Software | Name | Version | Classification |
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Aimless | 0.7.4data scalingPHENIX | 1.11.1_2575refinementPDB_EXTRACT | 3.25 | data extractionXDS | | data reductionPHENIX | | phasing | | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ks3 Resolution: 1.36→39.87 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.31
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.1643 | 2005 | 3.98 % |
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Rwork | 0.1485 | - | - |
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obs | 0.1492 | 50384 | 95.8 % |
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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: 86.57 Å2 / Biso mean: 18.8117 Å2 / Biso min: 6.33 Å2 |
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Refinement step | Cycle: final / Resolution: 1.36→39.87 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2059 | 0 | 8 | 211 | 2278 |
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Biso mean | - | - | 35.83 | 26.71 | - |
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Num. residues | - | - | - | - | 258 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.007 | 2237 | X-RAY DIFFRACTION | f_angle_d1.295 | 3051 | X-RAY DIFFRACTION | f_chiral_restr0.089 | 313 | X-RAY DIFFRACTION | f_plane_restr0.013 | 401 | X-RAY DIFFRACTION | f_dihedral_angle_d14.707 | 833 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.3556-1.3895 | 0.2183 | 103 | 0.1945 | 2454 | 2557 | 68 | 1.3895-1.4271 | 0.2085 | 134 | 0.1773 | 3415 | 3549 | 95 | 1.4271-1.4691 | 0.1845 | 156 | 0.1638 | 3493 | 3649 | 98 | 1.4691-1.5165 | 0.1868 | 132 | 0.1597 | 3534 | 3666 | 98 | 1.5165-1.5707 | 0.1627 | 155 | 0.162 | 3451 | 3606 | 97 | 1.5707-1.6336 | 0.1763 | 150 | 0.1507 | 3481 | 3631 | 98 | 1.6336-1.708 | 0.1823 | 140 | 0.1537 | 3532 | 3672 | 98 | 1.708-1.798 | 0.1558 | 145 | 0.1495 | 3534 | 3679 | 98 | 1.798-1.9107 | 0.1631 | 142 | 0.1455 | 3485 | 3627 | 97 | 1.9107-2.0582 | 0.1549 | 149 | 0.1421 | 3577 | 3726 | 99 | 2.0582-2.2653 | 0.1481 | 144 | 0.1379 | 3561 | 3705 | 99 | 2.2653-2.593 | 0.1513 | 151 | 0.1436 | 3570 | 3721 | 99 | 2.593-3.2667 | 0.1712 | 152 | 0.1527 | 3629 | 3781 | 99 | 3.2667-41.02 | 0.16 | 152 | 0.143 | 3663 | 3815 | 99 |
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Refinement TLS params. | Method: refined / Origin x: -9.657 Å / Origin y: -1.764 Å / Origin z: 16.06 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.0688 Å2 | -0.0039 Å2 | 0.0016 Å2 | - | 0.0697 Å2 | 0.0016 Å2 | - | - | 0.0645 Å2 |
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L | 0.6336 °2 | -0.0181 °2 | 0.0422 °2 | - | 0.8644 °2 | 0.1723 °2 | - | - | 0.4688 °2 |
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S | -0.0208 Å ° | -0.0275 Å ° | 0.0132 Å ° | -0.0849 Å ° | 0.0279 Å ° | -0.0139 Å ° | -0.0235 Å ° | 0.0113 Å ° | 0.0139 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 | ( CHAIN A AND ( RESID 3:261 OR RESID 401:611 OR RESID 301:301 ) )A3 - 261 | 2 | X-RAY DIFFRACTION | 1 | ( CHAIN A AND ( RESID 3:261 OR RESID 401:611 OR RESID 301:301 ) )A401 - 611 | 3 | X-RAY DIFFRACTION | 1 | ( CHAIN A AND ( RESID 3:261 OR RESID 401:611 OR RESID 301:301 ) )A301 | | | | | | |
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