EMD-11145 › Validation analysis
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SARS CoV-2 Spike protein, Closed conformation, C3 symmetry
Validation summary
Additional validation information
Please find validation analyses used for peer review in the wwPDB validation reports for this entries map (EMD-11145) and model-map (6zb5 and EMD-11145). 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 | 0.006 | - | - |
| Number of grid points | 220 × 220 × 220 | 220 × 220 × 220 | 220 × 220 × 220 |
| Voxel size (Å) | 1.050 × 1.050 × 1.050 | 1.050 × 1.050 × 1.050 | 1.050 × 1.050 × 1.050 |
| Minimum value | -0.197 | -0.044 | -0.045 |
| Maximum value | 0.316 | 0.103 | 0.108 |
| Average value | 0.001 | -0.000 | -0.000 |
| Standard deviation | 0.012 | 0.006 | 0.006 |
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Orthogonal projection
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More projections
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Orthogonal projection (false-colour)
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Orthogonal maximum-value
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Orthogonal standard-deviation
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Orthogonal minimum-value
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Orthogonal median-value projections
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Central slices
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Largest variance slices
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X Index: 116
Y Index: 115
Z Index: 150
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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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More projections
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Orthogonal projections of raw map
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Orthogonal projections of raw map
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Orthogonal maximum-value projections of
raw
map
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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 | -0.56 % | 5.17 % | 66.99 % |
| Raw map | 0.41 % | 0.47 % | 10.76 % |
* 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 | 3.08 | 2.91 | 2.91 | 2.84 |
Map and 1 fitted model
Model-map evaluation bars:
| Model | Metric | Evaluation bar | Average value |
|---|---|---|---|
| 6zb5 | Q-score |
0.619
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| Atom Inclusion |
0.992
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| CCC |
CCC bar not available
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| SMOC |
0.668
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Map with model 6zb5 (SARS CoV-2 Spike protein, Closed conformation, C3 symmetry)
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Chain scores summary
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Atom inclusion at 0.006 contour level
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Residue fit view
based on Q-score
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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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