Software | Name | Version | Classification |
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X-PLOR | | model building X-PLOR | 3.851 | refinementDENZO | | data reductionSCALEPACK | | data scaling X-PLOR | | phasing | | | | |
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Refinement | Resolution: 2→30 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.219 | 3439 | 5 % | SHELLS |
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Rwork | 0.187 | - | - | - |
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obs | 0.187 | 68596 | 81.2 % | - |
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all | - | 74777 | - | - |
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Displacement parameters | Biso mean: 30.6 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 | 0.26 Å | 0.23 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.29 Å | 0.27 Å |
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 6968 | 0 | 54 | 300 | 7322 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | x_bond_d0.006 | | X-RAY DIFFRACTION | x_angle_deg1.2 | | X-RAY DIFFRACTION | x_dihedral_angle_d25.2 | | X-RAY DIFFRACTION | x_improper_angle_d0.63 | | X-RAY DIFFRACTION | x_mcbond_it2.11 | 1.5 | X-RAY DIFFRACTION | x_mcangle_it3.24 | 2 | X-RAY DIFFRACTION | x_scbond_it4 | 2 | X-RAY DIFFRACTION | x_scangle_it6.1 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.285 | 393 | 5.1 % |
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Rwork | 0.274 | 7239 | - |
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obs | - | - | 54.8 % |
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Xplor file | Refine-ID | Serial no | Param file | Topol file |
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X-RAY DIFFRACTION | 1 | PROTEIN_REP.PARAMTOPHCSDX.PROX-RAY DIFFRACTION | 2 | PGA.PARTOPH19.SOLX-RAY DIFFRACTION | 3 | | PGA.TOP | | | | |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement |
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Refinement | *PLUS σ(F): 2 / % reflection Rfree: 5 % |
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Solvent computation | *PLUS |
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Displacement parameters | *PLUS Biso mean: 30.6 Å2 |
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Refine LS restraints | *PLUS Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | x_angle_deg1.2 | | X-RAY DIFFRACTION | x_dihedral_angle_d | | X-RAY DIFFRACTION | x_dihedral_angle_deg25.2 | | X-RAY DIFFRACTION | x_improper_angle_d | | X-RAY DIFFRACTION | x_improper_angle_deg0.63 | | X-RAY DIFFRACTION | x_mcbond_it | 1.5 | X-RAY DIFFRACTION | x_scbond_it | 2 | X-RAY DIFFRACTION | x_mcangle_it | 2 | X-RAY DIFFRACTION | x_scangle_it | 2.5 | | | | | | | | | |
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LS refinement shell | *PLUS Rfactor Rfree: 0.285 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.274 / Rfactor obs: 0.279 |
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