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A handful of misplaced waters with extremely high B-factors can shift
the average by several squared Angstroems. It is probably better to
compare the median temperature factor of the model with the value from
the Wilson plot.
On 21 Dec 2006, at 10:14, Eleanor Dodson wrote:
B factors reflect the quality of your measured data. Assuming that is
properly processed the average B for the model should more or less
match the Wilson B
You will always get quite a range between the interior of the protein,
and the surface residues which may well be in multiple conformations.
Eleanor
Zhongli Cui wrote:
Dear all,
I am refining the models of a glucosidase, one is native form and the
other is a complex. Here are statistcs results of the 2 models:
for native
working set= 0.1835 test set= 0.2140
luzzati coordinate error (5.0 - 1.9 A ): 0.21 A
cross-validated luzzati coordinate error (5.0 - 1.9 A
): 0.24 A
sigmaa coordinate error (5.0 - 1.9 A ): 0.20 A
cross-validated sigmaa coordinate error (5.0 - 1.9 A
): 0.21 A
rmsd bonds= 0.005098 with 0 bond violations > 0.05
rmsd angles= 1.30986 with 65 angle violations > 8.0
rmsd dihedrals= 23.97789 with 5 angle violations >
60.0
rmsd improper= 0.76021 with 61 angle violations >
3.0
average B-factor= 30.0377
minimum B-factor= 2.55649
maximum B-factor= 95.0965
B rmsd for bonded mainchain atoms= 1.155
B rmsd for bonded sidechain atoms= 1.792
B rmsd for angle mainchain atoms= 1.722
B rmsd for angle sidechain atoms= 2.549
For complex
working set= 0.1973 test set= 0.2374
luzzati coordinate error (5.0 - 2.1 A ): 0.25 A
cross-validated luzzati coordinate error (5.0 - 2.1 A
): 0.30 A
sigmaa coordinate error (5.0 - 2.1 A ): 0.25 A
cross-validated sigmaa coordinate error (5.0 - 2.1 A
): 0.30 A
rmsd bonds= 0.005633 with 0 bond violations > 0.05
rmsd angles= 1.32029 with 55 angle violations > 8.0
rmsd dihedrals= 24.05490 with 4 angle violations >
60.0
rmsd improper= 0.76886 with 61 angle violations >
3.0
================================== B-factors
=================================
average B-factor= 40.2614
minimum B-factor= 13.7972
maximum B-factor= 84.5672
B rmsd for bonded mainchain atoms= 1.145
B rmsd for bonded sidechain atoms= 1.764
B rmsd for angle mainchain atoms= 1.712
B rmsd for angle sidechain atoms= 2.410
I wold like to know if the models are acceptable? Does the high
B-factor matter? what caused the high values of B-factors?
Thanks in advance for any comment.
Cheers
Zhongli
<ccp4.vcf>
--
http://www.ysbl.york.ac.uk/~emsley
Structural Biology Laboratory, University of York, York, YO10 5YW, UK
