Software | Name | Version | Classification |
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CNS | 1.1 | refinementDENZO | | data reductionSCALEPACK | | data scalingSHARP | | phasing | | | |
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Refinement | Method to determine structure: SAD, MIR / Resolution: 2.5→19.68 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1725937.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.284 | 480 | 5.2 % | RANDOM |
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Rwork | 0.216 | - | - | - |
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obs | 0.216 | 9259 | 97.1 % | - |
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all | - | 9536 | - | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.075 Å2 / ksol: 0.35419 e/Å3 |
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Displacement parameters | Biso mean: 41.2 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 2.95 Å2 | 4.65 Å2 | 0 Å2 |
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2- | - | 2.95 Å2 | 0 Å2 |
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3- | - | - | -5.91 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.44 Å | 0.31 Å |
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Luzzati d res low | - | 6 Å |
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Luzzati sigma a | 0.56 Å | 0.41 Å |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.68 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2061 | 0 | 58 | 58 | 2177 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.009 | | X-RAY DIFFRACTION | c_angle_deg1.2 | | X-RAY DIFFRACTION | c_dihedral_angle_d22.5 | | X-RAY DIFFRACTION | c_improper_angle_d0.87 | | X-RAY DIFFRACTION | c_mcbond_it0.89 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it1.6 | 2 | X-RAY DIFFRACTION | c_scbond_it1.07 | 2 | X-RAY DIFFRACTION | c_scangle_it1.77 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.355 | 81 | 5.6 % |
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Rwork | 0.309 | 1374 | - |
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obs | - | - | 94.2 % |
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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 | GTP2.PARAMGTP2.TOPX-RAY DIFFRACTION | 3 | WATER_REP.PARAMWATER.TOPX-RAY DIFFRACTION | 4 | ION.PARAMION.TOPX-RAY DIFFRACTION | 5 | SAH.PARAMSAH.TOP | | | | | | | | | |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.22 |
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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_deg1.21 | X-RAY DIFFRACTION | c_dihedral_angle_d | X-RAY DIFFRACTION | c_dihedral_angle_deg22.5 | X-RAY DIFFRACTION | c_improper_angle_d | X-RAY DIFFRACTION | c_improper_angle_deg0.87 | | | | | |
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LS refinement shell | *PLUS Rfactor Rfree: 0.36 / Rfactor Rwork: 0.31 |
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