Re: [ccp4bb] question of extra high B factor

[Kay Diederichs]

Hi Pavel,






best,

Kay

Pavel Afonine schrieb:

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?

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

     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





Pavel.

PS>

     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:

     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

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 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 -:) 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 Mean B-factor value Number of structures in PDB

--
Kay Diederichs                http://strucbio.biologie.uni-konstanz.de
email: kay.diederi...@uni-konstanz.de    Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz

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