Software | Name | Version | Classification |
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PHASES | | phasingCNS | 1 | refinementFRAMBO | | data collectionSAINT | | data scaling | | | |
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Refinement | Method to determine structure: MIR / Resolution: 2→14.99 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 763581.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure.
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.239 | 3151 | 9.8 % | RANDOM |
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Rwork | 0.185 | - | - | - |
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all | - | 31853 | - | - |
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obs | - | 28703 | 81.8 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.7433 Å2 / ksol: 0.337425 e/Å3 |
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Displacement parameters | Biso mean: 29.6 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 2.18 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 3.79 Å2 | 0 Å2 |
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3- | - | - | -5.97 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.31 Å | 0.3 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.32 Å | 0.27 Å |
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Refinement step | Cycle: LAST / Resolution: 2→14.99 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 4046 | 0 | 1 | 151 | 4198 |
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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_deg1.3 | | X-RAY DIFFRACTION | c_dihedral_angle_d22.1 | | X-RAY DIFFRACTION | c_improper_angle_d0.8 | | X-RAY DIFFRACTION | c_mcbond_it3.87 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it4.72 | 2 | X-RAY DIFFRACTION | c_scbond_it5.99 | 2 | X-RAY DIFFRACTION | c_scangle_it7.5 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 2→2.12 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.288 | 384 | 9.9 % |
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Rwork | 0.243 | 4163 | - |
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obs | - | 3481 | 72.7 % |
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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 | WATER_REP.PARAM | X-RAY DIFFRACTION | 3 | CARBOHYDRATE.PARAM | X-RAY DIFFRACTION | 4 | ION.PARAM | | | | | |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 15 Å / Num. reflection obs: 31854 / Rfactor obs: 0.183 / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.185 |
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Solvent computation | *PLUS |
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Displacement parameters | *PLUS |
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Refine LS restraints | *PLUS Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.0061 | | X-RAY DIFFRACTION | c_angle_deg1.29 | | X-RAY DIFFRACTION | c_dihedral_angle_d | | X-RAY DIFFRACTION | c_dihedral_angle_deg22.1 | | X-RAY DIFFRACTION | c_improper_angle_d | | X-RAY DIFFRACTION | c_improper_angle_deg0.8 | | X-RAY DIFFRACTION | c_mcbond_it3.87 | 1.5 | X-RAY DIFFRACTION | c_scbond_it5.99 | 2 | X-RAY DIFFRACTION | c_mcangle_it4.72 | 2 | X-RAY DIFFRACTION | c_scangle_it7.5 | 2.5 | | | | | | | | | | |
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LS refinement shell | *PLUS Rfactor Rfree: 0.288 / Rfactor Rwork: 0.243 |
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