Software | Name | Version | Classification |
---|
PHENIX | 1.10_2155refinementPDB_EXTRACT | 3.25 | data extractionHKL-3000 | | data reductionHKL-3000 | | data scalingPHENIX | | phasing | | | | | |
|
---|
Refinement | Method to determine structure: SAD / Resolution: 2.198→24.284 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.08 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
---|
Rfree | 0.2107 | 1967 | 9.46 % |
---|
Rwork | 0.1811 | 18815 | - |
---|
obs | 0.184 | 20782 | 86.61 % |
---|
|
---|
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL |
---|
Displacement parameters | Biso max: 97.13 Å2 / Biso mean: 33.2002 Å2 / Biso min: 16.23 Å2 |
---|
Refinement step | Cycle: final / Resolution: 2.198→24.284 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
---|
Num. atoms | 2224 | 0 | 50 | 161 | 2435 |
---|
Biso mean | - | - | 21.73 | 41.46 | - |
---|
Num. residues | - | - | - | - | 288 |
---|
|
---|
Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
---|
X-RAY DIFFRACTION | f_bond_d0.009 | 2304 | X-RAY DIFFRACTION | f_angle_d0.899 | 3112 | X-RAY DIFFRACTION | f_chiral_restr0.051 | 332 | X-RAY DIFFRACTION | f_plane_restr0.005 | 404 | X-RAY DIFFRACTION | f_dihedral_angle_d16.544 | 1365 | | | | | |
|
---|
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 (%) |
---|
2.1983-2.2533 | 0.2525 | 68 | 0.2035 | 650 | 44 | 2.2533-2.3141 | 0.2413 | 78 | 0.2075 | 761 | 50 | 2.3141-2.3822 | 0.2585 | 91 | 0.2108 | 884 | 59 | 2.3822-2.459 | 0.2925 | 122 | 0.2211 | 1151 | 75 | 2.459-2.5468 | 0.2534 | 147 | 0.2106 | 1392 | 92 | 2.5468-2.6487 | 0.2418 | 154 | 0.1972 | 1473 | 97 | 2.6487-2.769 | 0.2372 | 157 | 0.1985 | 1490 | 98 | 2.769-2.9148 | 0.221 | 159 | 0.1901 | 1520 | 99 | 2.9148-3.0971 | 0.2464 | 163 | 0.193 | 1544 | 99 | 3.0971-3.3357 | 0.2019 | 159 | 0.1792 | 1528 | 99 | 3.3357-3.6703 | 0.2134 | 162 | 0.1752 | 1557 | 100 | 3.6703-4.199 | 0.1935 | 165 | 0.1576 | 1576 | 100 | 4.199-5.2814 | 0.173 | 167 | 0.1548 | 1605 | 100 | 5.2814-24.284 | 0.1926 | 175 | 0.1906 | 1684 | 98 |
|
---|
Refinement TLS params. | Method: refined / Origin x: -32.6595 Å / Origin y: -17.6333 Å / Origin z: -0.9014 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
---|
T | 0.1829 Å2 | -0.086 Å2 | 0.0253 Å2 | - | 0.2924 Å2 | -0.0109 Å2 | - | - | 0.2602 Å2 |
---|
L | 0.6113 °2 | -0.3612 °2 | -0.0949 °2 | - | 0.7 °2 | 0.0628 °2 | - | - | 1.3417 °2 |
---|
S | 0.0136 Å ° | 0.0527 Å ° | -0.0143 Å ° | 0.0451 Å ° | -0.0482 Å ° | 0.1103 Å ° | -0.0513 Å ° | -0.3711 Å ° | -0.0085 Å ° |
---|
|
---|
Refinement TLS group | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
---|
1 | X-RAY DIFFRACTION | 1 | allA1 - 308 | 2 | X-RAY DIFFRACTION | 1 | allA309 | 3 | X-RAY DIFFRACTION | 1 | allZ6 - 14 | 4 | X-RAY DIFFRACTION | 1 | allS1 - 161 | | | | | | | | |
|
---|