Table 1. Resolution metrics for selected examples.
| Maps | ||||
|---|---|---|---|---|
| Not masked | Masked | |||
| Map, model and metrics | Reported d FSC | Original | Original | Sharpened |
| PDB entry 5UAR †, EMDB code 8461 | ||||
| d 99 | 1.9 | 6.5 | 4.7 | |
| d model (B, Å2) | 3.7 | 6.7 (−60) | 6.7 (−10) | 6.6 (−90) |
| d model(B=0) | 6.6 | 6.7 | 6.5 | |
| d FSC_model | 3.6 | 3.3 | 3.4 | |
| PDB entry 5LDF ‡, EMDB code 4039 | ||||
| d 99 | 4.4 | 4.9 | 4.1 | |
| d model (B, Å2) | 6.2 | 4.0 (220) | 4.1 (220) | 4.1 (−10) |
| d model(B=0) | 7.5 | 7.4 | 4.2 | |
| d FSC_model | 3.6 | 3.5 | 3.5 | |
| PDB entry 5K12 §, EMDB code 8194 | ||||
| d 99 | 1.9 | 2.5 | 2.8 | |
| d model (B, Å2) | 1.8 | 3.0 (20) | 3.0 (20) | 3.0 (10) |
| d model(B=0) | 3.4 | 3.4 | 3.3 | |
| d FSC_model | 1.8 | 1.8 | 2.0 | |
| PDB entry 5K7L ¶, EMDB code 8215 | ||||
| d 99 | 7.4 | 6.9 | 3.9 | |
| d model (B, Å2) | 3.8 | 3.6 (260) | 3.6 (300) | 3.8 (40) |
| d model(B=0) | 8.3 | 8.6 | 4.0 | |
| d FSC_model | 3.5 | 3.2 | 3.4 | |
The original map for PDB entry 5UAR contains high-resolution features (likely to be noise) outside the model. These features can be removed by masking (compare d 99 for the masked and unmasked maps). The unsharpened map does not show higher resolution details (see d model). The model reproduces all details up to d FSC (compare d FSC and d FSC_model). High-resolution filtering followed by sharpening may be required to build and confirm these details.
The original map for PDB entry 5LDF contains details of a resolution higher than d FSC (compare d FSC and d 99); the molecular region also contains these details (compare d 99 for the masked and unmasked maps). The unsharpened map indeed looks like a map nearer 6 Å resolution (the difference between d model calculated with underestimated B = 0 and overestimated B = 220 Å2). The model reproduces details up to a resolution slightly higher than 4 Å (see d FSC_model), which is confirmed by all metrics calculated for the sharpened map. It is possible that d FSC is underestimated.
The original map for PDB entry 5K12 contains high-resolution details up to d FSC (d 99 for the unmasked map). Inside the molecular region neither the original nor the sharpened map show such details (d 99 for masked maps) and the map itself looks like a 3 Å resolution map (see d model). At the same time, the model reproduces the data up to a resolution near d FSC (d FSC_model). To visualize these details, the default sharpening is insufficient and omitting dominating lower resolution data may be needed.
The original data for PDB entry 5K7L are weak at higher resolution and the original map shows limited detail (low d 99 for unsharpened maps); these details do appear in the sharpened map (compare d 99 and d FSC, also compare d 99 for sharpened and unsharpened maps). Indeed, the original map in the molecular region is blurred by very large B [compare d model and d model(B=0)]. The sharpened map looks like a map at d FSC [compare d FSC with d model and d model(B=0) for sharpened maps]. The model reproduces the map details well (compare d FSC_model and d FSC).