Software | Name | Version | Classification |
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Adxv | | data processingSCALEPACK | | data scalingSOLVE | | phasingCNS | 1 | refinement | | | |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→45 Å / Rfactor Rfree error: 0.005 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.27 | 2868 | 10.1 % | RANDOM |
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Rwork | 0.227 | - | - | - |
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all | - | 29225 | - | - |
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obs | - | 28384 | 86.8 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.7353 Å2 / ksol: 0.368334 e/Å3 |
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Displacement parameters | Biso mean: 29.9 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 3.1 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -3.57 Å2 | 0 Å2 |
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3- | - | - | 0.47 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.41 Å | 0.33 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.39 Å | 0.36 Å |
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Refinement step | Cycle: LAST / Resolution: 2.5→45 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 3206 | 0 | 0 | 129 | 3335 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.011 | | X-RAY DIFFRACTION | c_angle_deg1.6 | | X-RAY DIFFRACTION | c_dihedral_angle_d25 | | X-RAY DIFFRACTION | c_improper_angle_d0.85 | | X-RAY DIFFRACTION | c_mcbond_it1.11 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it1.87 | 2 | X-RAY DIFFRACTION | c_scbond_it2.73 | 2 | X-RAY DIFFRACTION | c_scangle_it2.59 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.368 | 330 | 8.8 % |
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Rwork | 0.317 | 3440 | - |
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obs | - | - | 69 % |
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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.PARAMWATER_REP.TOP | | | |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 45 Å / % reflection Rfree: 10 % / Rfactor obs: 0.227 / Rfactor Rfree: 0.27 |
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Solvent computation | *PLUS |
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Displacement parameters | *PLUS |
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Refine LS restraints | *PLUS Refine-ID | Type | Dev ideal |
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X-RAY DIFFRACTION | c_dihedral_angle_d | X-RAY DIFFRACTION | c_dihedral_angle_deg25 | X-RAY DIFFRACTION | c_improper_angle_d | X-RAY DIFFRACTION | c_improper_angle_deg0.85 | | | | |
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LS refinement shell | *PLUS Rfactor obs: 0.317 |
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