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| Crystal Structure of Human Complement C3b in Complex with MCP (CCP1-4) |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 2.2 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 21 2 21 | a: 82.830 Å | b: 130.630 Å | c: 233.830 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 2.40 Å | Reflections | 98774 | Test set | 4928 (5.0%) | ||
| R | 0.1879 | R-free | 0.2188 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.40 Å | Reflections | 98774 | Test set |
4927 (5.0%)
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 | 0.2102 | 0.2075 |
| R-free |
0.2511
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2492 |
| Bond length RMS Z-score | 0.615 | 0.394 |
| Bond angle RMS Z-score | 0.641 | 0.570 |
| Model quality | ||
| Ramachandran plot normality | -0.790 61 | -1.311 47 |
| Rotamer normality | -1.754 56 | -1.981 51 |
| Coarse packing | -0.129 43 | -0.196 40 |
| Fine packing | -1.473 33 | -1.453 34 |
| Bump severity | 0.120 8 | 0.090 11 |
| Hydrogen bond satisfaction | 0.702 2 | 0.864 19 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 28 |
| Side chains built | 1 |
| Waters removed | 57 |
| Peptides flipped | 2 |
| Chiralities fixed | 0 |
| Residues fitting density better | 10 |
| Residues fitting density worse | 2 |