Software | Name | Classification |
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CNS | refinementSCALEPACK | data scalingCNS | phasing | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→25.15 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 331602.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.262 | 2621 | 8.1 % | RANDOM |
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Rwork | 0.215 | - | - | - |
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obs | 0.215 | 32516 | 94.1 % | - |
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all | - | 32516 | - | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.59 Å2 / ksol: 0.346 e/Å3 |
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Displacement parameters | Biso mean: 42.8 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 1.29 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 6.54 Å2 | 0 Å2 |
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3- | - | - | -7.83 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.35 Å | 0.28 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.36 Å | 0.31 Å |
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Refinement step | Cycle: LAST / Resolution: 2.15→25.15 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 4122 | 0 | 75 | 192 | 4389 |
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Refine LS restraints | Refine-ID | Type | Dev ideal |
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X-RAY DIFFRACTION | c_bond_d0.01 | X-RAY DIFFRACTION | c_angle_deg1.6 | X-RAY DIFFRACTION | c_dihedral_angle_d22.5 | X-RAY DIFFRACTION | c_improper_angle_d0.94 | | | | |
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LS refinement shell | Resolution: 2.15→2.23 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.342 | 379 | 8.1 % |
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Rwork | 0.316 | 4325 | - |
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obs | - | 3209 | 83 % |
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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_REP.PARAMPROTEIN.LINKX-RAY DIFFRACTION | 3 | ION.PARAMWATER.TOPX-RAY DIFFRACTION | 4 | ADP_ALF.PARAMION.TOPX-RAY DIFFRACTION | 5 | | ADP_ALF.TOP | | | | | | | | |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement |
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Refinement | *PLUS σ(F): 2 / % reflection Rfree: 8.1 % |
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Solvent computation | *PLUS |
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Displacement parameters | *PLUS Biso mean: 42.8 Å2 |
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Refine LS restraints | *PLUS Refine-ID | Type | Dev ideal |
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X-RAY DIFFRACTION | c_angle_deg1.6 | 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_deg0.94 | | | | | |
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LS refinement shell | *PLUS Rfactor Rfree: 0.342 / % reflection Rfree: 8.1 % / Rfactor Rwork: 0.316 |
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