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| STRUCTURE OF LINEAR GRAMICIDIN D OBTAINED USING TYPE I CRYSTALS GROWN IN A monovaccenin LIPID CUBIC PHASE |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 2.2 |
| From original header | |||||
|---|---|---|---|---|---|
| Spacegroup | P 1 21 1 | a: 23.960Å b: 41.981Å c: 32.429Å | α: 90.00° β: 107.25° γ: 90.00° | ||
| Resolution | 1.70 Å | Reflections | 6601 | Test set | 0 (0.0%) |
| R | 0.1662 | R-free | 0.2112 | ||
| According to PDB-REDO | |||||
| Resolution | 1.70 Å | Reflections | 6601 | Test set |
659 (10%)
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 | Proteopedia | |||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.1627 | 0.1589 |
| R-free |
0.1923
R-free was considered biased, the
estimated unbiased R-free was used
|
0.1684 |
| Bond length RMS Z-score | 1.763 | 0.342 |
| Bond angle RMS Z-score | 1.333 | 0.530 |
| Model quality | ||
| Ramachandran plot normality | -12.707 0 | -12.400 0 |
| Rotamer normality | -7.042 2 | -6.809 2 |
| Coarse packing | N/A N/A | N/A N/A |
| Fine packing | N/A N/A | N/A N/A |
| Bump severity | 0.003 81 | 0.000 95 |
| Hydrogen bond satisfaction | 0.250 0 | 0.286 0 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 0 |
| Side chains built | 0 |
| Waters removed | 0 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |