PowerFit - Results 2ykr without RsgA

GTPase RsgA-30S ribosomal subunit-GMPPNP complex

In this example the 30S ribosomal subunit-GMPPNP complex (PDB entry 2ykr) without the GTPase RsgA (chain W) 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. For this example Powerfit only reports one acceptable solution fitting well into the provided density map.

Run 2ykr without RsgA - EMD-1884 (Example2)

Status: FINISHED

Your PowerFit run has successfully completed.

Archive of the complete run:	Example2.tgz
Archive of all autogenerated images:	Example2_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.

Note: Your results will be stored for 14 days before being removed from the server, please make a backup as soon as possible.

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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	0.666	0.804	183.8	0.00

Images were generated with UCSF Chimera.

Fit 1

Rank	1
Cross Correlation Score	0.666
Fisher z-score	0.804
z-score/σ	183.8
Sigma difference (z_N-z_N+1)/σ	0.00
PDB	Download