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 | |||||||
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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) |
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Links | |||||||
PDBe | RCSB PDB | 3D bionotes | Proteopedia |
Original | PDB-REDO | |
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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 flipped | 1 |
Waters removed | 57 |
Peptides flipped | 2 |
Chiralities fixed | 0 |
Residues fitting density better | 10 |
Residues fitting density worse | 2 |