cases refine a group occupancy for the ligand. If this is done correctly, I would expect that both structures will look very similar and provide independent proof for the binding mode of your ligand. One question is: what to do with ambiguities in the low-occupancy structure? I would look in the high-occupancy structure for hints how to resolve these, but more puritan crystallographers may have different opinions. Also 88% completeness is not great, but also not that bad. If the electron density looks good, I would trust it.
However, if both independently refined structures show a very different binding mode, I would get suspicious. In this case I would not just ignore the low-occupancy structure but would try to find out what happened: was the ligand incorrectly fitted? Where the soaking conditions (precipitant, buffer, pH) different, could it be that the ligand was degraded/turned over during the long soak? Best, Herman Von: CCP4 bulletin board [mailto:[email protected]] Im Auftrag von Monica Mittal Gesendet: Mittwoch, 13. August 2014 07:48 An: [email protected] Betreff: [ccp4bb] Protein_Ligand Suggestion Dear all I have solved a structure of protein with ligand at 2.7 and 2.8 A. Both have ligand bound in it as i soaked it. For the first structure i soaked for lesser time and lesser concentration of ligand and solved it at 2.7 A resolution. Although the ligand has good density (2Fo-Fc at 0.9 sigma) but it is little unconnected from its middle portion. Its RSCC value is 0.76 and B-factor of 70.0. Overall completeness of structure is > 91%. So If i decrease the occupancy of ligand here, will it improve the ligand statistics esp. the Real space R-value?? However for the second structure, i soaked for longer time and higher ligand concentration, so the ligand is perfect with clear 2Fo-Fc map at 1.2 sigma and Fo-Fc map at 2.8 sigma along with well defined simulated annealing and composite omit maps. The RSCC value is 0.81 with B-factor of 40.1.The only issue is the overall completeness of the structure is 88%. But if i get evrything OK at this completeness, den can i consider the second structure with ligand as the correct one?? Thanks in advance. Monica
