Software | Name | Version | Classification |
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MOSFLM | | data reductionSCALA | | data scalingPHENIX | 1.6.4_486refinementPDB_EXTRACT | 3.24 | data extractionAutoSol | | phasing | | | | | |
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Refinement | Method to determine structure: SAD / Resolution: 2.299→57.779 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.28 / Phase error: 26.7
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2771 | 2419 | 7.44 % |
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Rwork | 0.249 | - | - |
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obs | 0.251 | 32492 | 95.59 % |
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Bsol: 59.91 Å2 / ksol: 0.381 e/Å3 |
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Displacement parameters | Biso max: 197.7 Å2 / Biso mean: 57.27 Å2 / Biso min: 20.57 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -9.0362 Å2 | 0 Å2 | -0.6789 Å2 |
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2- | - | 16.9343 Å2 | 0 Å2 |
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3- | - | - | -7.8981 Å2 |
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Refinement step | Cycle: final / Resolution: 2.299→57.779 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2462 | 445 | 0 | 103 | 3010 |
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Biso mean | - | - | - | 44.88 | - |
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Num. residues | - | - | - | - | 331 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.002 | 2980 | X-RAY DIFFRACTION | f_angle_d0.69 | 4072 | X-RAY DIFFRACTION | f_chiral_restr0.035 | 460 | X-RAY DIFFRACTION | f_plane_restr0.001 | 457 | X-RAY DIFFRACTION | f_dihedral_angle_d18.875 | 1219 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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2.299-2.3812 | 0.2708 | 240 | 0.2349 | 3056 | 3296 | 95 | 2.3812-2.4765 | 0.2911 | 233 | 0.253 | 2801 | 3034 | 91 | 2.4765-2.5893 | 0.3506 | 236 | 0.2521 | 2943 | 3179 | 94 | 2.5893-2.7258 | 0.289 | 240 | 0.2568 | 3118 | 3358 | 97 | 2.7258-2.8965 | 0.2954 | 243 | 0.2523 | 3063 | 3306 | 98 | 2.8965-3.1202 | 0.2752 | 248 | 0.2729 | 2983 | 3231 | 96 | 3.1202-3.4341 | 0.3267 | 236 | 0.2892 | 2980 | 3216 | 94 | 3.4341-3.931 | 0.2608 | 250 | 0.2382 | 3133 | 3383 | 98 | 3.931-4.9522 | 0.2417 | 237 | 0.2127 | 2923 | 3160 | 94 | 4.9522-57.7974 | 0.2659 | 256 | 0.257 | 3073 | 3329 | 97 |
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Refinement TLS params. | Method: refined / Origin x: -5.9818 Å / Origin y: 6.3674 Å / Origin z: 28.8691 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.1741 Å2 | 0.0077 Å2 | 0.0011 Å2 | - | 0.1581 Å2 | -0.0121 Å2 | - | - | 0.1771 Å2 |
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L | 0.2302 °2 | 0.0938 °2 | 0.2132 °2 | - | 0.1494 °2 | 0.0674 °2 | - | - | 0.2685 °2 |
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S | -0.0678 Å ° | 0.0137 Å ° | -0.007 Å ° | 0.0119 Å ° | 0.0013 Å ° | -0.0042 Å ° | 0.0057 Å ° | -0.0387 Å ° | -0 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 | allA12 - 88 | 2 | X-RAY DIFFRACTION | 1 | allB12 - 88 | 3 | X-RAY DIFFRACTION | 1 | allD12 - 88 | 4 | X-RAY DIFFRACTION | 1 | allE12 - 89 | 5 | X-RAY DIFFRACTION | 1 | allC3 - 13 | 6 | X-RAY DIFFRACTION | 1 | allF7 - 17 | 7 | X-RAY DIFFRACTION | 1 | allS1 - 104 | | | | | | | | | | | | | | |
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