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
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