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Dear all
I am refining a protein structure in which dithiothreitol (DTT) is
contained. The resolution is 2.1 A and the 2Fo - Fc electron density map is
clear. After several cycle refmac5 refinements, we found negative Fo -Fc
map near a sulfur of DTT using coot. The map was generated by AUTO OPEN MTZ
on coot. This negative density is NOT overlapped with the sulfur. The
distance between the center of the density and the sulfur is approximately
2.1 A. Another sulfur of DTT is bound to a heme iron. Now free-R factor is
dropped to 22.2 % (R = 18 %).
The intensity data was collected with a wavelength 1.0A.
What should I interpret the residual negative density ? Can I neglect of it
?
Any help will be welcome.
Best regards.
==========================
Masaki UNNO Ph.D.
Institute of Multidisciplinary Research
for Material
Tohoku University
tel +81-22-217-5117 or
+81-22-217-5749
fax +81-22-217-5118
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