Software | Name | Version | Classification |
---|
PHENIX | 1.9_1692refinementPDB_EXTRACT | 3.24 | data extractionxia2 | | data reductionxia2 | | data scalingPHASER | | phasing | | | | | |
|
---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→25.784 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.79 / Phase error: 26.07
| Rfactor | Num. reflection | % reflection |
---|
Rfree | 0.2522 | 983 | 4.93 % |
---|
Rwork | 0.2039 | - | - |
---|
obs | 0.2063 | 19954 | 99.73 % |
---|
|
---|
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å |
---|
Displacement parameters | Biso max: 115.93 Å2 / Biso mean: 27.6515 Å2 / Biso min: 2.77 Å2 |
---|
Refinement step | Cycle: final / Resolution: 1.92→25.784 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
---|
Num. atoms | 1924 | 0 | 0 | 198 | 2122 |
---|
Biso mean | - | - | - | 34.4 | - |
---|
Num. residues | - | - | - | - | 250 |
---|
|
---|
Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
---|
X-RAY DIFFRACTION | f_bond_d0.01 | 1966 | X-RAY DIFFRACTION | f_angle_d1.19 | 2668 | X-RAY DIFFRACTION | f_chiral_restr0.046 | 286 | X-RAY DIFFRACTION | f_plane_restr0.007 | 358 | X-RAY DIFFRACTION | f_dihedral_angle_d15.215 | 720 | | | | | |
|
---|
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
---|
1.92-2.0212 | 0.3394 | 131 | 0.2997 | 2676 | 2807 | 100 | 2.0212-2.1478 | 0.3188 | 127 | 0.2561 | 2666 | 2793 | 100 | 2.1478-2.3135 | 0.2744 | 157 | 0.2303 | 2642 | 2799 | 100 | 2.3135-2.5462 | 0.2733 | 155 | 0.2063 | 2679 | 2834 | 100 | 2.5462-2.9142 | 0.2488 | 133 | 0.2011 | 2704 | 2837 | 100 | 2.9142-3.6698 | 0.2269 | 142 | 0.1806 | 2741 | 2883 | 100 | 3.6698-25.7862 | 0.2109 | 138 | 0.169 | 2863 | 3001 | 99 |
|
---|
Refinement TLS params. | Method: refined / Origin x: -5.9072 Å / Origin y: -18.3631 Å / Origin z: 23.7083 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
---|
T | 0.0461 Å2 | -0.01 Å2 | 0.0068 Å2 | - | 0.0346 Å2 | 0.0017 Å2 | - | - | 0.0372 Å2 |
---|
L | 0.5795 °2 | 0.1416 °2 | -0.071 °2 | - | 0.5999 °2 | 0.129 °2 | - | - | 0.3454 °2 |
---|
S | -0.0477 Å ° | 0.0511 Å ° | -0.0421 Å ° | -0.1197 Å ° | 0.0621 Å ° | -0.0006 Å ° | -0.0307 Å ° | -0.0157 Å ° | 0.0192 Å ° |
---|
|
---|
Refinement TLS group | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
---|
1 | X-RAY DIFFRACTION | 1 | allA3 - 127 | 2 | X-RAY DIFFRACTION | 1 | allB3 - 127 | 3 | X-RAY DIFFRACTION | 1 | allS1 - 198 | | | | | | |
|
---|