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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