Software | Name | Version | Classification |
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CNS | | refinement CCP4 | (SCALA)data scalingCNS | | phasing | | | |
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Refinement | Starting model: PDB ENTRY 1VXH Resolution: 2.3→9.18 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 762440.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: residue 153 was disordered
| Rfactor![](img/lk-wikipe.gif) | Num. reflection | % reflection | Selection details |
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Rfree![](img/lk-wikipe.gif) | 0.218 | 633 | 10.9 % | RANDOM |
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Rwork![](img/lk-wikipe.gif) | 0.162 | - | - | - |
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obs | - | 5811 | 97.7 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 17.7685 Å2 / ksol: 0.397049 e/Å3 |
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Displacement parameters | Biso mean: 16.9 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.54 Å2 | 0 Å2 | -0.78 Å2 |
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2- | - | 1.97 Å2 | 0 Å2 |
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3- | - | - | -1.44 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.29 Å | 0.21 Å |
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Luzzati d res low | - | 9.2 Å |
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Luzzati sigma a | 0.21 Å | 0.11 Å |
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Refinement step | Cycle: LAST / Resolution: 2.3→9.18 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 1212 | 0 | 53 | 54 | 1319 |
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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 | | X-RAY DIFFRACTION | c_dihedral_angle_d17.2 | | X-RAY DIFFRACTION | c_improper_angle_d1.02 | | X-RAY DIFFRACTION | c_mcbond_it1.22 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it1.87 | 2 | X-RAY DIFFRACTION | c_scbond_it2.23 | 2 | X-RAY DIFFRACTION | c_scangle_it3.39 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.224 | 93 | 10.5 % |
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Rwork | 0.166 | 791 | - |
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obs | - | - | 91.8 % |
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Xplor file | Refine-ID | Serial no | Param file | Topol file |
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X-RAY DIFFRACTION | 1 | PROTEIN.PARAMPROTEIN.TOPX-RAY DIFFRACTION | 2 | WATER.PARAMWATER.TOPX-RAY DIFFRACTION | 3 | HEME.PARAMHEME.TOPX-RAY DIFFRACTION | 4 | SO4.PARAMSO4.TOP | | | | | | | |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement |
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Refinement | *PLUS Lowest resolution: 9.2 Å / Num. reflection obs: 5853 / σ(F): 2 / % reflection Rfree: 10.9 % / Rfactor obs: 0.16 / Rfactor Rfree : 0.217 |
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Solvent computation | *PLUS |
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Displacement parameters | *PLUS Biso mean: 16.9 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_bond_d0.006 | | X-RAY DIFFRACTION | c_angle_deg1.021 | | X-RAY DIFFRACTION | c_dihedral_angle_d | | X-RAY DIFFRACTION | c_dihedral_angle_deg17.2 | | X-RAY DIFFRACTION | c_improper_angle_d | | X-RAY DIFFRACTION | c_improper_angle_deg1.02 | | X-RAY DIFFRACTION | c_mcbond_it1.22 | 1.5 | X-RAY DIFFRACTION | c_scbond_it2.23 | 2 | X-RAY DIFFRACTION | c_mcangle_it1.87 | 2 | X-RAY DIFFRACTION | c_scangle_it3.39 | 2.5 | | | | | | | | | | |
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LS refinement shell | *PLUS Rfactor Rfree: 0.224 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.166 |
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