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| Crystal structure of the eukaryotic initiation factor |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 1.2 |
| From original header | |||||
|---|---|---|---|---|---|
| Spacegroup | P 31 2 1 | a: 93.443Å b: 93.443Å c: 269.387Å | α: 90.00° β: 90.00° γ: 120.00° | ||
| Resolution | 2.51 Å | Reflections | 47722 | Test set | 2412 (5.1%) |
| R | 0.2382 | R-free | 0.2584 | ||
| According to PDB-REDO | |||||
| Resolution | 2.51 Å | Reflections | 47722 | Test set | 2412 (5.1%) |
| Twin | true | Radiation damage | 73 | ||
| 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 | 0.2442 | 0.1931 |
| R-free |
0.2913
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2576 |
| Bond length RMS Z-score | 0.491 | 0.432 |
| Bond angle RMS Z-score | 0.601 | 0.665 |
| Model quality | ||
| Ramachandran plot normality | -3.222 15 | -2.650 21 |
| Rotamer normality | -2.993 32 | -3.468 25 |
| Coarse packing | -1.208 8 | -0.823 16 |
| Fine packing | -1.611 27 | -0.922 56 |
| Bump severity | 0.134 8 | 0.040 21 |
| Hydrogen bond satisfaction | 0.818 7 | 0.857 16 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 14 |
| Side chains built | 0 |
| Waters removed | 3 |
| Peptides flipped | 7 |
| Chiralities fixed | 0 |
| Residues fitting density better | 17 |
| Residues fitting density worse | 1 |