Software | Name | Version | Classification |
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ADSC | Quantumdata collectionPHASER | | phasingPHENIX | (phenix.refine: 1.7.3_928)refinementHKL-2000 | | data reductionHKL-2000 | | data scaling | | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→35.689 Å / SU ML: 0.29 / σ(F): 1.35 / Phase error: 29.37 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2534 | 1186 | 4.99 % |
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Rwork | 0.1909 | - | - |
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obs | 0.1941 | 23775 | 82.64 % |
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all | - | 23792 | - |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL |
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Displacement parameters | | Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.8829 Å2 | -0 Å2 | -0.6509 Å2 |
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2- | - | -3.5115 Å2 | -0 Å2 |
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3- | - | - | 4.3945 Å2 |
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Refinement step | Cycle: LAST / Resolution: 2.42→35.689 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2530 | 590 | 41 | 256 | 3417 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.011 | 3286 | X-RAY DIFFRACTION | f_angle_d1.578 | 4560 | X-RAY DIFFRACTION | f_dihedral_angle_d21.974 | 1257 | X-RAY DIFFRACTION | f_chiral_restr0.086 | 498 | X-RAY DIFFRACTION | f_plane_restr0.006 | 480 | | | | | |
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LS refinement shell | Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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2.4201-2.5302 | 0.2442 | 82 | 0.179 | 1588 | X-RAY DIFFRACTION | 46 | 2.5302-2.6635 | 0.2883 | 93 | 0.2248 | 2025 | X-RAY DIFFRACTION | 59 | 2.6635-2.8303 | 0.296 | 110 | 0.2526 | 2471 | X-RAY DIFFRACTION | 73 | 2.8303-3.0488 | 0.3828 | 154 | 0.2624 | 3048 | X-RAY DIFFRACTION | 89 | 3.0488-3.3554 | 0.3125 | 187 | 0.2184 | 3337 | X-RAY DIFFRACTION | 98 | 3.3554-3.8404 | 0.242 | 179 | 0.1776 | 3383 | X-RAY DIFFRACTION | 99 | 3.8404-4.8366 | 0.2106 | 176 | 0.1461 | 3359 | X-RAY DIFFRACTION | 99 | 4.8366-35.6933 | 0.2034 | 205 | 0.1724 | 3378 | X-RAY DIFFRACTION | 98 |
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Refinement TLS params. | Method: refined / Origin x: 20.7701 Å / Origin y: -11.232 Å / Origin z: 3.2541 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.2225 Å2 | -0.0145 Å2 | -0.0207 Å2 | - | 0.2641 Å2 | 0.0191 Å2 | - | - | 0.307 Å2 |
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L | 4.0515 °2 | -0.4929 °2 | 0.0298 °2 | - | 3.399 °2 | 0.0121 °2 | - | - | 0.6611 °2 |
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S | -0.0029 Å ° | -0.1698 Å ° | 0.0972 Å ° | 0.1344 Å ° | 0.0419 Å ° | -0.8623 Å ° | -0.0101 Å ° | 0.1512 Å ° | -0.0067 Å ° |
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Refinement TLS group | Selection details: all |
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