Dear Jain, The Wilson plot is based on the assumption that you can model your structure with a collection of atoms randomly distributed in the unit cell. This model is very poor at low resolution, say, 4.5A and lower. Since the Wilson B depends on the change in scattering as a function of resolution, a Wilson B calculated for 3A data will be very unreliable, being based only on the data from 4.5A to 3A.
Once you begin refinement you have a proper model of your crystal and all the low resolution data can be used to estimate the average B. At this point the Wilson B should be ignored, it was only a stepping stone to get you here. A Wilson B of 50 to 60A^2 for a 3A data set collected on frozen crystals at a synchrotron (I'm making an assumption here.) is quite surprising. 137A^2 seems much more likely to me. I'd trust CNS's results. The overall anisotropic correction should be fine at this resolution too. Dale Tronrud Jian Wu wrote: > Dear all, > > Recently we have collected one set of data which is processed to 2.9A > and 3.0A and the Wilson-B values are 50.1 and 59.1, respectively. As for > the completeness of the highest shell is only 66% in 2.9A (80% in 3.0A), > we use the dataset with 3.0A for phasing and refinement. > > Everything is OK during phasing. Routinely, we use CNS (rigid, minimize > and bgroup) for primary refinement and the R and freeR values go to 31.1 > and 34.1. Surprisingly, the B-factor is 137.2. I have modified the > B-factor to a fixed value (59.1 A^2) in the searching model coordinate > file, however it changed to 127.6 after 'rigid' and subsequently to > 131.9 after 'minimize'. In all the scripts above I used the default > option "anisotrpic" at "overall B-factor correction". I don't know > whether it is right to use this option at low resolution, so I have > tried the other two options "no" and "isotropic". In the 1st choice, the > B-factor is seemingly reasonable (55~59) but the R and freeR are very > high (45.9 and 51.9). In the 2nd choice, the B-factor, R and freeR > values are between those of the other two options (111.3, 40.6, and > 45.3). I want to know what cause these surprising changes especially for > B-factor value. > > Any suggestion is appreciated. > > Jian Wu > > -- > Jian Wu > > Ph.D. Student > Institute of Biochemistry and Cell Biology > Shanghai Institutes for Biological Sciences > Chinese Academy of Sciences (CAS) > Tel: 0086-21-54921117 > Email: prote...@gmail.com <mailto:prote...@gmail.com> >
