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| Structure of the nanobody stablized properdin bound alternative pathway proconvertase C3b:FB:FP |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 1.3 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 21 21 2 | a: 148.690 Å | b: 179.460 Å | c: 192.600 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 3.90 Å | Reflections | 47651 | Test set | 1853 (3.9%) | ||
| R | 0.2488 | R-free | 0.2654 | ||||
| According to PDB-REDO | |||||||
| Resolution | 3.90 Å | Reflections | 47651 | Test set | 1853 (3.9%) | ||
| Twin | false | Radiation damage | 47 | ||||
| PDB-REDO files | |||||||
| Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
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| Links | |||||||
| PDBe | RCSB PDB | 3D bionotes | Proteopedia | ||||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.3130 | 0.2751 |
| R-free | 0.3285 | 0.3055 |
| Bond length RMS Z-score | 0.511 | 0.189 |
| Bond angle RMS Z-score | 0.673 | 0.385 |
| Model quality | ||
| Ramachandran plot normality | -3.304 14 | -2.827 19 |
| Rotamer normality | -2.022 50 | -1.402 63 |
| Coarse packing | -2.105 2 | -1.705 3 |
| Fine packing | -3.007 2 | -2.498 5 |
| Bump severity | 0.198 5 | 0.193 5 |
| Hydrogen bond satisfaction | 0.764 3 | 0.777 4 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 15 |
| Side chains built | 0 |
| Waters removed | 0 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 494 |
| Residues fitting density worse | 238 |