says that the structures have the wrong hand and topology
due to an "in-house" program that inverted the signs on the anomalous
pairs.
I had a similar experience of swapped F+ and F- from data collected
at a synchrotron (Someone there forgot to upload the correct geometry
files after they switched detectors). My student traced and fitted
the chain but the the structure failed the preXPLOR geometry check
since the helices had the wrong hand. When we saw this we swapped F+
and F- and everything worked out. I would think if F+ and F- were
swapped you would get an inverted structure that geometry checks
should flag.
Alternatively, the initial structure of the histone octomer was
phased on a Patterson analysis that had the heavy atom positioned
incorrectly. This affected the structure by reinforcing the
incorrect image and suppressing the correct image in the electron
density map see Wang, et al., J. Mol. Biol. 236: 179‑188 (1994).
In this case the helices had the correct hand but the structure was
incorrect.
Finally, during the 90's I consulted at the PDB working on processing
difficult structures and streamlining processing. This was the
period where crystallographers were first required to deposit
coordinates to publish. There was a definite correlation between
journal (Science, Nature, etc) and problems with the structure
reflecting the rush to publish. I think this may have also played a
part in this unfortunate event.
Just my 2 cents
John
On Dec 24, 2006, at 4:04 AM, Bernhard Rupp wrote:
*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
says that the structures have the wrong hand and topology
due to an "in-house" program that inverted the signs on the anomalous
pairs.
Hmm...the model helices are right handed. If you swap sign (such as in
earlier days by placing image plates wrong way in reader), the whole
structure is invers and the helices have wrong hand.
I can't see this in 1z2r. If right handed helices were built
into initially left handed (poor) density, then the RSCC would scream
(as it did, if I interpret the remark about EDS correctly).
There got to be more to this story?
Merry Christmas, BR
