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Dear fellow
crystallographers, This is only partially
related to CCP4, but I hope my fellow crystallographers subscribed to CCP4 list-server would like to give me help
and advices. I have a protein of the size
of about 90 kDa. I have been able
to grow very tiny crystals from this protein (about 0.1x0.1x0.05 mm3 in
dimension). The crystals diffracted
X-ray better than 3 A. Even though
the diffraction spots are pretty weak, the scaling of the data was pretty good
to 3 A with the r-merge of 0.12 and completeness of 99%. The space group of the crystals is
I4. Analysis of the systematic
absence reflections indicated that there is no screw axis, i.e., the space group
cannot be I4(1). I have a structure model
from the same kind protein from a different species that was refined to 2.0
A. The sequence alignment of the
two proteins indicated that all important structure elements are conserved. They share 44% identity in sequence with
very few deletions or insertions (3%).
Thus, I thought it would be easy and straightforward to solve the new
structure using the MR method. However, all of my efforts
using either CNS or AMORE programs to find the structure solution have failed so
far. Using CNS, the rotation
function search yielded a list of solutions in which the top peaks (over ten
peaks) always have the RF-function value of 1.000 (I don¡¯t know what it means
here). The subsequent translation
search yielded a list of results with very poor monitor values and packing
value. For space group I4, the
translation search should carry out only along x- and y-axes. But CNS also does the translation search
along z-axis.
Using AMORE, both rotation
function search and translation function search resulted no outstanding
peaks. Most of the peaks in the
list had correlation coefficient around 0.3-0.4 and R-factor around 0.55. I am wondering if there is
something wrong with my data or there are other problems too. Does anyone in the community have
similar experience? Does anyone have any clue on what¡¯s going wrong here? Or does anyone have any suggestions and
advices for me? Thank you very much in
advance for your help. Sincerely
yours, Jianping
Ding
CABM
and Rutgers University
679
Hoes Lane
Piscataway,
NJ 08854
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