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: 2.4→19.73 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1565132.54 / 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 | 0.271 | 490 | 5.2 % | RANDOM |
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Rwork | 0.215 | - | - | - |
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obs | 0.215 | 9395 | 86.6 % | - |
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all | - | 10849 | - | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.7414 Å2 / ksol: 0.358191 e/Å3 |
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Displacement parameters | Biso mean: 47.5 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 3.94 Å2 | 6.76 Å2 | 0 Å2 |
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2- | - | 3.94 Å2 | 0 Å2 |
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3- | - | - | -7.88 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.38 Å | 0.29 Å |
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Luzzati d res low | - | 6 Å |
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Luzzati sigma a | 0.35 Å | 0.25 Å |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.73 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2061 | 0 | 27 | 80 | 2168 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.008 | | X-RAY DIFFRACTION | c_angle_deg1.2 | | X-RAY DIFFRACTION | c_dihedral_angle_d23 | | X-RAY DIFFRACTION | c_improper_angle_d0.81 | | X-RAY DIFFRACTION | c_mcbond_it0.92 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it1.67 | 2 | X-RAY DIFFRACTION | c_scbond_it1.06 | 2 | X-RAY DIFFRACTION | c_scangle_it1.75 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.323 | 55 | 4.5 % |
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Rwork | 0.246 | 1159 | - |
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obs | - | - | 68.4 % |
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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 | NUC.PARAMNUC.TOPX-RAY DIFFRACTION | 3 | WATER_REP.PARAMWATER.TOPX-RAY DIFFRACTION | 4 | ION.PARAMION.TOPX-RAY DIFFRACTION | 5 | SAM.PARAMSAM.TOP | | | | | | | | | |
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Refinement | *PLUS Highest resolution: 2.4 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_deg1.15 | X-RAY DIFFRACTION | c_dihedral_angle_d | X-RAY DIFFRACTION | c_dihedral_angle_deg23 | X-RAY DIFFRACTION | c_improper_angle_d | X-RAY DIFFRACTION | c_improper_angle_deg0.81 | | | | | |
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LS refinement shell | *PLUS Rfactor Rfree: 0.32 / Rfactor Rwork: 0.25 |
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