Dear all,
That's the kind of interesting question that triggers me to have a
closer look at PDB entries ... just to convince myself that a value of
30% RSRZ outliers really is as disturbing as I initially thought.
One can go through all available validation reports of X-Ray PDB
structures and extract the
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers
value. This gives the attached plot percent_RSRZ_outliers.png (with
the same plot also on logscale and as a close-up to zoom into the >20%
range).
* Looking at it his way, only 0.32% of current PDB entries have a
RSRZ outlier of 30% or higher.
Unless one has e.g. a 3-residue small peptide structure with one
poor residue I would be very reluctant to stick with the model/data
in its current shape ;-)
* Most of those very high values seem very suspect and are most
likely due to problems with the reflection data (or the use of it
in the validation software), i.e. deposited CIF file is
corrupted compared to the original file a user tried to deposit:
* out of the 193 structures with a value of 50% or higher, there
are 8 structures with a reported resolution below 4A
* but there are also 70 structures of 1.5A or better
* 8 of the apparently "worst" structures (100% RSRZ outliers) have
a reported resolution of 1.32-0.96A ... unlikely that those
density-fit parts of the validation reports are correctly
reflecting the model [1].
Not sure that helps much, but it satisfied my curiosity at least :-)
Cheers
Clemens
[1] Looking at those high-resolution, poor density fit structures is
quite entertaining: some have all density shifted (maybe deposited
the wrong reflection data for the correct model, which can happen
for large group depositions). Others have some really dodgy
look-n-feel on the PDBpeep server that analyses the deposited
data.
On Wed, Jan 29, 2025 at 11:43:15PM +0800, 白雪慧 wrote:
> Happy New Year, everyone.
>
> Recently, I have encountered some problems when submitting PDB, and I have
> seen some discussions about these problems before.
>
> Meanwhile, I still want to ask how to reduce the RSRZ outliers in the wwPDB
> validation report, is there any good way to reduce the RSRZ outliers
>
> in the WWPDB Validation report? I enclose my alidation report.
>
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--
*--------------------------------------------------------------
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
* Global Phasing Ltd., Sheraton House, Castle Park
* Cambridge CB3 0AX, UK www.globalphasing.com
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