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| Crystal structure of 60-mer BFDV Capsid Protein |
| This entry was created with PDB-REDO version 8.08 using the deposited PDB model version 1.3 |
| From original header | |||||
|---|---|---|---|---|---|
| Spacegroup | F 4 3 2 | a: 377.310Å b: 377.310Å c: 377.310Å | α: 90.00° β: 90.00° γ: 90.00° | ||
| Resolution | 2.55 Å | Reflections | 74619 | Test set | 3733 (5.0%) |
| R | 0.1912 | R-free | 0.2162 | ||
| According to PDB-REDO | |||||
| Resolution | 2.55 Å | Reflections | 74619 | Test set |
3728 (5.0%)
New test set, PDB-REDO compensated for this
|
| Twin | false | Radiation damage | 86 | ||
| 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 | 0.1977 | 0.1886 |
| R-free |
0.2348
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2057 |
| Bond length RMS Z-score | 0.439 | 0.392 |
| Bond angle RMS Z-score | 0.614 | 0.570 |
| Model quality | ||
| Ramachandran plot normality | -1.327 46 | -1.114 52 |
| Rotamer normality | 0.852 97 | 0.088 91 |
| Coarse packing | -0.564 25 | -0.811 16 |
| Fine packing | -1.549 30 | -1.571 29 |
| Bump severity | 0.006 68 | 0.003 81 |
| Hydrogen bond satisfaction | 0.917 73 | 0.901 51 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 20 |
| Side chains built | 0 |
| Waters removed | 6 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 1 |
| Residues fitting density worse | 0 |