Software | Name | Version | Classification |
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SOLVE | | phasingCNS | 0.9 | refinementDENZO | | data reductionSCALEPACK | | data scaling | | | |
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Refinement | Method to determine structure : MAD / Resolution: 2.1→29.26 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 564210.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| Rfactor![](img/lk-wikipe.gif) | Num. reflection | % reflection | Selection details |
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Rfree![](img/lk-wikipe.gif) | 0.247 | 8539 | 9.8 % | RANDOM |
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Rwork![](img/lk-wikipe.gif) | 0.215 | - | - | - |
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all![](img/lk-wikipe.gif) | 0.215 | 92597 | - | - |
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obs | 0.215 | 87277 | 94.4 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.92 Å2 / ksol: 0.36 e/Å3 |
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Displacement parameters | Biso mean: 41 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 5.3 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -3.2 Å2 | 0 Å2 |
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3- | - | - | -2.1 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 | 0.26 Å | 0.21 Å |
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Refinement step | Cycle: LAST / Resolution: 2.1→29.26 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 5104 | 0 | 6 | 248 | 5358 |
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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_deg1.4 | | X-RAY DIFFRACTION | c_dihedral_angle_d28.3 | | X-RAY DIFFRACTION | c_improper_angle_d0.71 | | X-RAY DIFFRACTION | c_mcbond_it3.59 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it5.75 | 2 | X-RAY DIFFRACTION | c_scbond_it5.84 | 2 | X-RAY DIFFRACTION | c_scangle_it8.26 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.305 | 1362 | 9.9 % |
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Rwork | 0.26 | 12340 | - |
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obs | - | - | 88.8 % |
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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 | ION.PARAMION.TOPX-RAY DIFFRACTION | 3 | WATER_REP.PARAMWATER_REP.TOP | | | | | |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement |
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Refinement | *PLUS σ(F): 0 / % reflection Rfree: 9.8 % |
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Solvent computation | *PLUS |
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Displacement parameters | *PLUS Biso mean: 41 Å2 |
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Refine LS restraints | *PLUS Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_angle_deg1.4 | | X-RAY DIFFRACTION | c_dihedral_angle_d | | X-RAY DIFFRACTION | c_dihedral_angle_deg28.3 | | X-RAY DIFFRACTION | c_improper_angle_d | | X-RAY DIFFRACTION | c_improper_angle_deg0.71 | | X-RAY DIFFRACTION | c_mcbond_it | 1.5 | X-RAY DIFFRACTION | c_scbond_it | 2 | X-RAY DIFFRACTION | c_mcangle_it | 2 | X-RAY DIFFRACTION | c_scangle_it | 2.5 | | | | | | | | | |
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LS refinement shell | *PLUS Rfactor Rfree: 0.305 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.26 |
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