Re: [ccp4bb] question of extra high B factor

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: question of extra high B factor
From: "Edward A {- dot -} Berry" BerryE {- at -} UPSTATE {- dot -} EDU
Date: 2009-08-01

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
>
>
>
>

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: OT - Acknowledgement of contributions to BMC
From: Bernhard Rupp br {- at -} RUPPWEB {- dot -} ORG
Date: 2009-07-31

Next message:
Subject: PhD position at Trinity College Dublin
From: Khan Amir Rafiq amirrafk {- at -} TCD {- dot -} IE
Date: 2009-08-01