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| Crystal structure of a recombinant Vatairea macrocarpa seed lectin complexed with Tn antigen |
| This entry was created with PDB-REDO version 7.32 using the deposited PDB model |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | I 2 2 2 | a: 56.093 Å | b: 86.024 Å | c: 128.877 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 1.97 Å | Reflections | 21798 | Test set | 1075 (4.9%) | ||
| R | 0.1980 | R-free | 0.2540 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.97 Å | Reflections | 21798 | Test set | 1075 (4.9%) | ||
| Twin | false | Radiation damage | N/A | ||||
| PDB-REDO files | |||||||
| Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
|||||
| Links | |||||||
| PDBe | RCSB PDB | 3D bionotes | Proteopedia | ||||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.1999 | 0.1870 |
| R-free |
0.2354
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2106 |
| Bond length RMS Z-score | 0.651 | 0.686 |
| Bond angle RMS Z-score | 0.737 | 0.821 |
| Model quality | ||
| Ramachandran plot normality | -1.153 49 | -0.459 69 |
| Rotamer normality | -1.992 58 | -1.551 67 |
| Coarse packing | 1.058 95 | 1.106 95 |
| Fine packing | -0.195 79 | -0.180 79 |
| Bump severity | 0.004 78 | 0.005 74 |
| Hydrogen bond satisfaction | 0.880 28 | 0.880 28 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 2 |
| Side chains flipped | 0 |
| Waters removed | 2 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 2 |
| Residues fitting density worse | 0 |