Software | Name | Version | Classification |
---|
PHENIX | 1.17.1_3660refinementPDB_EXTRACT | 3.27 | data extractionHKL-3000 | | data reductionAimless | | data scalingPHASER | | phasing | | | | | |
|
---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DRX Resolution: 2.02→47.49 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 31.68 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
---|
Rfree | 0.2459 | 1667 | 4.93 % |
---|
Rwork | 0.2083 | 32157 | - |
---|
obs | 0.2101 | 33824 | 99.22 % |
---|
|
---|
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL |
---|
Displacement parameters | Biso max: 92.3 Å2 / Biso mean: 51.7191 Å2 / Biso min: 32.09 Å2 |
---|
Refinement step | Cycle: final / Resolution: 2.02→47.49 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
---|
Num. atoms | 3328 | 0 | 0 | 128 | 3456 |
---|
Biso mean | - | - | - | 52.67 | - |
---|
Num. residues | - | - | - | - | 438 |
---|
|
---|
Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
---|
X-RAY DIFFRACTION | f_bond_d0.007 | 3433 | X-RAY DIFFRACTION | f_angle_d0.949 | 4689 | X-RAY DIFFRACTION | f_dihedral_angle_d6.682 | 481 | X-RAY DIFFRACTION | f_chiral_restr0.056 | 529 | X-RAY DIFFRACTION | f_plane_restr0.006 | 597 | | | | | |
|
---|
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | % reflection obs (%) |
---|
2.02-2.08 | 0.3725 | 127 | 0.3264 | 2608 | 97 | 2.08-2.15 | 0.3026 | 160 | 0.2744 | 2659 | 100 | 2.15-2.23 | 0.3452 | 130 | 0.2576 | 2634 | 100 | 2.23-2.32 | 0.2985 | 151 | 0.2659 | 2635 | 100 | 2.32-2.42 | 0.2834 | 139 | 0.2474 | 2651 | 99 | 2.42-2.55 | 0.2688 | 135 | 0.2304 | 2657 | 100 | 2.55-2.71 | 0.2753 | 142 | 0.2325 | 2660 | 100 | 2.71-2.92 | 0.2456 | 148 | 0.2379 | 2654 | 99 | 2.92-3.21 | 0.2751 | 142 | 0.2327 | 2700 | 100 | 3.21-3.68 | 0.2754 | 136 | 0.2115 | 2701 | 99 | 3.68-4.63 | 0.2164 | 122 | 0.1773 | 2747 | 99 | 4.63-4.749 | 0.1847 | 135 | 0.1723 | 2851 | 98 |
|
---|