There was a case a few years ago (not too many though) where a 1.6 Å structure
had been solved using an incorrect value for the wavelength (~5% too low,
leading to a cell that was slightly too small for its contents to be
comfortable). It was later corrected so we could compare their validation
statistics. Some interesting observations:
- the geometry had been very tightly restrained so that didn't give a clue
about the cell error (WhatCheck only suggested a very small change)
- somewhat surprisingly (I thought) the Ramachandran plot did not improve in
the correct model (0.3% outliers in the wwPDB validation report), and the
sidechain rotamer outliers even got worse (from 1.5 to 2.5 %)
- the map looked surprisingly good for the incorrect cell
- however, RSR-Z told clearly that the map was not good enough for the claimed
resolution - the model had 24% outliers! (3% in the corrected model which
still only put it at the ~50th percentile)
- another good indicator was the clashscore (went from 44 to 7)
- the original model did not include an Rfree, but the R-value (>0.3 at 1.6Å
resolution) ought to have provided a clue to the crystallographers and
reviewers one would think
It would be interesting to see what would happen if the wavelength would be
set 5% too high.
--Gerard
On Thu, 16 Jul 2020, Clemens Vonrhein wrote:
Hi Robbie,
On Wed, Jul 15, 2020 at 07:23:15PM +0000, Robbie Joosten wrote:
At the same time if you have a a more relaxed approach to restraints
than you might find systematic deviations in bond lengths. A test
for that has been in WHAT_CHECK for decades and it actually works
surprisingly well to detect cell dimension problems.
Indeed.
That said, the problem is uncommon now.
Not so sure about that: we all rely on an accurate value of the
energy/wavelength from the instrument/beamline - and if that is off
(for whatever reasons) it will result in incorrect cell dimensions and
a systematic deviation from the various restraints.
This would even affect the best experiment done on the best crystal
... so fairly easy to spot at the refinement stage, especially if such
an energy/wavelength offset is constant over a long period of time on
a given instrument. To spot this at the data collection stage one
would hope that at some point a crystal with very pronounced ice-rings
will be looked at properly (and the fact these are not where we expect
them to should cause some head-scratching).
Cheers
Clemens
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Best wishes,
--Gerard
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Gerard J. Kleywegt
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