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Re: chloride ions
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> What is the best way to judge whether a given electron density in a protein
> crystal structure can be modelled as a cholride ion or a water molecule ?
Depends a lot in terms of what resolution you are working at:
1. Chemical environment - local compensating groups, distance of
"hydrogen bonds", no nearby Glu/Asp/Cter.
2. Bigger than average electron density cloud (often a judgement call)
3. The "water" refines with an abnormally low B-factor.
4. The "water" refines with an abnormally high occupancy [not that I
advocate refining occupancies of waters in general - just in this case as
a test, and a couple of other waters as a control]
5. Presence of Chloride in your xtallisation medium ;)
If at lowish resolution (worse than 2.5A) be paranoid.
If at highish resolution (better than 2.0A) you should be able to tell.
phil
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| Phil Jeffrey | |
| Crystallography Facility Manager | If you lie to the compiler, |
| Memorial Sloan-Kettering Cancer Center, NYC | it will get its revenge |
| phil@xray2.mskcc.org | - Henry Spencer |
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