I think I wasn't totally clear. The structure was refined
with the correct cell dimensions and those fractional
coordinates then were converted to orthogonal as the last
step before sending them to the PDB. Had the depositor
simply sent us the fractional data, we would have changed
them to orthogonal and there would have been no problem.
Instead the depositor used an incorrect matrix to make the
orthogonal data that was sent to us.
The depositor told me that something looked wrong in the
active site graphically and that is how s/he realized that
there was a problem.
I think that this occurred before we did packing analysis
as the letter we sent was short with just the outlier distances
and angles. The depositor would have had to send a new magnetic
tape to us and it was trivial to just do the requisite math
myself.
Frances
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On Thu, 16 Jul 2020, Gerard DVD Kleywegt wrote:
Hi Frances,
I'm not surprised. Just correcting (from old orthogonal via fractional to new
orthogonal) will "stretch" bonds ever so slightly. I would have done
rigid-body followed by some all-atom refinement and maybe checked the map and
model fit afterwards (esp. at crystal contacts), and if necessary rebuilt
some residues followed by more refinement.
--Gerard
On Thu, 16 Jul 2020, Frances C. Bernstein wrote:
I do not remember the date or the PDB entry but it was during
the time that the PDB at BNL was including distance and angle
outliers in the checking report sent back to the depositor.
It was a not-too-large protein and there were perhaps half a
dozen outliers each on distances and angles which was typical of
an entry without 'problems'. So I sent the proposed entry to the
depositor and got a panicked call that something was wrong based
on the depositor looking at a display of the entry. By the next
day the depositor had figured out that s/he had decided to convert
to orthogonal for deposition and mistyped one of the cell dimensions
by 1 Angstrom. That length was about 135 so the error was less than
1% in one direction and I was very impressed that the depositor had
spotted it graphically.
After I did the appropriate linear algebra to correct the coordinates
I took a look at the distance and angle outliers. Of course they
were different but to my great surprise there were about the same
number of outliers for the 'bad' and the corrected entries. So based
on the checking at that time we could not tell the bad from the good.
I would be interested to know what would happen now with all the
additional checking that is available. Perhaps someone should do
that experiment.
Frances
=====================================================
**** Bernstein + Sons
* * Information Systems Consultants
**** 5 Brewster Lane, Bellport, NY 11713-2803
* * ***
**** * Frances C. Bernstein
* *** f...@bernstein-plus-sons.com
*** *
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=====================================================
On Thu, 16 Jul 2020, Gerard DVD Kleywegt wrote:
There was a case a few years ago (not too many though) where a 1.6 ?
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
1.6?
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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--Gerard
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