Software | Name | Version | Classification |
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CCP4 | | model buildingCNS | 1 | refinementMOSFLM | | data reduction CCP4 | (SCALA)data scaling CCP4 | | phasing | | | | | |
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Refinement | Method to determine structure: MIR / Resolution: 1.95→19.68 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3832033.19 / Data cutoff high rms absF: 3832033.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.231 | 2835 | 5.1 % | RANDOM |
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Rwork | 0.196 | - | - | - |
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all | 0.196 | 55315 | - | - |
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obs | 0.196 | 55315 | 98.1 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 67.13 Å2 / ksol: 0.38 e/Å3 |
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Displacement parameters | Biso mean: 35.4 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -2.39 Å2 | -0.09 Å2 | 0 Å2 |
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2- | - | -2.39 Å2 | 0 Å2 |
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3- | - | - | 4.78 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.26 Å | 0.22 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.2 Å | 0.18 Å |
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Refinement step | Cycle: LAST / Resolution: 1.95→19.68 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 4077 | 0 | 73 | 566 | 4716 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.01 | | X-RAY DIFFRACTION | c_angle_deg1.5 | | X-RAY DIFFRACTION | c_dihedral_angle_d23.6 | | X-RAY DIFFRACTION | c_improper_angle_d0.96 | | X-RAY DIFFRACTION | c_mcbond_it1.39 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it2.08 | 2 | X-RAY DIFFRACTION | c_scbond_it2.15 | 2 | X-RAY DIFFRACTION | c_scangle_it3.06 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.279 | 449 | 4.9 % |
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Rwork | 0.244 | 8767 | - |
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obs | - | 8767 | 98.6 % |
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Xplor file | Refine-ID | Serial no | Param file | Topol file |
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X-RAY DIFFRACTION | 1 | PROTEIN_REP.PAPROTEIN.TOPX-RAY DIFFRACTION | 2 | WATER_REP.PARAWATER.TOPX-RAY DIFFRACTION | 3 | ION.PARAMION.TOPX-RAY DIFFRACTION | 4 | ACY.PARACY.TOPX-RAY DIFFRACTION | 5 | TRS.PARTRS.TOP | | | | | | | | | |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement |
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Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5.1 % |
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Solvent computation | *PLUS |
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Displacement parameters | *PLUS Biso mean: 35.4 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_angle_deg1.5 | | X-RAY DIFFRACTION | c_dihedral_angle_d | | X-RAY DIFFRACTION | c_dihedral_angle_deg23.6 | | X-RAY DIFFRACTION | c_improper_angle_d | | X-RAY DIFFRACTION | c_improper_angle_deg0.96 | | X-RAY DIFFRACTION | c_mcbond_it | 1.5 | X-RAY DIFFRACTION | c_scbond_it | 2 | X-RAY DIFFRACTION | c_mcangle_it | 2 | X-RAY DIFFRACTION | c_scangle_it | 2.5 | | | | | | | | | |
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LS refinement shell | *PLUS Rfactor Rfree: 0.279 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.244 |
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