Software | Name | Version | Classification |
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DENZO | | data reductionSCALEPACK | | data scalingSHARP | | phasingCNS | 0.9 | refinement | | | |
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Refinement | Method to determine structure: MIR / Resolution: 2.4→38.48 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 444544.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.273 | 3236 | 10 % | RANDOM |
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Rwork | 0.23 | - | - | - |
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obs | 0.232 | 32279 | 95 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 30.19 Å2 / ksol: 0.319 e/Å3 |
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Displacement parameters | Biso mean: 45 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 0 Å2 | 0 Å2 |
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3- | - | - | 0 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.41 Å | 0.35 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.51 Å | 0.47 Å |
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Refinement step | Cycle: LAST / Resolution: 2.4→38.48 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 4154 | 0 | 80 | 126 | 4360 |
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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_deg1.4 | | X-RAY DIFFRACTION | c_dihedral_angle_d23.7 | | X-RAY DIFFRACTION | c_improper_angle_d1.02 | | X-RAY DIFFRACTION | c_mcbond_it1.2 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it2.06 | 2 | X-RAY DIFFRACTION | c_scbond_it1.77 | 2 | X-RAY DIFFRACTION | c_scangle_it2.65 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.367 | 460 | 10.4 % |
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Rwork | 0.352 | 3947 | - |
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obs | - | 3947 | 79 % |
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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.PARAMWATER.TOPX-RAY DIFFRACTION | 3 | SAH.PARAMSAH.TOPX-RAY DIFFRACTION | 4 | SKF_NEW.PARAMSKF.TOP | | | | | | | |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement |
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Refinement | *PLUS Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.231 / Rfactor Rfree: 0.272 / Rfactor Rwork: 0.23 |
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Solvent computation | *PLUS |
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Displacement parameters | *PLUS Biso mean: 45 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_angle_deg1.45 | | 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_deg1.02 | | X-RAY DIFFRACTION | c_mcbond_it1.2 | 1.5 | X-RAY DIFFRACTION | c_scbond_it1.77 | 2 | X-RAY DIFFRACTION | c_mcangle_it2.06 | 2 | X-RAY DIFFRACTION | c_scangle_it2.65 | 2.5 | | | | | | | | | |
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LS refinement shell | *PLUS Rfactor Rfree: 0.367 / % reflection Rfree: 10.4 % / Rfactor Rwork: 0.352 |
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