Software | Name | Version | Classification |
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CNS | 0.9 | refinementd*TREK | | data reductionHKL-2000 | | data scalingCNS | | phasing | | | |
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Refinement | Method to determine structure: MAD / Resolution: 2→42.09 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The number of reflections for refinement is greater than the number of reflections for data collection, because in CNS (hlml taget) refinement, the Friedel's pair was treated as two seperated reflections.
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.248 | 2466 | 4.9 % | RANDOM |
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Rwork | 0.237 | - | - | - |
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obs | 0.237 | 50697 | 89.6 % | - |
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all | - | 56561 | - | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 82.368 Å2 / ksol: 0.431764 e/Å3 |
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Displacement parameters | Biso mean: 31.7 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 11.56 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -8.3 Å2 | 0 Å2 |
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3- | - | - | -3.26 Å2 |
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Refine analyze | Luzzati coordinate error free: 0.31 Å / Luzzati sigma a free: 0.39 Å |
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Refinement step | Cycle: LAST / Resolution: 2→42.09 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 3492 | 0 | 0 | 307 | 3799 |
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Refine LS restraints | Refine-ID | Type | Dev ideal |
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X-RAY DIFFRACTION | c_bond_d0.009 | X-RAY DIFFRACTION | c_angle_deg1.3 | X-RAY DIFFRACTION | c_dihedral_angle_d23.7 | X-RAY DIFFRACTION | c_improper_angle_d0.75 | | | | |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.357 | 348 | 5 % |
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Rwork | 0.352 | 6563 | - |
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obs | - | - | 73.7 % |
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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 | | | |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 50 Å |
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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 |
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X-RAY DIFFRACTION | c_dihedral_angle_d | X-RAY DIFFRACTION | c_dihedral_angle_deg23.7 | X-RAY DIFFRACTION | c_improper_angle_d | X-RAY DIFFRACTION | c_improper_angle_deg0.75 | | | | |
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