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: 3→46.2 Å / Occupancy max: 1 / Occupancy min: 1
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.226 | 323 | 9.9 % |
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Rwork | 0.209 | - | - |
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obs | - | 3262 | 99.6 % |
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Solvent computation | Bsol: 35.1879 Å2 |
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Displacement parameters | Biso max: 140.99 Å2 / Biso mean: 80.8589 Å2 / Biso min: 42.29 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.68 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 26.859 Å2 | 0 Å2 |
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3- | - | - | -27.54 Å2 |
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Refinement step | Cycle: LAST / Resolution: 3→46.2 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 0 | 942 | 62 | 9 | 1013 |
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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_d1.124 | | X-RAY DIFFRACTION | c_mcbond_it0 | 1.5 | X-RAY DIFFRACTION | c_scbond_it1.4 | 2 | X-RAY DIFFRACTION | c_mcangle_it0 | 2 | X-RAY DIFFRACTION | c_scangle_it2.271 | 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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3-3.11 | 0.3556 | 35 | 0.3799 | 294 | 329 | 100 | 3.11-3.23 | 0.3024 | 26 | 0.2965 | 278 | 304 | 100 | 3.23-3.38 | 0.2667 | 33 | 0.2778 | 295 | 328 | 99.7 | 3.38-3.56 | 0.3072 | 37 | 0.2469 | 266 | 303 | 100 | 3.56-3.78 | 0.2727 | 32 | 0.2197 | 299 | 331 | 100 | 3.78-4.07 | 0.2155 | 43 | 0.2204 | 268 | 311 | 100 | 4.07-4.48 | 0.1887 | 27 | 0.2293 | 307 | 334 | 100 | 4.48-5.13 | 0.2145 | 33 | 0.1915 | 289 | 322 | 100 | 5.13-6.46 | 0.2146 | 26 | 0.1724 | 314 | 340 | 100 | 6.46-100 | 0.1696 | 31 | 0.16 | 329 | 360 | 97 |
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Xplor file | Refine-ID | Serial no | Param file |
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X-RAY DIFFRACTION | 1 | dna-rna_free.param | X-RAY DIFFRACTION | 2 | water_rep.paramX-RAY DIFFRACTION | 3 | ion.paramX-RAY DIFFRACTION | 4 | 115_xplor.param | | |
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