Dear all
The P21 unit cell is a=86.499 b=38.554 c=94.027 al=90.0 be=97.92 ga=90.0
The C2 unit cell is a=103.932 b=62.253 c=96.305 al=90.0 be=111.934
ga=90.0
Phaser and the other programs do give me solutions but the LLG in
Phaser is about -1000's and the highest TFZ score I get is 4.9, and
for molrep the Rfac is about 0.600's. I even tried to do rigid body
with the solutions obtained and I get an increase value for Rfact and
Rfree of 55-56%.
Thank you all for your suggestions. I'll use them right now.
Teresa
On Aug 23, 2010, at 11:43 AM, Peter Zwart wrote:
can you list you cell constants?
On 23 August 2010 09:10, Teresa De la Mora <[email protected]> wrote:
Dear all
I have a molecular replacement problem and I really need your help
with this
one. My protein crystallized in C2 instead of P21 like it did
before. Now
when I tried to do MR to place it in C2 it doesn't work, I get no
solution.
This protein has been crystallized in P212121, P31, P43 and C2 and
it has
two loops in different regions that depending on the packing,
they'll show
density so it is flexible. When I crystallized it the first time in
P21 and
used a publish model I had no problem at all to place it, just
right now.
I've have tried molrep, phaser and phenix with different resolution
ranges
(40-3.0, 20-3.0, 10-3.0) and different models, i.e. publish
structures or
the one I got at P21. I also tried doing rotation first at different
resolutions then compare the peaks obtained and picked the ones
that are
consistent and give that for translation search and yet no
solution. The
resolution is 2.4 A and the Matthews coefficient predicts 3
molecules in ASU
with 43.6% solvent. I also tried searching for 2 molecules just in
case that
it is high solvent content (62.5%) as monomer and as dimer and yet no
solution. The data itself processed well and I've processed in HKL
and
d*trek and used both processed files and yet no solution.
Completeness is
96.9% overall and 82% (2.49-2.40) shell. Redundancy is 3.5 overall
and 2.6
at the(2.49-2.40) shell. Here is the table from HKL:
Lower Upper Average Average Norm. Linear Square
Angstrom I error stat. Chi**2 R-fac R-
fac
50.00 5.17 901.9 35.9 10.2 1.105 0.041 0.051
5.17 4.10 962.8 47.7 11.6 0.971 0.045 0.049
4.10 3.58 496.4 25.9 9.2 1.194 0.063 0.067
3.58 3.26 309.9 15.2 8.4 1.360 0.069 0.067
3.26 3.02 153.9 9.9 7.2 1.456 0.105 0.098
3.02 2.85 100.8 7.3 6.9 1.864 0.141 0.120
2.85 2.70 57.4 7.0 6.8 1.584 0.200 0.162
2.70 2.59 41.9 7.5 7.0 1.348 0.246 0.220
2.59 2.49 30.5 7.4 7.3 1.526 0.329 0.285
2.49 2.40 22.5 8.0 7.8 1.347 0.388 0.361
All reflections 319.9 17.6 8.3 1.366 0.065 0.056
Would you please, please give me some tips, tricks, advice,
encouragement?
:-)
Thank you so much
Teresa
Teresa De la Mora-Rey Ph.D.
Dept. Medicinal Chemistry
University of Minnesota
8-101 Weaver-Densford Hall
308 Harvard St. SE, Minneapolis, MN 55455
Lab phone (612) 626-5226
"If you never did you should. These things are fun and fun is good"
Dr.
Seuss
--
-----------------------------------------------------------------
P.H. Zwart
Research Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
SASTBX: http://sastbx.als.lbl.gov
-----------------------------------------------------------------
Teresa De la Mora-Rey Ph.D.
Dept. Medicinal Chemistry
University of Minnesota
8-101 Weaver-Densford Hall
308 Harvard St. SE, Minneapolis, MN 55455
Lab phone (612) 626-5226
"If you never did you should. These things are fun and fun is good"
Dr. Seuss
