hard to believe changes in Rfree

Dr. John Badger jb at MSI.COM
Fri Jul 17 12:31:44 EST 1998


 Regarding Na+ in proteins. We looked at this a while back
 in cubic insulin crystals. It's quite likely that there will
 be some sodiums bound in many proteins. In our case, the hallmark of
 sodium binding sites that contain well-ordered sodium was
 several backbone carbonyls pointing to the water/sodium atom (and,
 after all, this is what ion channels and carriers have). 

 At 1.7A we also had similer clues that the water was really
 sodium (B-factor abnormally low, position refined too close
 to ligating groups in the protein). Experimentally we nailed
 it by replacing the sodium with other monovalent ions (Li, K,
 Rb, Tl) and computing the difference map - you only need low
 resolution data to do this.


 Regarding the differential in free R of 0.2%:

 If you use the equation on page 161 of Blundell and Johnson
 to estimate the average change in intensity (i.e. assume
 that water>Na adds about 1/5 of an atom to the 900 atom model) you
 get intensity changes of about 2%. How this will translate
 into F's and differences in free-R isn't so clear but the
 effect might not be completely negligable.

 I don't think it is at all impossible that the small change
 in free R is due to the change in scattering factor and
 the structural changes that result from the water>sodium swap.

 Another calculation you could do is the simple point replacement
 of water with sodium to see how big a change you get just
 from change in scattering factor.

 Having said all that, I would also be relying on stereochemical
 arguments to decide what to do.

 John Badger

 Product Development Manager, Macromolecular Crystallography

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