Dear Afonine, Thanks for your kind help. Best wishes. On Fri, Jul 31, 2009 at 10:38 AM, Pavel Afonine <[email protected]> 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 > > > > > -- Jiamu Du, Ph.D. State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 320 Yue-Yang Road Shanghai 200031 P. R. China Tel: +86-21-5492-1117 E-mail: [email protected]
