This entry is not up to date with the most recent version of PDB-REDO.
Please log in
to request an update.
| Crystal structure of minichromosome maintenance protein MCM/DNA complex |
| This entry was created with PDB-REDO version 8.04 using the deposited PDB model version 1.3 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 41 21 2 | a: 186.665 Å | b: 186.665 Å | c: 281.489 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 3.15 Å | Reflections | 84178 | Test set | 4259 (5.1%) | ||
| R | 0.1881 | R-free | 0.2413 | ||||
| According to PDB-REDO | |||||||
| Resolution | 3.14 Å | Reflections | 84178 | Test set | 4259 (5.1%) | ||
| 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 | 3D bionotes | Proteopedia | ||||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.2150 | 0.2383 |
| R-free | 0.2612 | 0.2801 |
| Bond length RMS Z-score | 0.677 | 0.672 |
| Bond angle RMS Z-score | 0.784 | 0.924 |
| Model quality | ||
| Ramachandran plot normality | -2.316 24 | -4.495 7 |
| Rotamer normality | -4.526 20 | -6.095 8 |
| Coarse packing | 0.549 84 | 0.085 66 |
| Fine packing | -1.519 31 | -2.592 4 |
| Base pair conformation | N/A N/A | N/A N/A |
| Bump severity | 0.047 20 | 0.609 1 |
| Hydrogen bond satisfaction | 0.824 8 | 0.813 6 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 35 |
| Side chains built | 0 |
| Waters removed | 0 |
| Peptides flipped | 80 |
| Chiralities fixed | 0 |
| Residues fitting density better | 75 |
| Residues fitting density worse | 269 |