Software | Name | Version | Classification |
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DENZO | | data reductionSCALEPACK | | data scalingSOLVE | | phasingCNS | 1 | refinement | | | |
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Refinement | Resolution: 1.75→19.58 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 578945.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.255 | 1362 | 10.2 % | RANDOM |
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Rwork | 0.211 | - | - | - |
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all | - | 13394 | - | - |
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obs | - | 13394 | 99.5 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 64.74 Å2 / ksol: 0.431 e/Å3 |
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Displacement parameters | Biso mean: 24.9 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 5.76 Å2 | 0 Å2 | 0.99 Å2 |
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2- | - | -2.71 Å2 | 0 Å2 |
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3- | - | - | -3.05 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.26 Å | 0.21 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.23 Å | 0.21 Å |
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Refinement step | Cycle: LAST / Resolution: 1.75→19.58 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 995 | 0 | 0 | 136 | 1131 |
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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_deg1.4 | | X-RAY DIFFRACTION | c_dihedral_angle_d23.9 | | X-RAY DIFFRACTION | c_improper_angle_d1.02 | | X-RAY DIFFRACTION | c_mcbond_it1.49 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it2.21 | 2 | X-RAY DIFFRACTION | c_scbond_it2.38 | 2 | X-RAY DIFFRACTION | c_scangle_it3.38 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.327 | 200 | 9.2 % |
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Rwork | 0.291 | 1985 | - |
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obs | - | - | 98.1 % |
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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_PI3.TOPX-RAY DIFFRACTION | 2 | WATER_REP.PARAMWATER.TOP | | | |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement |
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Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10.2 % / Rfactor obs: 0.215 |
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Solvent computation | *PLUS |
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Displacement parameters | *PLUS Biso mean: 24.9 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_deg1.4 | | X-RAY DIFFRACTION | c_dihedral_angle_d | | X-RAY DIFFRACTION | c_dihedral_angle_deg23.9 | | X-RAY DIFFRACTION | c_improper_angle_d | | X-RAY DIFFRACTION | c_improper_angle_deg1.02 | | 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: 0.327 / % reflection Rfree: 9.2 % / Rfactor Rwork: 0.291 |
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