Hello Mudassar ali Khan,
these R-values after refinement rather indicate a failure of Molecular
Replacement.
Did you see in aimless.pdf:
"WARNING: the L-test suggests that the data may be twinned
so the indicated Laue symmetry may be too high
Rough estimated twin fraction alpha from cumulative N(|L|) plot 0.215 +/-
(0.013)
Estimated twin fraction alpha from 0.209
Estimated twin fraction alpha from 0.199"
In case of twinning, a subgroup of P63 could be the correct spacegroup.
Subgroups of P63 are P3 and P21.
I'd try Molecular Replacement in these two spacegroups, and twin refinement.
Best wishes,
Kay
On Mon, 7 Mar 2022 14:09:40 +0530, Mudassar Ali Khan <[email protected]>
wrote:
>Dear all,
>
>I am trying to solve an x-ray structure of a protein for which the
>structure is not available. I have performed data reduction using XDS
>followed by Aimless (output file attached herewith). Molecular replacement
>was performed using Phaser MR (CCP4i) with modelled structure followed by
>rigid body and restrained refinement. In coot, the electron density is
>fitting well with the structure, however, I am not able to reduce the
>R-work and R-free beyond 0.43 and 0.46 respectively.
>
>I have also tried the same with Phenix, but the R-work and R-free were
>almost the same as obtained from ccp4i.
>Any suggestion to reduce R-work and R-free will be greatly appreciated.
>
>Thanks!
>
>Regards,
>Mudassar Ali Khan
>Graduate student
>KS-101, Varma Lab
>Advanced Centre for Treatment Education and Research in Cancer (ACTREC)
>Navi-Mumbai, India
>
>########################################################################
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
>This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing
>list hosted by www.jiscmail.ac.uk, terms & conditions are available at
>https://www.jiscmail.ac.uk/policyandsecurity/
>
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
