Software | Name | Version | Classification |
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BUSTER | 2.10.4refinementautoPROC | | data reductionXDS | Jun 30, 2023data reductionautoPROC | 1.0.5data scalingAimless | 0.7.15data scalingPHASER | | phasing | | | | | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.813→63.09 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.15 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.13 / SU Rfree Blow DPI: 0.127 / SU Rfree Cruickshank DPI: 0.12
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.2371 | 1927 | - | RANDOM |
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Rwork | 0.1946 | - | - | - |
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obs | 0.1966 | 38503 | 98.6 % | - |
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Displacement parameters | Biso mean: 53.89 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -3.8479 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -3.8479 Å2 | 0 Å2 |
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3- | - | - | 7.6958 Å2 |
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Refine analyze | Luzzati coordinate error obs: 0.23 Å |
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Refinement step | Cycle: LAST / Resolution: 1.813→63.09 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2571 | 0 | 38 | 348 | 2957 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number | Restraint function | Weight |
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X-RAY DIFFRACTION | t_bond_d0.01 | 5207 | HARMONIC2 | X-RAY DIFFRACTION | t_angle_deg0.95 | 9368 | HARMONIC2 | X-RAY DIFFRACTION | t_dihedral_angle_d | 1563 | SINUSOIDAL2 | X-RAY DIFFRACTION | t_gen_planes | 874 | HARMONIC5 | X-RAY DIFFRACTION | t_it | 5207 | HARMONIC10 | X-RAY DIFFRACTION | t_chiral_improper_torsion | 346 | SEMIHARMONIC5 | X-RAY DIFFRACTION | t_sum_occupancies | 1 | HARMONIC1 | X-RAY DIFFRACTION | t_ideal_dist_contact | 4901 | SEMIHARMONIC4 | X-RAY DIFFRACTION | t_omega_torsion3.5 | | | | X-RAY DIFFRACTION | t_other_torsion15.7 | | | | | | | | | | | | | | | | | | | | | |
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LS refinement shell | Resolution: 1.813→1.83 Å
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.3693 | 42 | - |
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Rwork | 0.3844 | - | - |
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obs | - | - | 80.82 % |
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Refinement TLS params. | Origin x: -0.4658 Å / Origin y: 23.2931 Å / Origin z: -3.5484 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | -0.0202 Å2 | 0.0304 Å2 | -0.0111 Å2 | - | 0.1103 Å2 | 0.0091 Å2 | - | - | 0.0882 Å2 |
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L | 0.7328 °2 | 0.2 °2 | -0.215 °2 | - | 0.8995 °2 | -0.119 °2 | - | - | 1.6725 °2 |
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S | 0.0232 Å ° | 0.0114 Å ° | -0.1268 Å ° | 0.0114 Å ° | 0.0137 Å ° | -0.4513 Å ° | -0.1268 Å ° | -0.4513 Å ° | -0.0368 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 | { A|* }A4 - 339 | 2 | X-RAY DIFFRACTION | 1 | { A|* }A1001 - 1005 | | | | |
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