Dont forget the confusing interaction between recorded B factors in a
PDB file and TLS parameters. This Q is still I think unresolved but you
need to be careful!
Eleanor
Edward A. Berry wrote:
> Interesting that the correlation between B-factor and
> resolution didn't show up in the QDB as recently as 2001.
> Or am I missing something?
> From what i understand this includes structures with
> resolution from 1.5 to 3.5 A.
>
> On Jan 4 2001 Gerard "CD" Kleywegt wrote:
>>
>> well, i had a quick look at the data stored in QDB
>> (gjk, acta cryst d52, 842-857) which shows that
>> for 435 structures the corr coeff between resolution
>> and average b is only 0.06, i.e. insignificant
>>
>> the only non-trivial correlate (using a 0.2 cut-off)
>> is the percentage of secondary structure (makes
>> sort of sense) with cc=0.20
>>
>> in my other large-scale test, mentioned a couple
>> of weeks ago, i found that essentially all temp-
>> factor-related staistics are "incorrectly"
>> correlated with measures of model accuracy
>> (e.g., higher average b tends to be accompanied
>> by higher accuracy !). average b is very strongly
>> correlated with completeness on the other hand.
>> i suspect that problems with data and/or restraints
>> (rather than physics) are a major determinant
>> of the temp-factors we calculate for our models ...
>>
>> --dvd
>>
>>
>> On Thu, 4 Jan 2001, Yu Wai Chen wrote:
>>>
>>> Does any one know if there is any correlation between the overall
>>> B-factor of a structure in relation to its resolution? Are there any
>>> publications on this topic?
>>>
>>> Also is there any correlation between the extent of disorder in a
>>> structure and the R-factor/Rfree?
>>>
>
> Pavel Afonine wrote:
>> 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
>>
>>
>>
>>
>
>
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