Hello,
I am doing structure refinement using only RDCs on a zinc coordinating
protein. I am getting a large number of violations in Bonds and Angles but
<5 violations in my RDCs. I thought it might have something to do with the
following message I get when I run Xplor...
AT_Build::buildNode: cycle link found between atoms 16 HIS 1 C and 4 HIS 1
CA
removing bond.
AT_Build::buildNode: cycle link found between atoms 262 CYS 17 CB and 260
CYS 17 CA
removing bond.
AT_Build::buildNode: cycle link found between atoms 478 CYS 31 C and 472 CYS
31 CA
removing bond.
AT_Build::buildNode: cycle link found between atoms 513 CYS 34 SG and 761
ZN2 301 ZN+2
removing bond.
AT_Build::buildNode: cycle link found between atoms 583 HIS 39 ND1 and 760
ZN2 300 ZN+2
removing bond.
AT_Build::buildNode: cycle link found between atoms 757 CYS 50 SG and 761
ZN2 301 ZN+2
removing bond.
I have 2 zinc atoms both are coordinated by 3 cys and 1 his. All of the
bonds removed above are in zinc coordinating residues but not all residues
that coordinate have bonds removed. Is this what could be causing my
structure to not refine properly? Thank you for your advice.
Mikaela
--
Mikaela Stewart
Graduate Student
Dr. Tatyana Igumenova Lab
Biochemistry & Biophysics
(979)845-6313
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