I believe that is so.
In this case the Rfactor against the deposited data is low. The question
to be addressed is whether the deposited data is of acceptable quality.
There are some poor distances but not many - the asymmetric unit is very
empty.
The Ramachandran plot is not good, and an author would be queried about
that. However you can choose to ignore their warnings.
Eleanor
Gina Clayton wrote:
I thought that when a structure is deposited the databank does run its
own
refinement validation and geometry checks and gives you back what it
finds i.e
distance problems etc and rfactor?
Quoting Eleanor Dodson <[EMAIL PROTECTED]>:
The weighting in REFMAC is a function of SigmA ( plotted in log file).
For this example it will be nearly 1 for all resolutions ranges so
the weights are pretty constant. There is also a contribution from
the "experimental" sigma, which in this case seems to be proportional
to |F|
Yesterday I attached the wrong TRUNCATE log file - here is the
correct one, and if you look at the plot
"Amplitude Analysis against resolution" it also includes a plot of
<F> <SigF>
Eleanor
Dominika Borek wrote:
There are many more interesting things about this structure -
obvious fake - refined against fabricated data.
After running refmac I have noticed discrepancies between R and
weighted R-factors. However, I do not know how the weights are
calculated and applied - it could maybe help to find out how these
data were created. Could you help?
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$
$$
0.005 2205 98.77 3800.5 3687.2 0.12 0.30 121 4133.9
4042.7 0.12 0.28
0.015 3952 99.90 1932.9 1858.7 0.20 0.60 197 2010.5
1880.5 0.21 0.40
0.025 5026 99.81 1577.9 1512.3 0.23 0.62 283 1565.0
1484.6 0.26 0.54
0.034 5988 99.76 1598.0 1541.5 0.23 0.61 307 1625.7
1555.6 0.23 0.42
0.044 6751 99.79 1521.2 1481.6 0.18 0.41 338 1550.3
1523.8 0.18 0.61
0.054 7469 99.81 1314.5 1291.2 0.14 0.29 391 1348.3
1337.7 0.15 0.27
0.064 8078 99.87 1111.5 1089.1 0.16 0.36 465 1096.1
1077.9 0.18 0.42
0.073 8642 99.84 976.7 959.2 0.15 0.32 488 995.3
988.4 0.16 0.50
0.083 9255 99.88 866.4 848.0 0.16 0.36 490 856.8
846.0 0.17 0.38
0.093 9778 99.88 747.6 731.4 0.16 0.36 515 772.8
747.3 0.18 0.38
0.103 10225 99.86 662.6 649.1 0.17 0.38 547 658.9
643.6 0.20 0.36
0.113 10768 99.83 597.2 584.7 0.18 0.42 538 593.4
590.0 0.20 0.49
0.122 11121 99.86 535.5 521.9 0.19 0.48 607 556.2
542.0 0.20 0.47
0.132 11692 99.85 489.3 479.2 0.19 0.46 607 476.4
467.3 0.23 0.42
0.142 11999 99.83 453.9 443.1 0.19 0.48 621 455.3
440.6 0.22 0.55
0.152 12463 99.79 419.2 407.3 0.19 0.44 655 435.3
424.3 0.22 0.53
0.162 12885 99.78 384.0 373.9 0.20 0.53 632 384.1
376.1 0.22 0.43
0.171 12698 95.96 357.2 348.5 0.21 0.57 686 353.9
338.6 0.24 0.51
0.181 11926 87.78 332.0 323.3 0.21 0.66 590 333.4
322.6 0.24 0.57
0.191 11204 80.39 309.9 299.6 0.22 0.59 600 302.1
296.3 0.26 0.77
$$
Eleanor Dodson wrote:
There is a correspondence in last weeks Nature commenting on the
disparities between three C3B structures. These are:
2icf solved at 4.0A resolution, 2i07 at 4.1A resolution, and 2hr0
at 2.26A resolution.
The A chains of all 3 structures agree closely, with each other and
other deposited structures.
The B chains of 2icf and 2i07 are in reasonable agreement, but
there are enormous differences to the B chain of 2hr0.
This structure is surprisingly out of step, and by many criteria
likely to be wrong.
There has been many articles written on validation and it seems
worth reminding crystallographers
of some of tests which make 2hr0 suspect.
1) The cell content analysis suggests there is 80% solvent in the
asymmetric unit.
Such crystals have been observed but they rarely diffract to 2.26A.
2) Data Analysis:
The reflection data has been deposited so it can be analysed.
The plots provided by TRUNCATE showing intensity statistic features
are not compatible with such a high solvent ratio. They are too
perfect; the moments are perfectly linear, unlikely with such large
volumes of the crystal containing solvent, and there is absolutely
no evidence of anisotropy, again unlikely with high solvent content.
3) Structure analysis
a) The Ramachandran plot is very poor ( 84% allowed) with many
residues in disallowed regions.
b) The distribution of residue B values is quite unrealistic. There
is a very low spread, which is most unusual for a structure with
long stretches of exposed chain. The baverage log file is attached.
c) There does not seem to be enough contacts to maintain the
crystalline state.
