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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 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         |
| Voice: (212) 639 8547   Fax: (212) 717 3135   |                             |