| Hadesarchaea YNP_N21 cytochrome b5 domain protein (KUO41884.1) |
| This entry was created with PDB-REDO version 8.22 using the deposited PDB model version 1.3 |
| From original header | |||||
|---|---|---|---|---|---|
| Spacegroup | P 63 | a: 72.170Å b: 72.170Å c: 22.810Å | α: 90.00° β: 90.00° γ: 120.00° | ||
| Resolution | 1.90 Å | Reflections | 5544 | Test set | 0 (0.0%) |
| R | 0.2206 | R-free | 0.2607 | ||
| According to PDB-REDO | |||||
| Resolution | 1.90 Å | Reflections | 5544 | Test set |
553 (10%)
New test set, PDB-REDO compensated for this
|
| Twin | false | Radiation damage | 78 | ||
| PDB-REDO files | |||||
| Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
|||
| Links | |||||
| PDBe | RCSB PDB | Proteopedia | |||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.2234 | 0.2217 |
| R-free |
0.2661
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2383 |
| Bond length RMS Z-score | 1.217 | 0.208 |
| Bond angle RMS Z-score | 0.992 | 0.476 |
| Model quality | ||
| Ramachandran plot normality | 1.802 98 | 2.495 99 |
| Rotamer normality | -0.751 77 | 0.948 97 |
| Coarse packing | -0.870 15 | -0.921 13 |
| Fine packing | -2.081 12 | -1.666 25 |
| MolProbity Clashscore | 4.770 55 | 5.560 48 |
| Hydrogen bond satisfaction | 0.937 92 | 0.926 83 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | N/A |
| Side chains built | 0 |
| Waters removed | N/A |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |