Software | Name | Classification |
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CNS | refinementDENZO | data reductionSCALEPACK | data scalingCNS | phasing | | | |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→42.42 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 632595.99 / Data cutoff high rms absF: 632595.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.267 | 3575 | 10.1 % | RANDOM |
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Rwork | 0.216 | - | - | - |
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all | 0.2326 | 41118 | - | - |
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obs | 0.216 | 35350 | 85.9 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.2979 Å2 / ksol: 0.324584 e/Å3 |
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Displacement parameters | Biso mean: 56.6 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.98 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 9.46 Å2 | 0 Å2 |
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3- | - | - | -10.44 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.36 Å | 0.28 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.24 Å | 0.17 Å |
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Refinement step | Cycle: LAST / Resolution: 2.3→42.42 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 5438 | 0 | 0 | 477 | 5915 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.007 | | X-RAY DIFFRACTION | c_angle_deg1.2 | | X-RAY DIFFRACTION | c_dihedral_angle_d25.7 | | X-RAY DIFFRACTION | c_improper_angle_d0.79 | | X-RAY DIFFRACTION | c_mcbond_it1.83 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it3.18 | 2 | X-RAY DIFFRACTION | c_scbond_it2.47 | 2 | X-RAY DIFFRACTION | c_scangle_it3.75 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.301 | 417 | 10.2 % |
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Rwork | 0.253 | 3664 | - |
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obs | - | 3664 | 60.7 % |
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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.PARAMWATER.TOPX-RAY DIFFRACTION | 3 | ION.PARAMION.TOP | | | | | |
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Refinement | *PLUS Highest resolution: 2.3 Å / % reflection Rfree: 10 % / Rfactor all: 0.2326 / Rfactor obs: 0.216 / Rfactor Rfree: 0.267 / Rfactor Rwork: 0.216 |
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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_angle_deg1.228 | X-RAY DIFFRACTION | c_dihedral_angle_d | X-RAY DIFFRACTION | c_dihedral_angle_deg25.7 | X-RAY DIFFRACTION | c_improper_angle_d | X-RAY DIFFRACTION | c_improper_angle_deg0.79 | | | | | |
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LS refinement shell | *PLUS Highest resolution: 2.3 Å / Rfactor Rfree: 0.301 / Rfactor Rwork: 0.253 |
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