Software | Name | Version | Classification |
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CNS | 1.1 | refinementCBASS | | data collectionHKL-2000 | | data scalingSHELXD | | phasing | | | |
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Refinement | Method to determine structure : SAD / Resolution: 2.15→45.77 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 394169.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: In all the chains, residue 416 and residues 376 to 379 were not modelled due to lack of electron density.
| Rfactor![](img/lk-wikipe.gif) | Num. reflection | % reflection | Selection details |
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Rfree![](img/lk-wikipe.gif) | 0.246 | 2517 | 2 % | RANDOM |
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Rwork![](img/lk-wikipe.gif) | 0.207 | - | - | - |
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obs | 0.207 | 126832 | 95.4 % | - |
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all | - | 126832 | - | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.3409 Å2 / ksol: 0.334343 e/Å3 |
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Displacement parameters | Biso mean: 34 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 4.43 Å2 | -0.15 Å2 | 1.98 Å2 |
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2- | - | -2.13 Å2 | 0.35 Å2 |
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3- | - | - | -2.31 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.33 Å | 0.27 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.3 Å | 0.25 Å |
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Refinement step | Cycle: LAST / Resolution: 2.15→45.77 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 19908 | 0 | 0 | 661 | 20569 |
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Refine LS restraints | Refine-ID | Type | Dev ideal |
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X-RAY DIFFRACTION | c_bond_d0.006 | X-RAY DIFFRACTION | c_angle_deg1.3 | X-RAY DIFFRACTION | c_dihedral_angle_d20.8 | X-RAY DIFFRACTION | c_improper_angle_d0.79 | | | | |
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LS refinement shell | Resolution: 2.15→2.28 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.32 | 356 | 1.9 % |
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Rwork | 0.284 | 18374 | - |
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obs | - | - | 84.3 % |
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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 | carbohydrate.paramcarbohydrate.topX-RAY DIFFRACTION | 3 | water_rep.paramwater.topX-RAY DIFFRACTION | 4 | ion.paramion.top | | | | | | | |
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