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| HUMAN BONE MORPHOGENETIC PROTEIN-2 (BMP-2) |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 1.5 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | H 3 2 | a: 91.440 Å | b: 91.440 Å | c: 107.750 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
| Resolution | 2.70 Å | Reflections | 5068 | Test set | 0 (0.0%) | ||
| R | 0.2420 | R-free | 0.2780 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.60 Å | Reflections | 5068 | Test set |
458 (9.0%)
New test set, PDB-REDO compensated for this
|
||
| Twin | false | Radiation damage | 8 | ||||
| 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 | 0.2881 | 0.2095 |
| R-free |
0.3470
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2387 |
| Bond length RMS Z-score | 0.690 | 0.171 |
| Bond angle RMS Z-score | 0.866 | 0.398 |
| Model quality | ||
| Ramachandran plot normality | -4.668 6 | -3.148 15 |
| Rotamer normality | -2.956 33 | -1.501 61 |
| Coarse packing | -0.981 12 | -1.202 8 |
| Fine packing | -1.061 51 | -1.222 44 |
| Bump severity | 0.023 34 | 0.003 81 |
| Hydrogen bond satisfaction | 0.865 19 | 0.908 61 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 5 |
| Side chains built | 0 |
| Waters removed | 3 |
| Peptides flipped | 1 |
| Chiralities fixed | 0 |
| Residues fitting density better | 1 |
| Residues fitting density worse | 0 |