Hi Pavel,
these are interesting tables ... but am I right that the low-B,
low-resolution structures in your 1st and 2nd table are fairly old -
refined at a time when crystallographers still thought that high B
factors should raise eyebrows?
Could it be that those structures that were refined with modern
software, and for which expt'l data were deposited, should give a more
consistent picture?
best,
Kay
Pavel Afonine schrieb:
> Hi,
>
>> all the errors go into B and so you can get decent R with wrong
>> structure. Glycosylated proteins have a large component totally
>> disordered - do you see any sugars?
>> with B~133 you uj is 3.7A which means that atom is all over the
>> place and meaningless
>> As a reviewer I would certainly question the interpretation of
>> such structure.
>> If the data collection was at 100K (or any cryo condition) one
>> expects B~20 for a good structure
>>
>
> I wouldn't interpret it that literally. The distribution of mean
> B-factors computed for structures in PDB at resolutions between 2.8 and
> 3..2A is:
> Mean B-factor value Number of structures
> in PDB
> 1.000 - 21.000 : 137
> 21.000 - 41.000 : 430
> 41.000 - 61.000 : 612
> 61.000 - 81.000 : 390
> 81.000 - 101.000 : 172
> 101.000 - 121.000 : 36
> 121.000 - 141.000 : 12
> 141.000 - 161.000 : 8
> 161.000 - 181.000 : 0
> 181.000 - 201.000 : 1
>
> There is good amount of models with mean B-factors well higher than 70.
> I doubt that PDB would accept a structure where atoms are "all over the
> place" -:) And I wouldn't claim that those models are all bad simply
> because they don't have B-factors~20.
> There is a number of publications that discuss this and show similar
> histograms, so there is no point to repeat it.
>
> So, Jiamu, *if* the high B-factors is the only issue with this part of
> your structure, then make sure that the domain in question is properly
> modeled, and keep the above histogram just in case should you run into a
> picky reviewer -:)
>
> Pavel.
>
> PS>
> Same histogram as above, but computed for all models in resolution range
> from 3 to 4A:
> Mean B-factor value Number of structures
> in PDB
> 0.000 - 22.720 : 90
> 22.720 - 45.440 : 250
> 45.440 - 68.160 : 295
> 68.160 - 90.880 : 271
> 90.880 - 113.600 : 131
> 113.600 - 136.320 : 73
> 136.320 - 159.040 : 32
> 159.040 - 181.760 : 13
> 181.760 - 204.480 : 8
> 204.480 - 227.200 : 5
>
> and finally, for high resolution models in 0.0 to 1.0A:
> Mean B-factor value Number of structures
> in PDB
> 1.800 - 4.190 : 3
> 4.190 - 6.580 : 4
> 6.580 - 8.970 : 18
> 8.970 - 11.360 : 41
> 11.360 - 13.750 : 50
> 13.750 - 16.140 : 34
> 16.140 - 18.530 : 9
> 18.530 - 20.920 : 3
> 20.920 - 23.310 : 3
> 23.310 - 25.700 : 5
>
>
>
>
--
Kay Diederichs http://strucbio.biologie.uni-konstanz.de
email: [log in to unmask] Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz
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