Crystal Structure of Human Complement C3b in complex with DAF (CCP2-4) |
This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 1.3 |
From original header | |||||||
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Spacegroup | P 21 2 21 | a: 117.429 Å | b: 142.378 Å | c: 323.697 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 4.19 Å | Reflections | 38982 | Test set | 1955 (5.0%) | ||
R | 0.2695 | R-free | 0.3073 | ||||
According to PDB-REDO | |||||||
Resolution | 4.19 Å | Reflections | 38982 | Test set | 1955 (5.0%) | ||
Twin | false | Radiation damage | N/A | ||||
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 | 0.2975 | 0.2604 |
R-free | 0.3331 | 0.3035 |
Bond length RMS Z-score | 1.024 | 0.370 |
Bond angle RMS Z-score | 1.280 | 0.594 |
Model quality | ||
Ramachandran plot normality | -4.043 9 | -3.727 11 |
Rotamer normality | -4.999 10 | -4.545 13 |
Coarse packing | -1.163 8 | -1.119 9 |
Fine packing | -3.133 2 | -2.810 3 |
Bump severity | 0.211 5 | 0.054 16 |
Hydrogen bond satisfaction | 0.779 4 | 0.797 5 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 9 |
Side chains flipped | 0 |
Waters removed | 0 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 188 |
Residues fitting density worse | 0 |