Software | Name | Version | Classification |
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SOLVE | | phasingRESOLVE | | model buildingCNS | 1 | refinementDENZO | | data reduction CCP4 | (SCALA)data scalingRESOLVE | | phasing | | | | | | |
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Refinement | Method to determine structure: Single Wavelength Anomalous Dispersion Resolution: 2.3→29.34 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1517194.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Used bulk solvent correction, simulated annealing, energy minimization, overall and indvidual B-factor refinement. A maximum likelihood refinent target was also used.
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.27 | 1518 | 5 % | RANDOM |
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Rwork | 0.238 | - | - | - |
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all | 0.242 | 31239 | - | - |
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obs | 0.242 | 31239 | 95 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 69.7635 Å2 / ksol: 0.366887 e/Å3 |
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Displacement parameters | Biso mean: 55.7 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 13.7 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -7.53 Å2 | 0 Å2 |
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3- | - | - | -6.17 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 | 0.29 Å | 0.25 Å |
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Refinement step | Cycle: LAST / Resolution: 2.3→29.34 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 3738 | 0 | 10 | 220 | 3968 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.005 | | X-RAY DIFFRACTION | c_angle_deg1 | | X-RAY DIFFRACTION | c_dihedral_angle_d21.1 | | X-RAY DIFFRACTION | c_improper_angle_d0.65 | | X-RAY DIFFRACTION | c_mcbond_it1.65 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it2.79 | 2 | X-RAY DIFFRACTION | c_scbond_it2.68 | 2 | X-RAY DIFFRACTION | c_scangle_it3.63 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.302 | 236 | 4.9 % |
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Rwork | 0.268 | 4551 | - |
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obs | - | 4787 | 90.5 % |
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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_REP.PARAMWATER.TOPX-RAY DIFFRACTION | 3 | ION.PARAMION.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 % / Rfactor obs: 0.238 / Rfactor Rfree: 0.27 |
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Solvent computation | *PLUS |
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Displacement parameters | *PLUS Biso mean: 55.7 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_angle_deg1 | | X-RAY DIFFRACTION | c_dihedral_angle_d | | X-RAY DIFFRACTION | c_dihedral_angle_deg21.1 | | X-RAY DIFFRACTION | c_improper_angle_d | | X-RAY DIFFRACTION | c_improper_angle_deg0.65 | | X-RAY DIFFRACTION | c_mcbond_it1.65 | 1.5 | X-RAY DIFFRACTION | c_scbond_it2.68 | 2 | X-RAY DIFFRACTION | c_mcangle_it2.79 | 2 | X-RAY DIFFRACTION | c_scangle_it3.63 | 2.5 | | | | | | | | | |
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LS refinement shell | *PLUS Rfactor Rfree: 0.302 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.268 |
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