This entry is not up to date with the most recent version of PDB-REDO.
Please log in
to request an update.
Ricin bound to VHH antibody V5G1 |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
---|---|---|---|---|---|---|---|
Spacegroup | P 1 | a: 44.345 Å | b: 77.438 Å | c: 101.577 Å | α: 89.97° | β: 90.18° | γ: 89.98° |
Resolution | 2.30 Å | Reflections | 57474 | Test set | 2742 (4.8%) | ||
R | 0.1870 | R-free | 0.2377 | ||||
According to PDB-REDO | |||||||
Resolution | 2.30 Å | Reflections | 57474 | Test set | 2742 (4.8%) | ||
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 | 0.2067 | 0.1876 |
R-free | 0.2564 | 0.2348 |
Bond length RMS Z-score | 1.597 | 0.400 |
Bond angle RMS Z-score | 0.747 | 0.575 |
Model quality | ||
Ramachandran plot normality | -1.300 45 | -1.113 50 |
Rotamer normality | -3.489 32 | -1.530 67 |
Coarse packing | 0.537 84 | 0.520 83 |
Fine packing | -0.731 63 | -0.310 76 |
Bump severity | 0.371 2 | 0.130 8 |
Hydrogen bond satisfaction | 0.848 13 | 0.904 56 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 20 |
Side chains flipped | 0 |
Waters removed | 20 |
Peptides flipped | 7 |
Chiralities fixed | 0 |
Residues fitting density better | 3 |
Residues fitting density worse | 0 |