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Re: [ccp4bb] question of extra high B factor |
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CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: question of extra high B factor From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK Date: 2009-08-03 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 >> >> >> >> > > CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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