B_sol from EDS

From: Bernhard Rupp (Hofkristallrat a.D.)
Date: 30 January 2012 19:10


Dear All,

when I plot bulk solvent B and K extracted from EDS, an improbable and
bimodal distribution appears.
In the B_sol vs k_sol PDF a sharp line of values with B-sol of 70 appears
(B-axis left to right, 0-200).

http://www.ruppweb.org/images/b_sol_contour.jpg
http://www.ruppweb.org/images/b_sol_surface.jpg

According to a quick peak at EDS instructions,
it uses the REFMAC flat bulk solvent model throughout  for bulk solvent
correction.

The main peak in fact has the expected distribution, but it seems that the
sharp peak at B_sol=70
represents some cut-off that in a certain set of calculations was used.

For data mining it would be useful to know where/when these cutoffs were
used.

Best regards, BR
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Bernhard Rupp
http://www.ruppweb.org/                
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From: Pavel Afonine


Hi Bernhard,

I just calculated k_sol and B_sol for all PDB entries that 

     - have reflection data available, 

     - I could re-compute the R-factor within 5%, and 

     - R-work<30% 

using a simple cctbx script. Here is what I get:

Distribution of k_sol:
     0.000 - 0.060      : 27
     0.060 - 0.120      : 12
     0.120 - 0.180      : 51
     0.180 - 0.240      : 182
     0.240 - 0.300      : 1770
     0.300 - 0.360      : 13819
     0.360 - 0.420      : 19731
     0.420 - 0.480      : 3039
     0.480 - 0.540      : 471
     0.540 - 0.600      : 256

Distribution of B_sol:
     0.000 - 31.300     : 4349
    31.300 - 62.600     : 29425
    62.600 - 93.900     : 4578
    93.900 - 125.200    : 597
   125.200 - 156.500    : 225
   156.500 - 187.800    : 84
   187.800 - 219.100    : 37
   219.100 - 250.400    : 23
   250.400 - 281.700    : 10
   281.700 - 313.000    : 30

It seems like the result of similar exercise done by Fokine and Urzhumtsev (Acta Cryst. (2002). D58, 1387-1392) still holds (see figure 3 on page 1390 there).

Pavel

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From: Bernhard Rupp (Hofkristallrat a.D.)

Yes, that is about what one would expect. I also checked a few of the extreme outliers, and almost always can come up with a reasonable value. Which does not remove my curiosity regarding the B_sol 70 cutoff and its purpose.

 

Cheers, BR