Re: [phenixbb] Difference in water molecules count

Hi Nat, The average B-factors for the protein and solvents are: Main chain 11.01 14.14 19.77 13.43 10.956 Side chain 13.07 17.22 21.44 16.76 12.648 Waters 30.22 29.39 28.49 30.23 26.08 Yes, the water molecules were identified automatically by phenix.refine programme. Regards, World Quoting Nathaniel Echols :

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I have been refining the mutant structures and at the end while making the comparative study I found that there is a large difference (almost half) number of water molecules in the protein strucutre of same mutant from different crystal conditions. The resolution of the structure, space group and no.of molecules in a.s.u is same.

Here is the data collection statistics and no.of water & protein atoms

On Tue, Feb 7, 2012 at 2:20 AM, wrote: present.

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I could also not understand the difference of unique and measured reflections at same resolution. Could anyone please explain me?

It depends on how many frames of data you collect and how well the integration worked. The fourth dataset in the list is both less redundant and less complete than the other two that go to 1.6A; the slightly lower data quality could have an impact on the map quality too. (Pavel and Sacha Urzhumtsev have found some interesting cases where a relatively small number of missing reflections really hurt the maps.) If you are using slightly different I/sigma cutoffs, that can also have a large effect, as can different levels of disorder in the crystal. What are the average protein and solvent B-factors for these structures?

The other thing to check: how were these waters identified? If you're relying on completely automatic water-picking methods like the one in phenix.refine, it's possible that it missed many weaker (but still valid) map peaks in one dataset - you can still fill these manually and turn the solvent update off.

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb