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 <[EMAIL PROTECTED]> 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. >>> >> >> -- 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)
