Are you *sure* there's no translational NCS ?
For example your first molecular replacement solution out of Phenix shows
EULER 293.6 27.7 288.7
FRAC -0.02 0.02 0.02
(that's "first molecule at origin in P1")
and
EULER 294.0 27.9 288.8
FRAC -0.37 0.02 0.02
which is essentially the same orientation, and a translation down one
crystallographic axis (a*)
And this suggests to me that either Xtriage or Phaser is missing
something here. Does Phaser find translational NCS in its initial data
analysis ? Unmodeled translational NCS could cause significant problems
with the molecular replacement search.
Phil Jeffrey
Princeton
On 8/29/19 11:28 AM, Napoleão wrote:
Deal all,
Sorry for the long post.
I have a data set obtained from a crystal produced after incubating a
protease with a protein which is mostly composed by an antiparallel beta
sheet. I have tried numerous approaches to solve it, and failed.
Molecular replacement using Phaser, and the protease or the protein as a
template yields no solution. However, molecular replacement using only
part of the beta sheet yields LLG=320 TFZ==28.0 (see below).
The apparently good data extends to 1.9 A, as processed by XDS, and the
space group is P1 (pointless agree). XDS info below:
SPACE_GROUP_NUMBER= 1
UNIT_CELL_CONSTANTS= 44.43 72.29 77.30 97.802 89.939 101.576
a b ISa
9.647E-01 3.176E-03 18.07
RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR
R-FACTOR COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano
LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed
expected Corr
1.90 24890 19149 23814 80.4% 58.1%
63.7% 11482 0.77 82.2% 63.8* 3 0.694 492
total 163756 125884 146938 85.7% 10.6%
10.8% 75744 3.78 15.0% 99.0* -3 0.761 5834
Xtriage in Phenix 1.16-3549 gives me all green lights (print below),
suggesting the data presents no twinning, no translational NCS, no ice
rings and is not anisotropic.
http://fullonline.org/science/phenix_xtriage_green.png
Molecular replacement in Phaser yields single solutions like:
Solution annotation (history):
SOLU SET RFZ=3.0 TFZ=* PAK=0 LLG=29 RFZ=2.8 TFZ=8.8 PAK=1 LLG=310
TFZ==27.6
LLG=320 TFZ==28.0
SOLU SPAC P 1
SOLU 6DIM ENSE ensemble1 EULER 293.6 27.7 288.7 FRAC -0.02
0.02 0.02 BFAC
-6.03
SOLU 6DIM ENSE ensemble1 EULER 294.0 27.9 288.8 FRAC -0.37
0.02 0.02 BFAC
-6.52
SOLU ENSEMBLE ensemble1 VRMS DELTA -0.1983 RMSD 0.49 #VRMS 0.21
or partial solutions like:
Partial Solution #1 annotation (history):
SOLU SET RFZ=3.7 TFZ=* PAK=0 LLG=32 RFZ=2.8 TFZ=13.0 PAK=0 LLG=317
TFZ==30.2
LLG=331 TFZ==30.5 RFZ=2.4 TFZ=7.2 PAK=0 LLG=464 TFZ==18.5 RFZ=2.7
TFZ=5.7 PAK=1
LLG=501 TFZ==6.8 LLG=509 TFZ==6.6
SOLU SPAC P 1
SOLU 6DIM ENSE ensemble1 EULER 85.4 153.0 138.5 FRAC -0.01 -0.00
-0.00 BFAC
-12.30
SOLU 6DIM ENSE ensemble1 EULER 86.2 153.2 139.5 FRAC -0.36 -0.01
-0.01 BFAC
-9.16
SOLU 6DIM ENSE ensemble1 EULER 83.8 152.3 135.9 FRAC -0.00 0.00
-0.25 BFAC
1.52
SOLU 6DIM ENSE ensemble1 EULER 191.2 109.1 39.3 FRAC -0.27
-0.01 0.22 BFAC
10.18
SOLU ENSEMBLE ensemble1 VRMS DELTA -0.0447 RMSD 0.49 #VRMS 0.44
However, after 1 refinement round in Phenix_Refine (Final: r_work =
0.4881 r_free = 0.5009) I got densities that are part good and part bad,
and if I delete the bad parts and refine again, the good parts become
bad. Please check the prints:
http://fullonline.org/science/good_part_of_density.png
http://fullonline.org/science/bad_part_of_density.png
What is the explanation for these molecular replacement results?
What else should I try? Arcimboldo takes 2 days+ to run and yields no
good solution.
Thank you!
Regards,
Napo
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