Hi Gerard,
fortunately I still have the data for this structure on my computer - and not
on tape or somesuch.
Below is the summary of the SCALA logfile, from which the statistics were
quoted. Collection was a single sweep of 180 degrees. I'll send you privately
the complete log file and the output mtz (happy to share with other people
also, but don't want to post big files to people to the BB in general).
Cell parameters are exactly the same, so I don't think we've submitted the
wrong mtz to the PDB by mistake.
Summary data for Project: D9-25 Crystal: nat Dataset: rm
Overall InnerShell OuterShell
Low resolution limit 22.00 22.00 2.32
High resolution limit 2.20 6.96 2.20
Rmerge 0.132 0.034 0.440
Rmerge in top intensity bin 0.052 - -
Rmeas (within I+/I-) 0.182 0.048 0.606
Rmeas (all I+ & I-) 0.177 0.048 0.598
Rpim (within I+/I-) 0.125 0.034 0.414
Rpim (all I+ & I-) 0.090 0.025 0.305
Fractional partial bias -0.030 -0.046 -0.056
Total number of observations 179203 5537 26037
Total number unique 47653 1546 6906
Mean((I)/sd(I)) 7.3 15.3 2.8
Completeness 99.9 96.8 99.9
Multiplicity 3.8 3.6 3.8
Anomalous completeness 84.5 92.1 80.0
Anomalous multiplicity 2.0 2.0 2.0
DelAnom correlation between half-sets -0.090 -0.032 -0.015
Mid-Slope of Anom Normal Probability 0.911 - -
Outlier rejection and statistics assume that there is anomalous scattering, ie
I+ differs from I-
Average unit cell: 157.34 53.98 112.75 90.00 100.43 90.00
Space group: C2
Average mosaicity: 0.68
Minimum and maximum SD correction factors: Fulls 1.04 6.74 Partials 1.63
13.05
Dataset: D9-25/nat/rm
written as averaged data to output file /tmp/mark/D9-25_14_2_mtz.tmp
Maximum resolution: 2.20A
Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
Section Editor Acta Crystallographica F
https://journals.iucr.org/f/
> On 22 Feb 2021, at 20:38, Gerard Bricogne <g...@globalphasing.com> wrote:
>
> Dear Patrick, Mark and colleagues,
>
> Examining the data associated to PDB entry 2XGF using the PDBpeep
> server, i.e. at
>
> http://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi?ID=2xgf
>
> shows a large region (marked up in dark blue) of missing measurements where
> the analysis of the trends in the distribution of the local average I/sig(I)
> would have led to expect statistically significant intensities. Such
> systematic patterns of missing data are never good news when it comes to
> maps.
>
> This raises a couple of questions for you, Mark:
>
> 1. this is not the shape of a standard cusp, so would there have been
> features of the crystal morphology that made some regions of reciprocal
> space hard to reach in an experiment, apart from the usual cusp caused by
> the 2-fold axis being too close to the rotation axis?
>
> 2. this pattern of missing data makes it rather surprising that the
> completeness reported in the paper is about 99%, all the way out to the
> outer resolution limit; the STARANISO logfile, accessible at
>
> http://staraniso.globalphasing.org/PDB/2xgf.log
>
> shows significantly lower values, even for the ellipsoidal completeness, of
> about 0.7 at the highest resolution, for the deposited data.
>
> Did you perhaps deposit only part of the data you collected for the
> remote wavelength? For example, only one of several orientations that you
> might have collected in order to try and fill the cusp?
>
> This may seem a digression from the original question about negative
> difference density, but clearly any systematically missing data can create
> additional artefacts in maps and difference maps, besides those originating
> from chemical or radiation damage related causes.
>
>
> With best wishes,
>
> Claus and Gerard.
>
> --
> On Mon, Feb 22, 2021 at 07:51:11PM +0100, Mark J van Raaij wrote:
>> Hi Patrick,
>> couldn't see any text in you email, just the subject and the picture, but
>> 2XGF is our T4 long tail fibre tail tip structure from 2010.
>> (2XGF stands for "2nd eXtraordinary Great Fibre", at least that's what I
>> *modestly* imagine..).
>> I think it's probably one or more of:
>> - noise (was this contoured at 3sigma? or at a specific e/Å3 level? at the
>> end of refinements 3sigma corresponds to less e/Å3 than at the start, or at
>> least it should).
>> - perhaps a small percentage of another metal than iron in the site (Co, Ni,
>> Cu, Zn?), it's quite clear most of it was iron though from the X-ray
>> fluorescence spectrum and the fact that the MAD phasing worked
>> - perhaps some radiation damage
>> - ripple effects around the heavy atom sites
>> Resolution was 2.2Å and data was 99.9% complete, multiplicity 3.8, more
>> statistics here: https://www.pnas.org/content/107/47/20287/tab-figures-data
>> <https://www.pnas.org/content/107/47/20287/tab-figures-data> (paper
>> https://www.pnas.org/content/107/47/20287).
>> We didn't consider lowering the occupancy of the irons, or changing from
>> Fe2+ to Fe3+, because that would have meant less electrons, not more as
>> suggested by the positive density.
>> In any case, happy that this thread serves to learn something more from the
>> comments by the experts.
>> Mark
>>
>> Mark J van Raaij
>> Dpto de Estructura de Macromoleculas
>> Centro Nacional de Biotecnologia - CSIC
>> calle Darwin 3
>> E-28049 Madrid, Spain
>> Section Editor Acta Crystallographica F
>> https://journals.iucr.org/f/
>>
>>
>>> On 22 Feb 2021, at 16:16, Patrick Needham <needh...@miamioh.edu> wrote:
>>>
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