Dear C-Daddy,
Did you look at the maps? Do you see any astonishing misinterpretations
there?
Do you think that the completeness in the last resolution shell would
affect the maps and the model? If so, why?
There are many possible reasons for the discrepancy you pointed out. In
I422 a=b, alpha=90.00, so typos in the table are the most probable
reason. I did look at the maps after running a quick refinement. Both
the structure and the ligand are fine. I would probably add solvent
molecules myself, but some conservative crystallographers prefer not to
do it, even at 2.5 A.
In other words, there is nothing wrong with this deposit. I would even
say that the level of sloppiness is below the average for this one.
D.
On 2017-06-29 11:07 AM, CDaddy wrote:
Dear colleagues,
I am really astonished by a recently released structure 5XQL. This
structure was just published in BBRC with a super fast process
(accepted overnight). Significant inconsistences were observed when I
compared the Data collection and refinement statistics in the paper
and at PDB website. The paper shows the crystal belong to I 4 2 2
with a=135.77, b=136.11, c=95.13 (Å) ; α=90.01. The resolution is
2.5Å with completeness of 99.7 (99.1). However when I checked the
released structure I got a= b=135.94, c=95.13 (Å) ; α=90.0. The
resolution is 2.5Å with completeness of 81.5 (44.0). The
completeness of the highest resolution shell is so low that 2.5Å
seems unreasonable. At first I thought that the authors could be
rookies in structural biology. But the molecular replacement in this
paper could be very difficult due to very low sequence identity
between the search model and the final structure. It was unlikely that
two new hands could solve it easily. Is there anyone who has this kind
of experience and know why?
With best wishes,
Richard
--
Dominika Borek, Ph.D. *** UT Southwestern Medical Center
5323 Harry Hines Blvd. *** Dallas, TX 75390-8816
214-645-9577 (phone) *** 214-645-6353 (fax)
