Software | Name | Version | Classification |
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DENZO | | data reductionSCALEPACK | | data scalingAMoRE | | phasingCNS | 1.1 | refinement | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1FX3 Resolution: 2.35→29.61 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 131500.99 / Data cutoff high rms absF: 131500.99 / 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 | 0.271 | 3103 | 10.3 % | SHELLS |
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Rwork | 0.234 | - | - | - |
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all | 0.238 | 31445 | - | - |
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obs | 0.234 | 30156 | 95.9 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.8554 Å2 / ksol: 0.334665 e/Å3 |
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Displacement parameters | Biso mean: 54 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 4.79 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 4.79 Å2 | 0 Å2 |
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3- | - | - | -9.57 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.38 Å | 0.31 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.34 Å | 0.26 Å |
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Refinement step | Cycle: LAST / Resolution: 2.35→29.61 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 4192 | 0 | 0 | 113 | 4305 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.011 | | X-RAY DIFFRACTION | c_angle_deg1.4 | | X-RAY DIFFRACTION | c_dihedral_angle_d25.3 | | X-RAY DIFFRACTION | c_improper_angle_d0.94 | | X-RAY DIFFRACTION | c_mcbond_it1.6 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it2.73 | 2 | X-RAY DIFFRACTION | c_scbond_it2.33 | 2 | X-RAY DIFFRACTION | c_scangle_it3.41 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 2.35→2.5 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.34 | 474 | 9.6 % |
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Rwork | 0.296 | 4475 | - |
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obs | - | 4475 | 96.7 % |
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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 | 3 | WATER_REP.PARAMWATER.TOP | | | |
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Software | *PLUS Name: CNS / Classification: refinement |
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Refinement | *PLUS Lowest resolution: 29.6 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.235 |
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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_angle_deg1.36 | X-RAY DIFFRACTION | c_dihedral_angle_d | X-RAY DIFFRACTION | c_dihedral_angle_deg25.3 | X-RAY DIFFRACTION | c_improper_angle_d | X-RAY DIFFRACTION | c_improper_angle_deg0.94 | | | | | |
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