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| Crystal structure of human Ig-beta homodimer |
| This entry was created with PDB-REDO version 8.12 using Foldit model 2013609 from player Galaxie |
| From original header | |||||
|---|---|---|---|---|---|
| Spacegroup | P 41 3 2 | a: 129.800Å b: 129.800Å c: 129.800Å | α: 90.00° β: 90.00° γ: 90.00° | ||
| Resolution | 3.20 Å | Reflections | 6407 | Test set | 0 (0.0%) |
| R | 0.1810 | R-free | 0.2630 | ||
| According to PDB-REDO | |||||
| Resolution | 3.20 Å | Reflections | 6407 | Test set |
642 (10.0%)
New test set, PDB-REDO compensated for this
|
| Twin | false | Radiation damage | 83 | ||
| 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 | 0.2080 | 0.1921 |
| R-free |
0.2520
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2463 |
| Bond length RMS Z-score | 0.704 | 0.533 |
| Bond angle RMS Z-score | 0.994 | 0.743 |
| Model quality | ||
| Ramachandran plot normality | -4.594 6 | -2.153 28 |
| Rotamer normality | -5.602 6 | -3.510 25 |
| Coarse packing | -2.164 1 | -1.139 9 |
| Fine packing | -2.642 4 | -1.241 43 |
| Bump severity | 0.084 11 | 0.025 32 |
| Hydrogen bond satisfaction | 0.781 4 | 0.861 18 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 0 |
| Side chains built | 0 |
| Waters removed | 2 |
| Peptides flipped | 6 |
| Chiralities fixed | 0 |
| Residues fitting density better | 2 |
| Residues fitting density worse | 0 |