RNA Polymerase III core
In this example the core 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 Example4
Status: FINISHED
Your PowerFit run has successfully completed.
Archive of the complete run: Example4.tgz
Archive of all autogenerated images: Example4_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 0.098 0.099 18.9 0.00
2 0.083 0.083 16.0 2.96
3 0.071 0.071 13.7 5.24
4 0.070 0.070 13.5 5.46
5 0.070 0.070 13.5 5.48
6 0.069 0.069 13.2 5.75
7 0.069 0.069 13.2 5.76
8 0.069 0.069 13.2 5.77
9 0.067 0.067 12.9 6.00
10 0.066 0.066 12.8 6.19
11 0.066 0.066 12.8 6.19
12 0.066 0.066 12.7 6.24
13 0.066 0.066 12.7 6.24
14 0.066 0.066 12.6 6.30
15 0.066 0.066 12.6 6.34
Images were generated with UCSF Chimera.
Fit 1
Rank 1
Cross Correlation Score 0.098
Fisher z-score 0.099
z-score/σ 18.9
Sigma difference (zN-zN+1)/σ 0.00
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Fit 2
Rank 2
Cross Correlation Score 0.083
Fisher z-score 0.083
z-score/σ 16.0
Sigma difference (zN-zN+1)/σ 2.96
PDB Download
Fit 3
Rank 3
Cross Correlation Score 0.071
Fisher z-score 0.071
z-score/σ 13.7
Sigma difference (zN-zN+1)/σ 5.24
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Fit 4
Rank 4
Cross Correlation Score 0.070
Fisher z-score 0.070
z-score/σ 13.5
Sigma difference (zN-zN+1)/σ 5.46
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Fit 5
Rank 5
Cross Correlation Score 0.070
Fisher z-score 0.070
z-score/σ 13.5
Sigma difference (zN-zN+1)/σ 5.48
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Fit 6
Rank 6
Cross Correlation Score 0.069
Fisher z-score 0.069
z-score/σ 13.2
Sigma difference (zN-zN+1)/σ 5.75
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Fit 7
Rank 7
Cross Correlation Score 0.069
Fisher z-score 0.069
z-score/σ 13.2
Sigma difference (zN-zN+1)/σ 5.76
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Fit 8
Rank 8
Cross Correlation Score 0.069
Fisher z-score 0.069
z-score/σ 13.2
Sigma difference (zN-zN+1)/σ 5.77
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Fit 9
Rank 9
Cross Correlation Score 0.067
Fisher z-score 0.067
z-score/σ 12.9
Sigma difference (zN-zN+1)/σ 6.00
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Fit 10
Rank 10
Cross Correlation Score 0.066
Fisher z-score 0.066
z-score/σ 12.8
Sigma difference (zN-zN+1)/σ 6.19
PDB Download