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| Crystal structure of 60-mer BFDV Capsid Protein in complex with single stranded DNA |
| This entry was created with PDB-REDO version 8.04 using the deposited PDB model version 1.3 |
| From original header | |||||
|---|---|---|---|---|---|
| Spacegroup | F 4 3 2 | a: 377.280Å b: 377.280Å c: 377.280Å | α: 90.00° β: 90.00° γ: 90.00° | ||
| Resolution | 2.30 Å | Reflections | 101174 | Test set | 5035 (5.0%) |
| R | 0.1735 | R-free | 0.1969 | ||
| According to PDB-REDO | |||||
| Resolution | 2.30 Å | Reflections | 101174 | Test set |
5030 (5.0%)
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 | 0.1799 | 0.1733 |
| R-free |
0.2117
R-free was considered biased, the
estimated unbiased R-free was used
|
0.1901 |
| Bond length RMS Z-score | 0.455 | 0.426 |
| Bond angle RMS Z-score | 0.650 | 0.597 |
| Model quality | ||
| Ramachandran plot normality | -1.147 49 | -1.101 50 |
| Rotamer normality | 0.458 96 | 0.587 96 |
| Coarse packing | -0.542 34 | -0.609 31 |
| Fine packing | -1.791 20 | -1.774 21 |
| Dinucleotide conformation (CONFAL) | 7.2 6 | 14.9 9 |
| Base pair conformation | N/A N/A | N/A N/A |
| Bump severity | 0.005 74 | 0.006 70 |
| Hydrogen bond satisfaction | 0.908 61 | 0.909 63 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 20 |
| Side chains built | 0 |
| Waters removed | 19 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |