Software | Name | Version | Classification |
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PHENIX | | refinementAimless | 0.5.27data scalingPHASER | 2.7.16phasingPDB_EXTRACT | 3.24 | data extractionDIALS | | data reduction | | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5BJP Resolution: 3.101→33.031 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.59 / Phase error: 24.76
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.3298 | 246 | 10 % |
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Rwork | 0.238 | - | - |
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obs | 0.2475 | 2459 | 99.27 % |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å |
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Displacement parameters | Biso max: 184.27 Å2 / Biso mean: 108.9614 Å2 / Biso min: 63.98 Å2 |
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Refinement step | Cycle: final / Resolution: 3.101→33.031 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 0 | 783 | 41 | 0 | 824 |
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Biso mean | - | - | 74.16 | - | - |
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Num. residues | - | - | - | - | 36 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.008 | 921 | X-RAY DIFFRACTION | f_angle_d1.688 | 1433 | X-RAY DIFFRACTION | f_chiral_restr0.066 | 180 | X-RAY DIFFRACTION | f_plane_restr0.008 | 42 | X-RAY DIFFRACTION | f_dihedral_angle_d22.025 | 433 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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3.1011-3.906 | 0.3682 | 120 | 0.2985 | 1083 | 1203 | 99 | 3.906-33.0327 | 0.3141 | 126 | 0.2128 | 1130 | 1256 | 100 |
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Refinement TLS params. | Method: refined / Origin x: 1.8666 Å / Origin y: 50.7071 Å / Origin z: 20.137 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.0712 Å2 | 0.6819 Å2 | -0.0834 Å2 | - | 2.6112 Å2 | -0.1542 Å2 | - | - | 0.864 Å2 |
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L | 0.3649 °2 | 0.3158 °2 | -0.4063 °2 | - | 0.3755 °2 | -0.1074 °2 | - | - | 0.8673 °2 |
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S | 0.2857 Å ° | 1.0915 Å ° | 0.2262 Å ° | 0.0552 Å ° | -0.2081 Å ° | 0.0306 Å ° | -0.8172 Å ° | -1.6858 Å ° | 0.0049 Å ° |
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Refinement TLS group | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | allA1 - 36 | 2 | X-RAY DIFFRACTION | 1 | allD2 | 3 | X-RAY DIFFRACTION | 1 | allB1 | | | | | | |
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