Table 1.
Statistics for the cryo-EM image reconstruction of PCV2d and refinement of its atomic coordinates.
| PCV2d | |
|---|---|
| Cryo-EM image reconstruction | |
| Number of Micrographs | 799 |
| Defocus range | −0.68 to −2.81 μm |
| Total dose | 64 e- Å−2 |
| Dose rate | 6.4 e− Å−2 sec−1 |
| Number of Frames | 50 |
| Particles extracted | 23,358 |
| Particles used for reconstruction | 4,442 |
| FSC resolution * | 3.3 Å |
| B-factor sharpening† | −125.9 Å2 |
| Coordinate refinement | |
| CC | 84.6% |
| B-factor average | 64.6 Å2 |
| Bond angles (rmsd degrees)‡ | 0.013 |
| Bond lengths (rmsd Å)§ | 1.38 |
| Molprobity¶ | 2.18 |
| EMRinger | 5.1 |
| Clashscore | 1.7 |
| Ramachandran favored (%) | 91.8% |
| Ramachandran allowed (%) | 8.2% |
| EMDB | 20113 |
| PDB | 6OLA |
*
Fourier shell correlation reported by Relion 3.0 using the gold standard method at a CC of 0.143.
†
The B-factor sharpening reported by Relion 3.0 during the post-refinement process
‡
The root-mean standard deviation for bonds reported by phenix.real_space_refine
§
The root-mean standard deviation for angles reported by phenix.real_space_refine
¶
Molprobity Overall score