EMD-19246 › Validation analysis
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NDH-PSI-LHCI supercomplex from S. oleracea: local refined membrane arm of NDH
Validation summary
Additional validation information
Please find validation analyses used for peer review in the wwPDB validation reports for this entries map (EMD-19246). Validation analysis of this entry is available in the main page. Documentation for the outputs of EMDB Validation Analysis can be found on the help page.
Deposited map parameters
| Primary map | Half map 1 | Half map 2 | |
|---|---|---|---|
| Recommended contour level | 0.29 | - | - |
| Number of grid points | 512 × 512 × 512 | 512 × 512 × 512 | 512 × 512 × 512 |
| Voxel size (Å) | 0.837 × 0.837 × 0.837 | 0.837 × 0.837 × 0.837 | 0.837 × 0.837 × 0.837 |
| Minimum value | -1.140 | -1.389 | -1.266 |
| Maximum value | 2.147 | 1.346 | 1.399 |
| Average value | 0.001 | 0.001 | 0.001 |
| Standard deviation | 0.078 | 0.143 | 0.144 |
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Central slices
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Largest variance slices
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X Index: 261
Y Index: 260
Z Index: 246
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Orthogonal projection (false-colour)
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Raw map visualisation (Raw map calculated from deposited two half-maps)
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Orthogonal maximum-value projections of
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Orthogonal minimum-value
projections of
raw map
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Orthogonal median-value projections
of
raw map
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Central slices of raw map
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Largest variance slices of raw map
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Orthogonal projections of raw map
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| Projection image zero values* | |||
|---|---|---|---|
| Map | Vertical % | Horizontal % | Overall % |
| Primary map | 0.37 % | -0.37 % | 18.39 % |
| Raw map | 0.0 % | 0.0 % | 0.0 % |
* measured on z-projection images. Zero(green) values on the image indicative of low signal or masked voxels
| Map resolution (Å) measured by Fourier Shell Correlation (FSC) | ||||
|---|---|---|---|---|
| EMDB calculated FSC | Author FSC | |||
| Threshold | Unmasked | Masked | Corrected | Author |
| FSC 0.143 | 4.52 | 3.52 | 3.52 | 4.50 |
Depositor mask(s)
Mask with primary map (msk_1)
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EMDB generated mask(s)
FSC mask with raw map
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