Software | Name | Version | Classification |
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SnB | | phasingSHARP | | phasingCNS | 1.1 | refinementDENZO | | data reductionSCALEPACK | | data scalingSHAKE-N-BAKE | | phasing | | | | | |
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Refinement | Method to determine structure: MAD / Resolution: 3→19.96 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 4863302.42 / 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 | 0.293 | 1570 | 5 % | RANDOM |
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Rwork | 0.26 | - | - | - |
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all | - | 31603 | - | - |
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obs | - | 31603 | 97.9 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.250818 e/Å3 |
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Displacement parameters | Biso mean: 57.3 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -15.91 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -25.74 Å2 | 0 Å2 |
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3- | - | - | 41.65 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.52 Å | 0.43 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.59 Å | 0.52 Å |
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Refinement step | Cycle: LAST / Resolution: 3→19.96 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 8907 | 0 | 8 | 58 | 8973 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.009 | | X-RAY DIFFRACTION | c_angle_deg1.2 | | X-RAY DIFFRACTION | c_dihedral_angle_d22.3 | | X-RAY DIFFRACTION | c_improper_angle_d0.79 | | X-RAY DIFFRACTION | c_mcbond_it1.08 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it1.92 | 2 | X-RAY DIFFRACTION | c_scbond_it1.63 | 2 | X-RAY DIFFRACTION | c_scangle_it2.63 | 2.5 | | | | | | | | |
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Refine LS restraints NCS | NCS model details: CONSTR |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.42 | 225 | 4.4 % |
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Rwork | 0.349 | 4878 | - |
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obs | - | - | 95.9 % |
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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 | GLYCEROL.PARGLYCEROL.TOPX-RAY DIFFRACTION | 4 | ION.PARAMION.TOP | | | | | | | |
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Software | *PLUS Name: CNS / Version: 1.1 / Classification: refinement |
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Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.26 / Rfactor Rwork: 0.26 |
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Solvent computation | *PLUS |
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Displacement parameters | *PLUS Biso mean: 57.3 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_deg1.2 | | X-RAY DIFFRACTION | c_dihedral_angle_d | | X-RAY DIFFRACTION | c_dihedral_angle_deg22.3 | | X-RAY DIFFRACTION | c_improper_angle_d | | X-RAY DIFFRACTION | c_improper_angle_deg0.79 | | 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: 0.42 / % reflection Rfree: 4.4 % / Rfactor Rwork: 0.349 |
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