Software | Name | Version | Classification |
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DENZO | | data reductionSCALEPACK | | data scalingAMoRE | | phasingCNS | 0.5 | refinement | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LMN Resolution: 2.4→100 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 227924.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.283 | 449 | 10.4 % | RANDOM |
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Rwork | 0.231 | - | - | - |
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obs | - | 4298 | 95.5 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.88 Å2 / ksol: 0.644 e/Å3 |
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Displacement parameters | Biso mean: 22.6 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.36 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -3.65 Å2 | 0 Å2 |
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3- | - | - | 4.02 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.44 Å | 0.31 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.44 Å | 0.32 Å |
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Refinement step | Cycle: LAST / Resolution: 2.4→100 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 961 | 0 | 0 | 58 | 1019 |
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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_deg1.6 | | X-RAY DIFFRACTION | c_dihedral_angle_d23.7 | | X-RAY DIFFRACTION | c_improper_angle_d0.77 | | X-RAY DIFFRACTION | c_mcbond_it5.26 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it8.16 | 2 | X-RAY DIFFRACTION | c_scbond_it5.71 | 2 | X-RAY DIFFRACTION | c_scangle_it8.35 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 2.4→2.54 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.307 | 71 | 10.4 % |
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Rwork | 0.291 | 611 | - |
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obs | - | - | 92.2 % |
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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 | WATER_REP.PARAMWATER_REP.TOP | | | |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement |
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Refinement | *PLUS Lowest resolution: 100 Å / σ(F): 0 / % reflection Rfree: 10.4 % / Rfactor obs: 0.238 / Rfactor Rfree: 0.27 |
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Solvent computation | *PLUS |
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Displacement parameters | *PLUS Biso mean: 22.6 Å2 |
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Refine LS restraints | *PLUS Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.008 | | X-RAY DIFFRACTION | c_angle_deg1.7 | | X-RAY DIFFRACTION | c_dihedral_angle_d | | X-RAY DIFFRACTION | c_dihedral_angle_deg23.7 | | X-RAY DIFFRACTION | c_improper_angle_d | | X-RAY DIFFRACTION | c_improper_angle_deg0.77 | | X-RAY DIFFRACTION | c_mcbond_it5.26 | 1.5 | X-RAY DIFFRACTION | c_scbond_it5.71 | 2 | X-RAY DIFFRACTION | c_mcangle_it8.16 | 2 | X-RAY DIFFRACTION | c_scangle_it8.35 | 2.5 | | | | | | | | | | |
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LS refinement shell | *PLUS Rfactor Rfree: 0.307 / % reflection Rfree: 10.4 % / Rfactor Rwork: 0.291 |
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