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
>
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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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>>
>>
>> Best wishes,
>>
>> --Gerard
>>
>> ******************************************************************
>> Gerard J. Kleywegt
>>
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Best wishes,
--Gerard
******************************************************************
Gerard J. Kleywegt
http://xray.bmc.uu.se/gerard mailto:[log in to unmask]
******************************************************************
The opinions in this message are fictional. Any similarity
to actual opinions, living or dead, is purely coincidental.
******************************************************************
Little known gastromathematical curiosity: let "z" be the
radius and "a" the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
******************************************************************
########################################################################
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