Software | Name | Version | Classification |
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DENZO | | data reductionSCALEPACK | | data scalingPHASES | | phasingCNS | 1 | refinement | | | |
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Refinement | Method to determine structure: MIR / Resolution: 2→19.95 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1799833.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.227 | 2933 | 5.1 % | RANDOM |
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Rwork | 0.186 | - | - | - |
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obs | 0.1861 | 58076 | 94.6 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.548 Å2 / ksol: 0.361371 e/Å3 |
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Displacement parameters | Biso mean: 23.9 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 4.66 Å2 | 0 Å2 | 2.03 Å2 |
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2- | - | -2.28 Å2 | 0 Å2 |
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3- | - | - | -2.38 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.27 Å | 0.21 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.27 Å | 0.19 Å |
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Refinement step | Cycle: LAST / Resolution: 2→19.95 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 6540 | 0 | 40 | 550 | 7130 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.009 | | X-RAY DIFFRACTION | c_angle_deg1.6 | | X-RAY DIFFRACTION | c_dihedral_angle_d23.3 | | X-RAY DIFFRACTION | c_improper_angle_d0.88 | | X-RAY DIFFRACTION | c_mcbond_it3.33 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it3.73 | 2 | X-RAY DIFFRACTION | c_scbond_it4.22 | 2 | X-RAY DIFFRACTION | c_scangle_it4.85 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.313 | 457 | 5 % |
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Rwork | 0.24 | 8613 | - |
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obs | - | - | 88.8 % |
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Xplor file | Refine-ID | Serial no | Param file | Topol file |
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X-RAY DIFFRACTION | 1 | PROTEIN_REP.PARAMPROTEIN.TOPX-RAY DIFFRACTION | 2 | WATER_REP.PARAMWATER.TOPX-RAY DIFFRACTION | 3 | TRS.PARTRS.TOPX-RAY DIFFRACTION | 4 | SUB.PARSUB.TOPX-RAY DIFFRACTION | 5 | PARAMETER_INFILE_5TOPOLOGY_INFILE_5 | | | | | | | | | |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 20 Å / Rfactor all: 4.8 |
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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_deg23.3 | X-RAY DIFFRACTION | c_improper_angle_d | X-RAY DIFFRACTION | c_improper_angle_deg0.88 | | | | |
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