Hi Marco,
Further to Zhen's comment, that can also happen if you have a cusp
containing one of the reciprocal lattice axes. The SG may be P212121 but
one of the 21 is never located due to the missing data.
You will always sort of get a solution from MR but you should look at
the Z-score of the translation function for the solution you get - if it
is below 8, it's very likely you have the wrong solution, and the most
likely culprit is the wrong phasing model. As Tom suggested, you should
validate the crystallized molecule - you might have purified the wrong
one (it happened to me a few times) even though the MW might be in the
right ballpark.
Best regards and good luck,
Pedro
On 20/02/2024 01:30, Gong, Zhen wrote:
Hello Marco,
I also feel that it might be due to the wrong space group because all
the homologous models and alphafold model did not improve the R
values. Make sure that you turn on “All possible in same pointgroup”
when you run Phenix.Phaser-MR. I work with P212121 crystals a lot.
Sometimes, if the diffraction quality was not good, the data will be
indexed as P222, or P21212 etc, and sometimes even C2221. Try all
possible in same pointgroup and see what happens. Good luck!
Zhen
*From: *CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Marco
Bravo <mbrav...@ucr.edu>
*Date: *Monday, February 19, 2024 at 20:17
*To: *CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>
*Subject: *[EXTERNAL] Re: [ccp4bb] Difficult Molecular replacement
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Hello Todd, I get the best solution for p22121 space group after MR
with an LLG score of 640 from phaser. and the Rfree is .4748. However
after MR refinement does not lower the Rfree and it appears to make
the Rfree worse. The XDS software indicates that my best solution is
P21 21 2. Often Phaser MR places the solution in P 21 21 2. The
helicase is a superfamily 2 helicase and is only monomeric. Its a
543aa long protein with a MW of 62Kda. It should have two RecA like
domains at the core but the protein I have crystallized has a
previously uncharacterized n-terminal domain responsible for tight
single stranded DNA binding. I have tried different space groups
manually but that resulted in clashing. I will be frank I do need to
work on my crystallography background as crystal lattices, space
group, and self-rotaion functions are limited. Thank you so far for
your help , I will try further trimming down my search model into
separate domain and trying that in the meantime.
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