Software | Name | Version | Classification |
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ADSC | Quantumdata collectionPHENIX | | model buildingCNS | 1.3 | refinementCrystalClear | | data reductionCrystalClear | | data scalingPHENIX | | phasing | | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→36.8 Å / Occupancy max: 1 / Occupancy min: 1
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.252 | 492 | 10.4 % |
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Rwork | 0.223 | - | - |
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obs | - | 4695 | 99.1 % |
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Solvent computation | Bsol: 37.9883 Å2 |
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Displacement parameters | Biso max: 104.2 Å2 / Biso mean: 67.4001 Å2 / Biso min: 34.75 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 27.418 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 3.896 Å2 | 0 Å2 |
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3- | - | - | -31.314 Å2 |
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Refinement step | Cycle: LAST / Resolution: 2.6→36.8 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 0 | 902 | 62 | 11 | 975 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.005 | | X-RAY DIFFRACTION | c_angle_d0.894 | | X-RAY DIFFRACTION | c_mcbond_it0 | 1.5 | X-RAY DIFFRACTION | c_scbond_it1.495 | 2 | X-RAY DIFFRACTION | c_mcangle_it0 | 2 | X-RAY DIFFRACTION | c_scangle_it2.239 | 2.5 | | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / 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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2.6-2.69 | 0.427 | 59 | 0.4543 | 409 | 468 | 100 | 2.69-2.8 | 0.4502 | 48 | 0.479 | 410 | 458 | 100 | 2.8-2.93 | 0.516 | 45 | 0.4001 | 417 | 462 | 100 | 2.93-3.08 | 0.382 | 44 | 0.3388 | 406 | 450 | 100 | 3.08-3.28 | 0.3231 | 42 | 0.2546 | 433 | 475 | 99.8 | 3.28-3.53 | 0.3485 | 50 | 0.2508 | 412 | 462 | 100 | 3.53-3.88 | 0.2366 | 49 | 0.2066 | 425 | 474 | 100 | 3.88-4.45 | 0.1661 | 51 | 0.1847 | 426 | 477 | 100 | 4.45-5.6 | 0.2257 | 56 | 0.1719 | 429 | 485 | 100 | 5.6-100 | 0.1842 | 48 | 0.1622 | 436 | 484 | 92.2 |
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Xplor file | Refine-ID | Serial no | Param file |
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X-RAY DIFFRACTION | 1 | dna-rna_rep.param | X-RAY DIFFRACTION | 2 | water_rep.paramX-RAY DIFFRACTION | 3 | ion.paramX-RAY DIFFRACTION | 4 | 115_xplor.param | | |
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