The pdb will give the depositor the results of their validation runs and identify problems - however they cannot force depositors to address those problems...
J
Gina Clayton <[log in to unmask]> 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 <[log in to unmask]>:
>
>> 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.
>>>
>>
>>
--
Professor James Whisstock
NHMRC Principal Research Fellow / Monash University Senior Logan fellow
Department of Biochemistry and Molecular Biology
Monash University, Clayton Campus, PO Box 13d, VIC, 3800, Australia
+613 9905 3747 (Phone)
+613 9905 4699 (Fax)
+61 418 170 585 (Mobile)
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