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: 2.8→44.5 Å / Occupancy max: 1 / Occupancy min: 1
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.265 | - | 10.1 % |
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Rwork | 0.226 | - | - |
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obs | - | 4352 | 97.1 % |
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Solvent computation | Bsol: 68.0444 Å2 |
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Displacement parameters | Biso max: 140.76 Å2 / Biso mean: 100.2348 Å2 / Biso min: 64.14 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -12.742 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 41.071 Å2 | 0 Å2 |
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3- | - | - | -28.33 Å2 |
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Refinement step | Cycle: LAST / Resolution: 2.8→44.5 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 0 | 900 | 62 | 3 | 965 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.006 | | X-RAY DIFFRACTION | c_angle_d1.025 | | X-RAY DIFFRACTION | c_mcbond_it0 | 1.5 | X-RAY DIFFRACTION | c_scbond_it1.49 | 2 | X-RAY DIFFRACTION | c_mcangle_it0 | 2 | X-RAY DIFFRACTION | c_scangle_it2.368 | 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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2.8-2.9 | 0.5668 | 47 | 0.5432 | 400 | 447 | 99.8 | 2.9-3.02 | 0.5097 | 51 | 0.4957 | 366 | 417 | 100 | 3.02-3.15 | 0.4066 | 48 | 0.3835 | 392 | 440 | 100 | 3.15-3.32 | 0.2818 | 50 | 0.2791 | 371 | 421 | 97.7 | 3.32-3.53 | 0.3474 | 39 | 0.2707 | 405 | 444 | 99.3 | 3.53-3.8 | 0.2728 | 43 | 0.2385 | 378 | 421 | 96.3 | 3.8-4.18 | 0.2465 | 48 | 0.2456 | 374 | 422 | 95 | 4.18-4.79 | 0.2507 | 34 | 0.1956 | 398 | 432 | 97.5 | 4.79-6.03 | 0.2188 | 48 | 0.1678 | 397 | 445 | 95.1 | 6.03-100 | 0.2089 | 43 | 0.1803 | 417 | 460 | 91.6 |
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Xplor file | Refine-ID | Serial no | Param file |
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X-RAY DIFFRACTION | 1 | sis_xplor.paramX-RAY DIFFRACTION | 2 | dna-rna.param | X-RAY DIFFRACTION | 3 | water_rep.paramX-RAY DIFFRACTION | 4 | ion.param | | |
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