Software | Name | Version | Classification |
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PHENIX | 1.12-2829 | refinementXDS | | data reductionAimless | 0.7.3data scalingPHASER | 2.8.0phasingPDB_EXTRACT | 3.27 | data extraction | | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6I8L Resolution: 1.42→81.655 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.83 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2059 | 2806 | 4.99 % |
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Rwork | 0.1801 | 53437 | - |
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obs | 0.1814 | 56243 | 99.91 % |
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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 | Biso max: 73.86 Å2 / Biso mean: 22.1735 Å2 / Biso min: 7.91 Å2 |
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Refinement step | Cycle: final / Resolution: 1.42→81.655 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 1559 | 0 | 145 | 173 | 1877 |
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Biso mean | - | - | 26.58 | 31.16 | - |
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Num. residues | - | - | - | - | 196 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.012 | 1703 | X-RAY DIFFRACTION | f_angle_d1.197 | 2317 | X-RAY DIFFRACTION | f_chiral_restr0.1 | 246 | X-RAY DIFFRACTION | f_plane_restr0.009 | 316 | X-RAY DIFFRACTION | f_dihedral_angle_d20.917 | 637 | | | | | |
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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 (%) |
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1.42-1.4441 | 0.299 | 132 | 0.299 | 2612 | 99 | 1.4441-1.4704 | 0.3327 | 149 | 0.2839 | 2609 | 100 | 1.4704-1.4987 | 0.3258 | 148 | 0.2624 | 2625 | 100 | 1.4987-1.5293 | 0.2382 | 138 | 0.2382 | 2613 | 100 | 1.5293-1.5625 | 0.2176 | 144 | 0.2122 | 2659 | 100 | 1.5625-1.5989 | 0.2217 | 136 | 0.2003 | 2613 | 100 | 1.5989-1.6389 | 0.2527 | 147 | 0.1964 | 2629 | 100 | 1.6389-1.6832 | 0.1829 | 137 | 0.1829 | 2673 | 100 | 1.6832-1.7327 | 0.199 | 131 | 0.1805 | 2635 | 100 | 1.7327-1.7887 | 0.2057 | 117 | 0.1741 | 2667 | 100 | 1.7887-1.8526 | 0.2004 | 144 | 0.1686 | 2641 | 100 | 1.8526-1.9268 | 0.1593 | 138 | 0.1593 | 2673 | 100 | 1.9268-2.0145 | 0.1956 | 141 | 0.1561 | 2656 | 100 | 2.0145-2.1207 | 0.1634 | 142 | 0.1551 | 2664 | 100 | 2.1207-2.2536 | 0.1616 | 135 | 0.1549 | 2692 | 100 | 2.2536-2.4276 | 0.1756 | 139 | 0.1655 | 2700 | 100 | 2.4276-2.6719 | 0.2001 | 134 | 0.1694 | 2691 | 100 | 2.6719-3.0585 | 0.2037 | 158 | 0.1714 | 2707 | 100 | 3.0585-3.8534 | 0.2247 | 141 | 0.1709 | 2774 | 100 | 3.8534-81.655 | 0.2141 | 155 | 0.1907 | 2904 | 100 |
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Refinement TLS params. | Method: refined / Origin x: -8.057 Å / Origin y: -33.889 Å / Origin z: 6.443 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.0722 Å2 | 0.0185 Å2 | -0.005 Å2 | - | 0.087 Å2 | -0.0066 Å2 | - | - | 0.0984 Å2 |
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L | 0.6292 °2 | -0.3869 °2 | -0.0583 °2 | - | 1.2765 °2 | -0.1239 °2 | - | - | 1.3106 °2 |
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S | 0.0289 Å ° | 0.0397 Å ° | 0.0458 Å ° | -0.0498 Å ° | -0.0317 Å ° | -0.0442 Å ° | -0.116 Å ° | -0.0664 Å ° | 0.0045 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 B AND ( RESID 301:301 OR RESID 303:304 OR RESID 52:269 OR RESID 302:302 OR RESID 306:306 OR RESID 305:305 OR RESID 307:308 OR RESID 401:573 ) )B301 | 2 | X-RAY DIFFRACTION | 1 | ( CHAIN B AND ( RESID 301:301 OR RESID 303:304 OR RESID 52:269 OR RESID 302:302 OR RESID 306:306 OR RESID 305:305 OR RESID 307:308 OR RESID 401:573 ) )B303 - 304 | 3 | X-RAY DIFFRACTION | 1 | ( CHAIN B AND ( RESID 301:301 OR RESID 303:304 OR RESID 52:269 OR RESID 302:302 OR RESID 306:306 OR RESID 305:305 OR RESID 307:308 OR RESID 401:573 ) )B52 - 269 | 4 | X-RAY DIFFRACTION | 1 | ( CHAIN B AND ( RESID 301:301 OR RESID 303:304 OR RESID 52: | | | | | | |
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