Structural parameters for the cryo-EM structure of the FVa-APC complex
| . | FVa-APC (PD) complex PDB ID 9MOT EMD-48481 . | FVa-APC complex PDB ID 9MOV EMD-48439 . |
|---|---|---|
| Data collection and processing | ||
| Nominal magnification | 75 000× | 75 000× |
| Voltage (kV) | 300 | 300 |
| Electron exposure (e−/Å2) | 51.86, 46.6, 46.89, 47.19, 52.8 | 51.86, 46.6, 46.89, 47.19, 52.8 |
| Defocus range (μm) | −1 to −2.4 | −1 to −2.4 |
| Pixel size (Å) | 0.8701 | 0.8701 |
| No. of images | 12 457 | 12 457 |
| Final particle images | 384 239 | 384 239 |
| Symmetry imposed | C1 | C1 |
| Resolution unmasked∗ (Å) | 3.1 | 3.5 |
| Resolution masked∗ (Å) | 3.1 | 2.9 |
| Model composition | ||
| Refinement program | Phenix (real space) | Phenix (real space) |
| No. of amino acid chains | 3 | 4 |
| No. of protein atoms (non-H) | 12 708 | 13 898 |
| Protein residues | 1 561 | 1 707 |
| Ligand molecules | NAG 8 | Ca2+ 7, NAG 9 |
| RMSD | ||
| Bond lengths (Å) | 0.005 | 0.005 |
| Bond angles (°) | 1.091 | 1.125 |
| Validation | ||
| All-atom clash score | 19.2 | 19.2 |
| Poor rotamers (%) | 0.29 | 0.33 |
| Ramachandran disallowed (%) | 0.0 | 0.0 |
| Ramachandran allowed (%) | 12.22 | 11.61 |
| Ramachandran favored (%) | 87.78 | 88.39 |
| MolProbity score | 2.38 | 2.37 |
| . | FVa-APC (PD) complex PDB ID 9MOT EMD-48481 . | FVa-APC complex PDB ID 9MOV EMD-48439 . |
|---|---|---|
| Data collection and processing | ||
| Nominal magnification | 75 000× | 75 000× |
| Voltage (kV) | 300 | 300 |
| Electron exposure (e−/Å2) | 51.86, 46.6, 46.89, 47.19, 52.8 | 51.86, 46.6, 46.89, 47.19, 52.8 |
| Defocus range (μm) | −1 to −2.4 | −1 to −2.4 |
| Pixel size (Å) | 0.8701 | 0.8701 |
| No. of images | 12 457 | 12 457 |
| Final particle images | 384 239 | 384 239 |
| Symmetry imposed | C1 | C1 |
| Resolution unmasked∗ (Å) | 3.1 | 3.5 |
| Resolution masked∗ (Å) | 3.1 | 2.9 |
| Model composition | ||
| Refinement program | Phenix (real space) | Phenix (real space) |
| No. of amino acid chains | 3 | 4 |
| No. of protein atoms (non-H) | 12 708 | 13 898 |
| Protein residues | 1 561 | 1 707 |
| Ligand molecules | NAG 8 | Ca2+ 7, NAG 9 |
| RMSD | ||
| Bond lengths (Å) | 0.005 | 0.005 |
| Bond angles (°) | 1.091 | 1.125 |
| Validation | ||
| All-atom clash score | 19.2 | 19.2 |
| Poor rotamers (%) | 0.29 | 0.33 |
| Ramachandran disallowed (%) | 0.0 | 0.0 |
| Ramachandran allowed (%) | 12.22 | 11.61 |
| Ramachandran favored (%) | 87.78 | 88.39 |
| MolProbity score | 2.38 | 2.37 |
NAG, N-acetylglucosamine; RMSD, root mean square deviation.
Calculated at the Fourier shell correlation threshold of 0.143.