Dear Robert,
In addition to the remarks and suggestions by others: How do your electron density maps look like? Do they look remotely reasonable, or do they look like they had gone through a meat grinder? If they look remotely ok, you could also try manual rebuilding, pruning etc. However, if they look chopped, there is no sense in trying to (re)build anything in it, either manually or automatically. I guess you tried all permutations and variations of P2221, with zero, one and two screw axes in all positions?
Best,
Herman
Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Robert S Phillips
Gesendet: Donnerstag, 18. Juni 2020 15:01
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] Molecular replacement problem
EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk
I've been pulling out my hair with this for a few months now. I have data sets to 2.6 A for a new enzyme in the aminotransferase superfamily. Unfortunately, the closest structure is only 25% identity. MR with PHASER using the monomer was a complete failure. Since the minimum structure of enzymes in the family is a dimer (the active site is formed at the monomer-monomer interface), I used dimers for MR with PHASER. Most of the results were marginal, but one looks good. However, it will not refine. Everything I have done with this solution has failed, simulated annealing, morphing, etc., it will not refine; AUTOBUILD and BUCCANEER with it do not give any useable models, since they have poor statistics and low completeness. The output from PHASER is below.
** SINGLE solution
** Solution written to PDB file: DGL_phaser.1.pdb
** Solution written to MTZ file: DGL_phaser.1.mtz
Solution annotation (history):
SOLU SET RFZ=18.9 TFZ=23.0 PAK=0 LLG=193 TFZ==8.3 LLG=994 TFZ==20.1 PAK=0 LLG=994 TFZ==20.1
SOLU SPAC P 2 2 21
SOLU 6DIM ENSE ense_1 EULER 360.0 0.0 0.0 FRAC -0.00 -0.00 -0.00 BFAC -0.12 MULT 2 #TFZ==20.1
SOLU ENSEMBLE ense_1 VRMS DELTA -3.5403 #RMSD 2.08 #VRMS 0.89
With LLG = 994 and TFZ = 20.1, isn't this a real solution?
Robert S. Phillips
Professor of Chemistry and of Biochemistry and Molecular Biology
University of Georgia
Athens, GA 30602
Phone: (706) 542-1996
Fax: (706) 542-9454
E-mail: rsphill...@chem.uga.edu
Web: http://tryptophan.net
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