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| crystal structure of a protein in the LRP/ASNC family from the hyperthermophilic archaeon Pyrococcus sp. OT3 |
| This entry was created with PDB-REDO version 8.13 using Foldit model 2013753 from player null |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 61 2 2 | a: 130.910 Å | b: 130.910 Å | c: 47.370 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
| Resolution | 2.70 Å | Reflections | 6903 | Test set | 0 (0.0%) | ||
| R | 0.2460 | R-free | 0.3140 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.70 Å | Reflections | 6903 | Test set |
697 (10.1%)
New test set, PDB-REDO compensated for this
|
||
| Twin | false | Radiation damage | 70 | ||||
| PDB-REDO files | |||||||
| Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
|||||
| Links | |||||||
| PDBe | RCSB PDB | 3D bionotes | Proteopedia | ||||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.2465 | 0.2118 |
| R-free |
0.2965
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2385 |
| Bond length RMS Z-score | 0.535 | 0.287 |
| Bond angle RMS Z-score | 0.704 | 0.510 |
| Model quality | ||
| Ramachandran plot normality | -4.677 6 | -2.334 25 |
| Rotamer normality | -3.960 19 | -0.740 77 |
| Coarse packing | -0.412 30 | 0.513 71 |
| Fine packing | 0.075 84 | 0.865 94 |
| Bump severity | 0.030 27 | 0.031 27 |
| Hydrogen bond satisfaction | 0.838 11 | 0.906 58 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 3 |
| Side chains built | 0 |
| Waters removed | 50 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 7 |
| Residues fitting density worse | 0 |