Software | Name | Version | Classification |
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CBASS | | data collectionSHELX | | model buildingSHARP | | phasingARP | | model buildingWARP | | model buildingCNS | 1.1 | refinementHKL-2000 | | data reductionHKL-2000 | | data scalingSHELX | | phasing | | | | | | | | |
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Refinement | Method to determine structure: SAD / Resolution: 2.06→36.25 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 224649.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.257 | 517 | 4.2 % | RANDOM |
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Rwork | 0.213 | - | - | - |
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all | 0.239 | 12920 | - | - |
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obs | 0.213 | 12412 | 94.2 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.3499 Å2 / ksol: 0.341256 e/Å3 |
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Displacement parameters | Biso mean: 30.4 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.15 Å2 | 0 Å2 | 5.19 Å2 |
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2- | - | -1.58 Å2 | 0 Å2 |
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3- | - | - | 1.43 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.32 Å | 0.26 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.29 Å | 0.21 Å |
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Refinement step | Cycle: LAST / Resolution: 2.06→36.25 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 1552 | 0 | 0 | 127 | 1679 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.007 | | X-RAY DIFFRACTION | c_angle_deg1.4 | | X-RAY DIFFRACTION | c_dihedral_angle_d23.3 | | X-RAY DIFFRACTION | c_improper_angle_d0.75 | | X-RAY DIFFRACTION | c_mcbond_it1.29 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it2.03 | 2 | X-RAY DIFFRACTION | c_scbond_it2.06 | 2 | X-RAY DIFFRACTION | c_scangle_it2.86 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 2.06→2.19 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.287 | 65 | 3.4 % |
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Rwork | 0.26 | 1863 | - |
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obs | - | - | 88 % |
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Xplor file | Refine-ID | Serial no | Param file | Topol file |
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X-RAY DIFFRACTION | 1 | protein_rep.paramprotein.topX-RAY DIFFRACTION | 2 | dna-rna_rep.param | dna-rna.top | X-RAY DIFFRACTION | 3 | water_rep.paramwater.topX-RAY DIFFRACTION | 4 | ion.paramion.top | | | | | |
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