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| The structure of nvBagel2 in the presence of Cd(II) |
| This entry was created with PDB-REDO version 8.11 using the deposited PDB model version 1.0 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | I 4 2 2 | a: 54.970 Å | b: 54.970 Å | c: 109.600 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 2.82 Å | Reflections | 2236 | Test set | 0 (0.0%) | ||
| R | 0.2302 | R-free | 0.3126 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.82 Å | Reflections | 2236 | Test set |
214 (9.6%)
New test set, PDB-REDO compensated for this
|
||
| 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 | 0.2395 | 0.2462 |
| R-free |
0.2802
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2773 |
| Bond length RMS Z-score | 0.873 | 0.187 |
| Bond angle RMS Z-score | 0.678 | 0.370 |
| Model quality | ||
| Ramachandran plot normality | -0.628 66 | -1.437 44 |
| Rotamer normality | -6.674 2 | -3.485 25 |
| Coarse packing | -0.988 12 | -1.019 11 |
| Fine packing | -0.133 80 | 0.185 86 |
| Bump severity | 0.003 81 | 0.000 95 |
| Hydrogen bond satisfaction | 0.898 47 | 0.898 47 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 1 |
| Side chains built | 0 |
| Waters removed | 0 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |