Software | Name | Version | Classification |
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CCP4 | suitemodel buildingO | | model buildingCNS | 1 | refinementDENZO | | data reductionSCALEPACK | | data scaling CCP4 | | phasing | | | | | | |
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Refinement | Method to determine structure: MIR / Resolution: 2.17→24.61 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2011306.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.253 | 4314 | 10.1 % | RANDOM |
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Rwork | 0.218 | - | - | - |
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all | 0.2213 | 43275 | - | - |
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obs | 0.218 | 42686 | 93.6 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.3493 Å2 / ksol: 0.3641 e/Å3 |
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Displacement parameters | Biso mean: 32.7 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -4.14 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 2.32 Å2 | 0 Å2 |
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3- | - | - | 1.82 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.31 Å | 0.28 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.25 Å | 0.27 Å |
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Refinement step | Cycle: LAST / Resolution: 2.17→24.61 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 4709 | 0 | 13 | 290 | 5012 |
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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_deg1.4 | | X-RAY DIFFRACTION | c_dihedral_angle_d22.1 | | X-RAY DIFFRACTION | c_improper_angle_d0.9 | | X-RAY DIFFRACTION | c_mcbond_it1.24 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it2.14 | 2 | X-RAY DIFFRACTION | c_scbond_it1.45 | 2 | X-RAY DIFFRACTION | c_scangle_it2.43 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 2.17→2.3 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.288 | 673 | 10.5 % |
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Rwork | 0.273 | 5766 | - |
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obs | - | - | 86.2 % |
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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 | ION.PARAMION.TOPX-RAY DIFFRACTION | 3 | WATER.PARAMWATER.TOPX-RAY DIFFRACTION | 4 | ACT.PARAMACT.TOP | | | | | | | |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement |
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Refinement | *PLUS Num. reflection obs: 43316 / σ(F): 2 / % reflection Rfree: 10 % / Rfactor Rfree: 0.252 |
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Solvent computation | *PLUS |
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Displacement parameters | *PLUS Biso mean: 32.7 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_dihedral_angle_d | | X-RAY DIFFRACTION | c_dihedral_angle_deg22.1 | | X-RAY DIFFRACTION | c_improper_angle_d | | X-RAY DIFFRACTION | c_improper_angle_deg0.9 | | X-RAY DIFFRACTION | c_mcbond_it1.24 | 1.5 | X-RAY DIFFRACTION | c_scbond_it1.45 | 2 | X-RAY DIFFRACTION | c_mcangle_it2.14 | 2 | X-RAY DIFFRACTION | c_scangle_it2.43 | 2.5 | | | | | | | | |
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LS refinement shell | *PLUS Rfactor Rfree: 0.288 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.273 |
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