PowerFit - Results 2ykr_W

GTPase RsgA-30S ribosomal subunit-GMPPNP complex

In this example, which is also used within the scope of the PowerFit web server tutorial, the putative ribosome biogenesis GTPase RsgA (chain W of PDB entry 2ykr) was fitted into the cryo-EM density map of the full RsgA-30S ribosomal subunit-GMPPNP complex (EMDB entry 1884 - 9.8 Å resolution) with the default server parameters. The best 3 Fits all occupy the expected part of the density map with powerfit clearly favoring one particular orientation based on cross correlation score and sigma difference.

Run 2ykr_W - EMD-1884 (Example1)

Status: FINISHED

Your PowerFit run has successfully completed.

Archive of the complete run:	Example1.tgz
Archive of all autogenerated images:	Example1_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-z_N)/σ
1	0.560	0.633	31.0	0.00
2	0.517	0.573	28.0	2.98
3	0.432	0.463	22.7	8.35
4	0.301	0.311	15.2	15.79
5	0.298	0.307	15.1	15.97
6	0.298	0.307	15.0	15.99
7	0.293	0.302	14.8	16.24
8	0.290	0.298	14.6	16.42
9	0.288	0.297	14.5	16.49
10	0.288	0.296	14.5	16.53
11	0.287	0.295	14.4	16.58
12	0.285	0.293	14.3	16.69
13	0.284	0.292	14.3	16.71
14	0.284	0.292	14.3	16.73
15	0.282	0.290	14.2	16.82