[ccp4bb] Molecular replacement problem
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 360.00.00.0 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<https://pod51004.outlook.com/owa/redir.aspx?C=ccbf42ffea5f48b1bf8e9bb950454bab=http%3a%2f%2ftryptophan.net> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
[ccp4bb] CCP4 7.1 problems
I installed CCP4 7.1 yesterday, and I have problems. On an Ubuntu 18.04 LTS
system, I get the following:
rob@rob-SA76R4:~$ ccp4i2
Running CCP4i2 browser from: /home/rob/CCP4/ccp4-7.1/share/ccp4i2
Python 2.7.16 (default, Apr 22 2020, 09:15:14)
[GCC 4.9.1 20140922 (Red Hat 4.9.1-10)]
Qt version 4.8.7
Illegal instruction
Then, back to the prompt.
Similarly, with COOT:
rob@rob-SA76R4:~$ coot
INFO:: Reading coordinate file:
/home/rob/CCP4/ccp4-7.1/share/coot/standard-residues.pdb
INFO:: file /home/rob/CCP4/ccp4-7.1/share/coot/standard-residues.pdb has been
read.
Spacegroup: P 1
/home/rob/CCP4/ccp4-7.1/bin/coot: line 333: 13382 Illegal instruction
$coot_bin "$@"
;;; note: source file /home/rob/CCP4/ccp4-7.1/share/guile/1.8/ice-9/boot-9.scm
;;; newer than compiled
/usr/lib/x86_64-linux-gnu/guile/2.2/ccache/ice-9/boot-9.go
Uncaught exception:
Throw to key syntax-error with args ("memoization" "In file ~S, line ~S: ~A
~S." ("/home/rob/CCP4/cc
p4-7.1/share/guile/1.8/ice-9/boot-9.scm" 103 "Bad define placement" (define
(syntax) (error "syntax
error in eval-case"))) #f)
I upgraded the system to Ubuntu 20.04 LTS (also released yesterday), and have
the same problems.
However, ccp4i starts normally.
Rob
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<https://pod51004.outlook.com/owa/redir.aspx?C=ccbf42ffea5f48b1bf8e9bb950454bab=http%3a%2f%2ftryptophan.net>
To unsubscribe from the CCP4BB list, click the following link:
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[ccp4bb] difficult molecular replacement solution
I have been working on a protein structure which has been hard to solve by molecular replacement. Unit cell: (60.6, 172.34, 196.42, 90, 90, 90) Space group: P 21 21 21 The problem is that the homologues have only ~20% identity, and there are multiple chains in the asymmetric unit. The question is how many. It could be 4, 5, or 6 chains. N solvent P 4 0.602 3.090.225 5 0.502 2.470.388 6 0.403 2.060.229 I have run PHASER with 4, 5 and 6 chains. I allowed it to search all possible space groups, and P212121 was the best solution. These are the results. N LLG TFZ 4 104.97.5 5 137.57.7 6 166.28.3 Am I correct to conclude that there are 6 chains in the asymmetric unit? Rob 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<https://pod51004.outlook.com/owa/redir.aspx?C=ccbf42ffea5f48b1bf8e9bb950454bab=http%3a%2f%2ftryptophan.net> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Rfree too high
I have several data sets of Salmonella tryptophan synthase with different ligands bound in the beta-site. The data look good, with high resolution, and reasonable Rmeas. The ligand density is very clear. However, refinement seems to be stuck at Rfree = 22%. For this resolution (~1.4 A) it should be much better. What could be the problem? SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION RESOLUTION NUMBER OF REFLECTIONSCOMPLETENESS R-FACTOR R-FACTOR COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr 3.36 326939651 10592 91.1% 4.4% 4.4% 32413 25.04 5.2%99.5* -250.6645619 2.37 60677 18085 18996 95.2% 7.3% 6.2% 60528 14.98 8.7%99.4* -110.8519578 1.94 75443 22363 24467 91.4% 19.2% 18.1% 749277.24 22.9%98.3* -120.746 12521 1.68 98569 27401 28903 94.8% 55.8% 61.7% 983062.95 65.8%92.5* -100.605 19049 1.50 92322 29771 32735 90.9% 126.4%149.8% 904801.04152.2%66.2* -110.556 14412 1.37 83172 33456 36126 92.6% 230.1%294.2% 795060.42291.8%30.0* -100.5227366 1.27 58312 26805 39186 68.4% 433.1%576.6% 525130.17561.4%12.4*-70.4873528 1.19 22864 13015 42131 30.9% 756.0% 1028.6% 178500.06 1021.4% 3.5 -40.469 546 1.1255564284 447859.6% 757.7%997.8% 25440.03 1071.6% 0.4 00.000 0 total 529608 184831277921 66.5% 10.2% 10.6% 5090674.36 12.2%99.7* -120.642 72619 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<https://pod51004.outlook.com/owa/redir.aspx?C=ccbf42ffea5f48b1bf8e9bb950454bab=http%3a%2f%2ftryptophan.net> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
