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: 2.25→40.29 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 87226.05 / 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 | 0.213 | 2652 | 9.9 % | RANDOM |
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Rwork | 0.207 | - | - | - |
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obs | 0.207 | 26697 | 97.4 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.6627 Å2 / ksol: 0.364427 e/Å3 |
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Displacement parameters | Biso mean: 37.7 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 4.3 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 0.74 Å2 | 0 Å2 |
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3- | - | - | -5.04 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.26 Å | 0.26 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.23 Å | 0.25 Å |
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Refinement step | Cycle: LAST / Resolution: 2.25→40.29 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 4032 | 0 | 10 | 229 | 4271 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.008 | | X-RAY DIFFRACTION | c_angle_deg1.3 | | X-RAY DIFFRACTION | c_dihedral_angle_d22.8 | | X-RAY DIFFRACTION | c_improper_angle_d0.89 | | X-RAY DIFFRACTION | c_mcbond_it3.43 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it5.57 | 2 | X-RAY DIFFRACTION | c_scbond_it6.22 | 2 | X-RAY DIFFRACTION | c_scangle_it9.56 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 2.25→2.39 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.254 | 401 | 9.7 % |
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Rwork | 0.25 | 3747 | - |
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obs | - | - | 92.4 % |
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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.top | | | | | |
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