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 yeast alpha1,2-mannosyltransferase Kre2p/Mnt1p: ternary complex with GDP/Mn and methyl-alpha-mannoside acceptor |
| This entry was created with PDB-REDO version 8.01. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 1 21 1 | a: 60.694 Å | b: 101.068 Å | c: 62.036 Å | α: 90.00° | β: 98.81° | γ: 90.00° |
| Resolution | 2.01 Å | Reflections | 47534 | Test set | 3280 (6.9%) | ||
| R | 0.2030 | R-free | 0.2560 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.97 Å | Reflections | 47534 | Test set | 3280 (6.9%) | ||
| 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 | 0.2066 | 0.1967 |
| R-free | 0.2539 | 0.2396 |
| Bond length RMS Z-score | 0.441 | 0.424 |
| Bond angle RMS Z-score | 0.735 | 0.697 |
| Model quality | ||
| Ramachandran plot normality | -1.505 40 | 0.064 81 |
| Rotamer normality | -2.002 58 | -0.736 82 |
| Coarse packing | 0.939 93 | 1.021 94 |
| Fine packing | -2.926 2 | -2.611 4 |
| Bump severity | 0.179 6 | 0.036 25 |
| Hydrogen bond satisfaction | 0.893 41 | 0.889 37 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 9 |
| Side chains flipped | 3 |
| Waters removed | 41 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |