RNA Polymerase III C82 domain
In this example the C82 domain of the RNA Polymerase III was fitted into a 9A cryo-EM density map of the full complex. This is related to our online RNA-Pol-III tutorial
Run Example5
Status: FINISHED
Your PowerFit run has successfully completed.
Archive of the complete run: Example5.tgz
Archive of all autogenerated images: Example5_images.tgz
Please cite the following papers in your work:
G.C.P. van Zundert, M. Trellet, J. Schaarschmidt, Z. Kurkcuoglu, M. David, M. Verlato, A. Rosato and A.M.J.J. Bonvin.
The DisVis and PowerFit web servers: Explorative and Integrative Modeling of Biomolecular Complexes. J. Mol. Biol., Advanced Online Publication (2016).

G.C.P. van Zundert and A.M.J.J. Bonvin (2015)
Fast and sensitive rigid-body fitting into cryo-EM density maps with PowerFit.
AIMS Biophysics 2, 73-87.
and add the following acknowledgment:
The FP7 WeNMR (project# 261572), H2020 West-Life (project# 675858), EOSC-hub (project# 777536) and the EGI-ACE (project# 101017567) European e-Infrastructure projects are acknowledged for the use of their web portals, which make use of the EGI infrastructure with the dedicated support of CESNET-MCC, INFN-LNL-2, NCG-INGRID-PT, TW-NCHC, CESGA, IFCA-LCG2, UA-BITP, TR-FC1-ULAKBIM, CSTCLOUD-EGI, IN2P3-CPPM, CIRMMP, SURFsara and NIKHEF, and the additional support of the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, Taiwan and the US Open Science Grid.
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Solutions
The table below lists the 15 best non-redundant solutions found by correlation score. The first column shows the rank, column 2 the correlation score, column 3 the Fisher z-score column 4 the zscore as factor of standard deviations (z/σ), and column 5 the sigma difference to the best fit. (see N. Volkmann 2009, and Van Zundert and Bonvin 2016).
Rank (N) Cross Correlation Score Fisher z-score z-score/σ Sigma difference
(z1-zN)/σ
1 0.263 0.269 17.2 0.00
2 0.260 0.266 17.0 0.20
3 0.235 0.240 15.3 1.88
4 0.233 0.238 15.2 2.01
5 0.231 0.235 15.0 2.16
6 0.231 0.235 15.0 2.17
7 0.225 0.229 14.7 2.54
8 0.224 0.228 14.6 2.62
9 0.224 0.228 14.6 2.65
10 0.223 0.226 14.5 2.72
11 0.223 0.226 14.5 2.74
12 0.222 0.226 14.5 2.74
13 0.222 0.226 14.4 2.76
14 0.221 0.225 14.4 2.83
15 0.221 0.225 14.4 2.83
Images were generated with UCSF Chimera.
Fit 1
Rank 1
Cross Correlation Score 0.263
Fisher z-score 0.269
z-score/σ 17.2
Sigma difference (zN-zN+1)/σ 0.00
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Fit 2
Rank 2
Cross Correlation Score 0.260
Fisher z-score 0.266
z-score/σ 17.0
Sigma difference (zN-zN+1)/σ 0.20
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Fit 3
Rank 3
Cross Correlation Score 0.235
Fisher z-score 0.240
z-score/σ 15.3
Sigma difference (zN-zN+1)/σ 1.88
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Fit 4
Rank 4
Cross Correlation Score 0.233
Fisher z-score 0.238
z-score/σ 15.2
Sigma difference (zN-zN+1)/σ 2.01
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Fit 5
Rank 5
Cross Correlation Score 0.231
Fisher z-score 0.235
z-score/σ 15.0
Sigma difference (zN-zN+1)/σ 2.16
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Fit 6
Rank 6
Cross Correlation Score 0.231
Fisher z-score 0.235
z-score/σ 15.0
Sigma difference (zN-zN+1)/σ 2.17
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Fit 7
Rank 7
Cross Correlation Score 0.225
Fisher z-score 0.229
z-score/σ 14.7
Sigma difference (zN-zN+1)/σ 2.54
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Fit 8
Rank 8
Cross Correlation Score 0.224
Fisher z-score 0.228
z-score/σ 14.6
Sigma difference (zN-zN+1)/σ 2.62
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Fit 9
Rank 9
Cross Correlation Score 0.224
Fisher z-score 0.228
z-score/σ 14.6
Sigma difference (zN-zN+1)/σ 2.65
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Fit 10
Rank 10
Cross Correlation Score 0.223
Fisher z-score 0.226
z-score/σ 14.5
Sigma difference (zN-zN+1)/σ 2.72
PDB Download