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Hi Sneha,<br>
<br>
typical R-factors at this resolution are (using
"phenix.r_factor_statistics 1.9" command):<br>
<br>
Histogram of Rwork for models in PDB at resolution 1.80-2.00 A:<br>
0.093 - 0.118 : 4<br>
0.118 - 0.143 : 216<br>
0.143 - 0.168 : 2142<br>
0.168 - 0.193 : 5011<br>
0.193 - 0.218 : 3592<br>
0.218 - 0.243 : 1090 <<< your case<br>
0.243 - 0.268 : 151<br>
0.268 - 0.293 : 20<br>
0.293 - 0.319 : 1<br>
0.319 - 0.344 : 3<br>
Histogram of Rfree for models in PDB at resolution 1.80-2.00 A:<br>
0.138 - 0.163 : 40<br>
0.163 - 0.189 : 651<br>
0.189 - 0.214 : 3178<br>
0.214 - 0.240 : 4512<br>
0.240 - 0.265 : 2809 <<< your case<br>
0.265 - 0.290 : 854<br>
0.290 - 0.316 : 159<br>
0.316 - 0.341 : 22<br>
0.341 - 0.367 : 3<br>
0.367 - 0.392 : 2<br>
Histogram of Rfree-Rwork for all model in PDB at resolution
1.80-2.00 A:<br>
0.000 - 0.010 : 97<br>
0.010 - 0.020 : 683<br>
0.020 - 0.030 : 2367<br>
0.030 - 0.040 : 3800 <<< your case<br>
0.040 - 0.050 : 3085<br>
0.050 - 0.060 : 1422<br>
0.060 - 0.070 : 511<br>
0.070 - 0.080 : 172<br>
0.080 - 0.090 : 73<br>
0.090 - 0.100 : 20<br>
Number of structures considered: 12230<br>
<br>
..so, in terms of R-factors your are fine.<br>
<br>
Run Comprehensive validation in Phenix GUI and check all "red
flags". I would say you need to be able to explain
rotamer/Ramachandran outliers or fix them otherwise.<br>
<br>
Pavel<br>
<br>
<br>
<br>
<div class="moz-cite-prefix">On 10/24/14 11:50 AM, Sneha Rangarajan
wrote:<br>
</div>
<blockquote
cite="mid:0F18166AABA9A440B2ECDE2A1F7F53EB0A5A1319@OITMX1006.AD.UMD.EDU"
type="cite">
<div class="WordSection1">
<p class="MsoNormal">Hi everyone,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">For a 1.9A dataset, here are my statistics-<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Rfactors: 22/26 <o:p></o:p></p>
<p class="MsoNormal">Ramachandran favored: 90.60%<o:p></o:p></p>
<p class="MsoNormal">Ramachandran outliers: 2.17%<o:p></o:p></p>
<p class="MsoNormal">Rotamer outliers: 4%<o:p></o:p></p>
<p class="MsoNormal">Clashscore: 8<o:p></o:p></p>
<p class="MsoNormal">Bonds: 0.007<o:p></o:p></p>
<p class="MsoNormal">Angles: 1.2<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I have tried a couple of things to refine
it further but nothing seems to improve all the parameters.<o:p></o:p></p>
<p class="MsoNormal">My question is what is an acceptable
Rfactor at this resolution for deposition in pdb?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks,<o:p></o:p></p>
<p class="MsoNormal">Sneha<o:p></o:p></p>
</div>
</blockquote>
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