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[ccp4bb]: Bulk solvent model in REFMAC
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Hello,
I have recently switched from CNS to using REFMAC for the final
refinement/analysis of several structures. I have almost immediately
come across two interesting cases where the Babinet Bulk Solvent model
in REFMAC does some interesting things. In the case of a high
resolution dimer structure (1.9 A) , refined with 4 TLS domains the
freeR factor dropped so that is was lower than the working R. Why would
this happen? In the second case, a moderate resolution structure (2.7
A) with five-fold NCS was refined with one TLS domain per chain. The
B-factors dropped and a large fraction of them were pinned at 2, when
the default Bbulk value of 200 was used. I have tried varying the Bbulk
values to minimize the freeR, with the results below. Note that the
test sets are the same in both CNS and REFMAC. This has raised several
questions:
Q1. Should the bulk solvent scale (ki) be interpreted to have a
physical meaning as suggested by Glykos & Kokkinidis (Acta Cryst. (200)
D56, 1070-72), where they say that ki and Bbulk are not independent and
Ki should be ~0.8 for most proteins? In this case why is ki=0.001 when
the freeR is a minimum for the dimer structure?
Q2. How can the free R refine to a value lower that the working R, when
its initial value is higher?
Q3. In the case of the low resolution pentamer structure with 5-fold
NCS, is it reasonable to use such a low Bbulk? The Ki for this case is
in closer agreement with that suggested by Glykos & Kokkinidis.
Certainly the refinements which result in many individual atomic
B-factors being pinned at 2.00 are not correct. Note that normally
REFMAC does not permit the Bbulk value to be set below 70.
1.9A dimer
Bbulk Overall Working Free R Mean B Babinet's
scale
CNS 50.77 Rw=21.73 Rf=24.44 <B>=38.50 ki=0.340#
0813x60. 60 Ro=21.773 Rw=21.807 Rf=21.143 <B>=24.856 ki=0.169
0813x80. 80 Ro=21.694 Rw=21.729 Rf=21.040 <B>=21.860 ki=0.017
0813x100 100 Ro=21.695 Rw=21.731 Rf=21.028 <B>=21.461 ki=0.001
0813x120 120 Ro=21.702 Rw=21.740 Rf=20.999 <B>=21.019 ki=0.001<<
0813x150 150 Ro=21.741 Rw=21.780 Rf=21.002 <B>=20.637 ki=0.001
080515x 200 Ro=21.796 Rw=21.837 Rf=21.028 <B>=20.211 ki=0.001
2.7 A pentamer with five-fold NCS
Bbulk Overall Working Free R Mean B Ki #B=2
CNS 34.75 R=22.08 Rf=24.32 <B>=47.5 0.359 #CNS
(ki=0.359)
080711x 200 Ro=23.322 R=23.232 Rf=25.000 <B>= 7.4 0.371 #(276)
0808125 125 Ro=23.174 R=23.086 Rf=24.795 <B>=11.3 0.465 #(25)
080616x 100 Ro=23.157 R=23.073 Rf=24.718 <B>=14.0 0.526 #(3)
080716x ~100.3 Ro=23.155 R=23.071 Rf=24.718 <B>=14.1 0.523 #(three
B=2)
0808090 90 Ro=23.155 R=23.071 Rf=24.694 <B>=15.5 0.555 #(one)
0808075 75 Ro=23.161 R=23.080 Rf=24.671 <B>=18.4 0.608 ###
081316 60 Ro=23.174 R=23.094 Rf=24.651 <B>=22.5 0.670 ###
081314 50 Ro=23.187 R=23.108 Rf=24.643 <B>=25.5 0.718 #<<
081310 40 Ro=23.203 R=23.125 Rf=24.644 <B>=29.0 0.769 ###
--
Best Regards,
Mark
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Mark A. White, Ph.D. Tel:
Sealy Center for Structural Biology (409) 747-4747
Dept. of Human Biological Chemistry & Genetics Fax:
Basic Science Building, Room 660C (409) 747-4745
University of Texas Medical Branch email:
Galveston, TX 77555-0647 mailto://white@xray.utmb.edu
http://xray.utmb.edu http://www.xray.utmb.edu/~white
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