Software | Name | Version | Classification |
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CNS | 1.1 | refinementHKL-2000 | | data collectionHKL-2000 | | data reductionSCALEPACK | | data scalingCNS | | phasing | | | | |
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Refinement | Method to determine structure : MOLECULAR REPLACEMENT Starting model: 2OHG Resolution: 2.5→39.87 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 93090.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| Rfactor![](img/lk-wikipe.gif) | Num. reflection | % reflection | Selection details |
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Rfree![](img/lk-wikipe.gif) | 0.237 | 1288 | 10.3 % | RANDOM |
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Rwork![](img/lk-wikipe.gif) | 0.226 | - | - | - |
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obs | 0.226 | 12501 | 99.1 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 66.2585 Å2 / ksol: 0.365511 e/Å3 |
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Displacement parameters | Biso mean: 56.1 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -5.73 Å2 | 3.06 Å2 | 0 Å2 |
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2- | - | -5.73 Å2 | 0 Å2 |
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3- | - | - | 11.46 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.35 Å | 0.33 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.45 Å | 0.44 Å |
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Refinement step | Cycle: LAST / Resolution: 2.5→39.87 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 1990 | 0 | 21 | 60 | 2071 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.006 | | X-RAY DIFFRACTION | c_angle_deg1.2 | | X-RAY DIFFRACTION | c_dihedral_angle_d22.1 | | X-RAY DIFFRACTION | c_improper_angle_d0.84 | | X-RAY DIFFRACTION | c_mcbond_it6.02 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it9.47 | 2 | X-RAY DIFFRACTION | c_scbond_it9.16 | 2 | X-RAY DIFFRACTION | c_scangle_it13.32 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.338 | 191 | 9.3 % |
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Rwork | 0.34 | 1858 | - |
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obs | - | - | 98.2 % |
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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.paramwater.topX-RAY DIFFRACTION | 3 | ion.paramion.topX-RAY DIFFRACTION | 4 | inh.paraminh.top | | | | | | | |
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