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
