Software | Name | Classification |
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CNS | refinementDENZO | data reductionSCALEPACK | data scalingCNS | phasing | | | |
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Refinement | Resolution: 1.9→40.82 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 906866.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.237 | 1769 | 9.6 % | RANDOM |
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Rwork | 0.204 | - | - | - |
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all | - | 18445 | - | - |
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obs | - | 18445 | 98.1 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 71.16 Å2 / ksol: 0.435 e/Å3 |
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Displacement parameters | Biso mean: 23.7 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -3.94 Å2 | 0 Å2 | -4.67 Å2 |
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2- | - | 4.43 Å2 | 0 Å2 |
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3- | - | - | -0.49 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.27 Å | 0.22 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.21 Å | 0.16 Å |
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Refinement step | Cycle: LAST / Resolution: 1.9→40.82 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 855 | 0 | 4 | 106 | 965 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.01 | | X-RAY DIFFRACTION | c_angle_deg1.2 | | X-RAY DIFFRACTION | c_dihedral_angle_d15.7 | | X-RAY DIFFRACTION | c_improper_angle_d0.81 | | X-RAY DIFFRACTION | c_mcbond_it2.55 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it3.33 | 2 | X-RAY DIFFRACTION | c_scbond_it6.39 | 2 | X-RAY DIFFRACTION | c_scangle_it8.75 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 1.9→1.99 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 8
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.344 | 167 | 8.1 % |
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Rwork | 0.273 | 1892 | - |
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obs | - | - | 88.6 % |
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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 | ION.PARAMION.TOPX-RAY DIFFRACTION | 3 | WATER_REP.PARAMWATER.TOPX-RAY DIFFRACTION | 4 | MPD_NEW.PARMPD_NEW.TOP | | | | | | | |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement |
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Refinement | *PLUS σ(F): 0 / % reflection Rfree: 9.6 % / Rfactor obs: 0.204 |
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Solvent computation | *PLUS |
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Displacement parameters | *PLUS Biso mean: 23.7 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_deg1.2 | | X-RAY DIFFRACTION | c_dihedral_angle_d | | X-RAY DIFFRACTION | c_dihedral_angle_deg15.7 | | X-RAY DIFFRACTION | c_improper_angle_d | | X-RAY DIFFRACTION | c_improper_angle_deg0.81 | | X-RAY DIFFRACTION | c_mcbond_it | 1.5 | X-RAY DIFFRACTION | c_scbond_it | 2 | X-RAY DIFFRACTION | c_mcangle_it | 2 | X-RAY DIFFRACTION | c_scangle_it | 2.5 | | | | | | | | | |
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LS refinement shell | *PLUS Rfactor Rfree: 0.344 / % reflection Rfree: 8.1 % / Rfactor Rwork: 0.273 |
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