Software | Name | Version | Classification |
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Blu-Ice | | data collectionPHASER | | phasingPHENIX | (phenix.refine: dev_572)refinementHKL-2000 | | data reductionHKL-2000 | | data scaling | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3Q7M Resolution: 2.091→19.85 Å / SU ML: 0.3 / σ(F): 0 / Phase error: 26.3 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2634 | 2000 | 9.17 % |
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Rwork | 0.1994 | - | - |
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obs | 0.2052 | 21810 | 99.7 % |
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all | - | 21724 | - |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20 Å2 / ksol: 0.326 e/Å3 |
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Displacement parameters | | Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 16.3648 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 16.3648 Å2 | 0 Å2 |
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3- | - | - | 16.3648 Å2 |
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Refinement step | Cycle: LAST / Resolution: 2.091→19.85 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2692 | 0 | 0 | 128 | 2820 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.011 | 2838 | X-RAY DIFFRACTION | f_angle_d1.024 | 3775 | X-RAY DIFFRACTION | f_dihedral_angle_d13.731 | 952 | X-RAY DIFFRACTION | f_chiral_restr0.063 | 443 | X-RAY DIFFRACTION | f_plane_restr0.004 | 492 | | | | | |
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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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2.0911-2.1658 | 0.3379 | 196 | 0.2945 | 1929 | X-RAY DIFFRACTION | 99 | 2.1658-2.2524 | 0.4223 | 196 | 0.3637 | 1956 | X-RAY DIFFRACTION | 99 | 2.2524-2.3547 | 0.2911 | 197 | 0.2894 | 1965 | X-RAY DIFFRACTION | 99 | 2.3547-2.4786 | 0.3338 | 198 | 0.2524 | 1962 | X-RAY DIFFRACTION | 100 | 2.4786-2.6336 | 0.3132 | 197 | 0.2235 | 1959 | X-RAY DIFFRACTION | 100 | 2.6336-2.8364 | 0.2992 | 202 | 0.2222 | 1974 | X-RAY DIFFRACTION | 100 | 2.8364-3.1209 | 0.2791 | 205 | 0.2102 | 1983 | X-RAY DIFFRACTION | 100 | 3.1209-3.5702 | 0.2199 | 203 | 0.1704 | 1992 | X-RAY DIFFRACTION | 100 | 3.5702-4.4895 | 0.2203 | 203 | 0.1503 | 2011 | X-RAY DIFFRACTION | 100 | 4.4895-19.8511 | 0.2262 | 203 | 0.1601 | 2079 | X-RAY DIFFRACTION | 100 |
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Refinement TLS params. | Method: refined / Origin x: -0.3397 Å / Origin y: -25.34 Å / Origin z: 12.0207 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | -0.0223 Å2 | 0.0643 Å2 | 0.0859 Å2 | - | -0.1256 Å2 | -0.0399 Å2 | - | - | -0.082 Å2 |
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L | 1.2184 °2 | -0.0524 °2 | 0.2097 °2 | - | 0.7024 °2 | -0.3261 °2 | - | - | 1.1356 °2 |
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S | -0.1334 Å ° | 0.1484 Å ° | -0.0017 Å ° | -0.1033 Å ° | 0.0553 Å ° | 0.0557 Å ° | -0.0692 Å ° | 0.1982 Å ° | 0.0026 Å ° |
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Refinement TLS group | Selection details: chain A |
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