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Typical R-factors for structures at around 1.45A are:<br>
<br>
phenix.r_factor_statistics 1.45<br>
<br>
Histogram of Rwork for models in PDB at resolution 1.35-1.55 A:<br>
0.092 - 0.122 : 40<br>
0.122 - 0.152 : 344<br>
0.152 - 0.183 : 743<br>
0.183 - 0.213 : 722 <<< your structure<br>
0.213 - 0.243 : 206<br>
0.243 - 0.273 : 18<br>
0.273 - 0.303 : 3<br>
0.303 - 0.334 : 0<br>
0.334 - 0.364 : 1<br>
0.364 - 0.394 : 1<br>
Histogram of Rfree for models in PDB at resolution 1.35-1.55 A:<br>
0.113 - 0.148 : 18<br>
0.148 - 0.183 : 333<br>
0.183 - 0.217 : 982<br>
0.217 - 0.252 : 607 <<< your structure<br>
0.252 - 0.287 : 125<br>
0.287 - 0.322 : 10<br>
0.322 - 0.357 : 1<br>
0.357 - 0.391 : 0<br>
0.391 - 0.426 : 0<br>
0.426 - 0.461 : 2<br>
Histogram of Rfree-Rwork for all model in PDB at resolution
1.35-1.55 A:<br>
0.001 - 0.011 : 82<br>
0.011 - 0.020 : 476<br>
0.020 - 0.030 : 666 <<< your structure<br>
0.030 - 0.040 : 381<br>
0.040 - 0.050 : 246<br>
0.050 - 0.059 : 121<br>
0.059 - 0.069 : 70<br>
0.069 - 0.079 : 26<br>
0.079 - 0.088 : 4<br>
0.088 - 0.098 : 6<br>
Number of structures considered: 2078<br>
<br>
So, your R-factors look quite normal given the resolution.<br>
<br>
Regarding Wilson vs Average B-factors, here is the statistics over
PDB:<br>
<br>
<small><font face="Courier New, Courier, monospace">Resolution_range
Wilson_B
Average_B Number_of_structures<br>
0.00 - 1.00 9.77 13.11 94<br>
1.00 - 1.25 10.58 16.44 401<br>
1.25 - 1.50 13.50 19.14 1050<br>
1.50 - 1.75 17.20 21.76 3600<br>
1.75 - 2.00 22.27 26.82 5510<br>
2.25 - 2.50 35.70 39.42 3385<br>
2.50 - 2.75 43.71 44.73 2844<br>
2.75 - 3.00 53.86 51.94 1628<br>
3.00 - 3.25 65.11 60.76 780<br>
3.25 - 3.50 81.69 78.70 165<br>
3.50 - 3.75 92.67 88.84 100<br>
3.75 - 4.00 111.83 102.29 30<br>
</font></small><br>
(*) Wilson_B is computed using phenix.model_vs_data<br>
Average_B is computed using phenix.model_vs_data from PDB file
(TLS is accounted for)<br>
Structures selected such that the recomputed R-factor matches
the
one in PDB file header within 1%.<br>
<br>
As you see, your B-factors are quite high. Should you worry about
it? I don't know. If everything else is done right and look good (as
good as R-factors), then no, otherwise I would think what might be
the cause for this. Although it's interesting to know why this
happens. I will probably look at the histogram of Wilson B and
average B around this resolution to see what people had in the past.<br>
<br>
Pavel.<br>
<br>
<br>
On 8/3/10 10:48 PM, Peter Zwart wrote:
<blockquote
cite="mid:AANLkTi=Qi4ym5Vuez6p5=vPYuujhSyxvS0zDiEaFzanc@mail.gmail.com"
type="cite">If you did use aniso B and are stuck at 19.8% for a
'true' 1.45 A data set, I suspect that something might be off ....
<div><br>
</div>
<div>did you check possibilities for twinning?</div>
<div><br>
</div>
<div>did you optimize weights properly?</div>
<div><br>
</div>
<div>P</div>
<div><br>
<div><br>
</div>
<div><br>
<div><br>
</div>
<div><br>
<br>
<div class="gmail_quote">2010/8/3 Geoffrey Feld <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:gkfeld@berkeley.edu">gkfeld@berkeley.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">Dear PhenixBBers,<br>
<br>
I'm working on a 1.45 A structure I solved using MR
(phaser) and I'm pretty close to finishing, just
plopping in waters and fixing rotamers. Rw = 19.8 Rfree=
22.8. I am a little concerned because my Wilson B is
27.00 while my average B for macromolecule is more like
43, and for solvent is 48. I have enough data to use
anisotropic ADP refinement, which was a big help in
bringing down the Rfree, but the average B hasn't really
moved much. Should I be concerned about this? Should I
try adjusting the wxu, or some other parameter? <br>
<br>
Thanks!<br>
<font color="#888888">-- <br>
Geoffrey K. Feld<br>
<br>
Department of Chemistry<br>
492 Stanley Hall<br>
University of California, Berkeley<br>
<br>
"Vigilia pretium libertatis"<br>
</font><br>
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<br>
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<br>
-- <br>
-----------------------------------------------------------------<br>
P.H. Zwart<br>
Research Scientist<br>
Berkeley Center for Structural Biology<br>
Lawrence Berkeley National Laboratories<br>
1 Cyclotron Road, Berkeley, CA-94703, USA<br>
Cell: 510 289 9246<br>
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