Hi Jiamu,
My question is: 1. How to reduce the B factor to a reasonable level?3. In the same of similar resolutionIs, is there some other structures like this situation?
POLYGON tool is (one of) your friend(s) to answer this question (apart from debatable one about "a reasonable level"):
Acta Cryst. D65, 297-300 (2009).Now it is available in PHENIX (from the latest nightly builds): http://www.phenix-online.org/
Please let me know if you have any questions about it. Pavel.