EMD-52237 › Validation analysis
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Cryo-EM structure of Pseudomonas aeruginosa tetrameric S-adenosyl-L-homocysteine hydrolase in the fully open state
Validation summary
Additional validation information
Please find validation analyses used for peer review in the wwPDB validation reports for this entries map (EMD-52237) and model-map (9hkv and EMD-52237). 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 | 0.1 | - | - |
| Number of grid points | 256 × 256 × 256 | 256 × 256 × 256 | 256 × 256 × 256 |
| Voxel size (Å) | 0.860 × 0.860 × 0.860 | 0.860 × 0.860 × 0.860 | 0.860 × 0.860 × 0.860 |
| Minimum value | -0.002 | -0.385 | -0.413 |
| Maximum value | 2.666 | 0.708 | 0.602 |
| Average value | 0.003 | 0.001 | 0.001 |
| Standard deviation | 0.043 | 0.037 | 0.037 |
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Orthogonal projection
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Orthogonal projection (false-colour)
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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: 147
Y Index: 137
Z Index: 113
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Orthogonal surface
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Raw map visualisation (Raw map calculated from deposited two half-maps)
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Orthogonal projections of raw map
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Orthogonal maximum-value projections of
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map
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Orthogonal minimum-value
projections of
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Orthogonal median-value projections
of
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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 | 0.07 % | 0.09 % | 82.73 % |
| 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 | 3.50 | 3.13 | 3.13 | 2.88 |
Map and 1 fitted model
Model-map evaluation bars:
| Model | Metric | Evaluation bar | Average value |
|---|---|---|---|
| 9hkv | Q-score |
0.37
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| Atom Inclusion |
0.741
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| CCC |
0.636
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| SMOC |
0.628
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Map with model 9hkv (Cryo-EM structure of Pseudomonas aeruginosa tetrameric S-adenosyl-L-homocysteine hydrolase in the fully open state)
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Threshold comparison:
Chain scores summary
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Atom inclusion at 0.1 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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