Software | Name | Version | Classification |
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CNS | 1 | refinementDENZO | | data reductionSCALEPACK | | data scalingEPMR | | phasing | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Ferredoxin from Allochromatium vinosum (PDB 1BLU) Resolution: 2.9→25.86 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 1092461.4 / 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 | 0.219 | 198 | 5.3 % | RANDOM |
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Rwork | 0.197 | - | - | - |
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all | 0.197 | 3753 | - | - |
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obs | 0.197 | 3753 | 91.1 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 28.1492 Å2 / ksol: 0.366861 e/Å3 |
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Displacement parameters | Biso mean: 48.7 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 3.31 Å2 | 9.98 Å2 | 0 Å2 |
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2- | - | 3.31 Å2 | 0 Å2 |
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3- | - | - | -6.63 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.34 Å | 0.34 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.19 Å | 0.49 Å |
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Refinement step | Cycle: LAST / Resolution: 2.9→25.86 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 621 | 0 | 16 | 0 | 637 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.007 | | X-RAY DIFFRACTION | c_angle_deg1.2 | | X-RAY DIFFRACTION | c_dihedral_angle_d23.3 | | X-RAY DIFFRACTION | c_improper_angle_d0.83 | | X-RAY DIFFRACTION | c_mcbond_it0.9 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it1.61 | 2 | X-RAY DIFFRACTION | c_scbond_it1.45 | 2 | X-RAY DIFFRACTION | c_scangle_it2.16 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.226 | 26 | 5.7 % |
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Rwork | 0.329 | 433 | - |
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obs | - | - | 68.2 % |
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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 | PARAM.FESTOPH.FESX-RAY DIFFRACTION | 3 | WATER_REP.PARAMWATER.TOPX-RAY DIFFRACTION | 4 | ION.PARAMION.TOP | | | | | | | |
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Refinement | *PLUS Highest resolution: 2.9 Å |
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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_angle_deg1.22 | X-RAY DIFFRACTION | c_dihedral_angle_d | X-RAY DIFFRACTION | c_dihedral_angle_deg23.3 | X-RAY DIFFRACTION | c_improper_angle_d | X-RAY DIFFRACTION | c_improper_angle_deg0.83 | | | | | |
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LS refinement shell | *PLUS Rfactor Rfree: 0.25 / Rfactor Rwork: 0.33 |
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