Software | Name | Version | Classification |
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HKL-2000 | | data collectionPHASER | | phasingPHENIX | (phenix.refine: 1.8.4_1496)refinementXDS | | data reductionSCALA | | data scaling | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2UVD Resolution: 2.5→51.274 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7203 / SU ML: 0.29 / σ(F): 1.35 / Phase error: 30.15 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.2707 | 341 | 4.64 % | RANDOM |
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Rwork | 0.2174 | - | - | - |
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obs | 0.22 | 7349 | 99.42 % | - |
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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: 150.09 Å2 / Biso mean: 67.4637 Å2 / Biso min: 26.11 Å2 |
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Refinement step | Cycle: LAST / Resolution: 2.5→51.274 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 1707 | 0 | 0 | 15 | 1722 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.006 | 1724 | X-RAY DIFFRACTION | f_angle_d1.142 | 2324 | X-RAY DIFFRACTION | f_chiral_restr0.037 | 272 | X-RAY DIFFRACTION | f_plane_restr0.003 | 306 | X-RAY DIFFRACTION | f_dihedral_angle_d15.084 | 628 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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2.5-3.1497 | 0.3474 | 161 | 0.2741 | 3425 | 3586 | 100 | 3.1497-51.2851 | 0.2483 | 180 | 0.199 | 3583 | 3763 | 99 |
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Refinement TLS params. | Method: refined / Origin x: 18.6926 Å / Origin y: -16.2395 Å / Origin z: -15.4302 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.3369 Å2 | 0.0541 Å2 | -0.0919 Å2 | - | 0.558 Å2 | 0.0525 Å2 | - | - | 0.4086 Å2 |
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L | 2.6928 °2 | -0.59 °2 | -0.0066 °2 | - | 2.2445 °2 | -0.1389 °2 | - | - | 3.1004 °2 |
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S | -0.123 Å ° | 0.7325 Å ° | 0.431 Å ° | -0.2929 Å ° | -0.17 Å ° | 0.2406 Å ° | -0.5254 Å ° | -0.5662 Å ° | 0.2332 Å ° |
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Refinement TLS group | Selection details: ALL |
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