Dear Jiang Yan,
 
The Matthews function is based on an average protein crystal with 50% solvent. However, crystals do exist with as little as 25% solvent or as much as 75% solvent, so if your structure refines to an Rfree of 20%, your structure is solved and you have a crystal with a high percentage of solvent (which may explain your low Rfree). Maps are usually contoured at sigma levels, based on the variation in the electron density map. So with an Rfree of 20%, your difference map will be very flat with and the sigma will be very low. Also the 3 sigma level usually used for difference maps will be very low and statistically, there are always some peaks at plus or minus 3 sigma, but they are nothing to worry about.
 
Best,
Herman

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Gesendet: Mittwoch, 26. Juni 2013 06:05
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Betreff: [ccp4bb] Rfree is 20%,why still green and red density?

Hi everyone,

I now meet some problems when trying to solve structure.Space group is P6422, and Mathews function shows there are 4 molecules in one asymmetry unit. However, Phenix-autobuild shows only 2 molecules in on one asymmetry unit, after refinement, Rfree=20%,(resolution is 2.8A). Although AA fit the map well, there are still some green and red density.
I wonder if anyone met this problem before? Any suggestion is welcome.

Best,
Jiang Yan