Software | Name | Version | Classification |
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MAR345 | | data collectiond*TREK | | data reductionSOLVE | | phasingCNS | 0.9 | refinementd*TREK | | data scaling | | | | |
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Refinement | Resolution: 2.3→9.94 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1501218.1 / Data cutoff high rms absF: 1501218.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: MLF Details: F48 has been fixed because it lies on a two fold symmetry element.
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.246 | 1391 | 10.1 % | RANDOM |
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Rwork | 0.214 | - | - | - |
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all | - | 13831 | - | - |
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obs | - | 13776 | 99.6 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.4068 Å2 / ksol: 0.371 e/Å3 |
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Displacement parameters | Biso mean: 34.3 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 0 Å2 | 0 Å2 |
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3- | - | - | 0 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.34 Å | 0.31 Å |
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Luzzati d res low | - | 10 Å |
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Luzzati sigma a | 0.24 Å | 0.22 Å |
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Refinement step | Cycle: LAST / Resolution: 2.3→9.94 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 1311 | 0 | 29 | 63 | 1403 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.006 | | X-RAY DIFFRACTION | c_angle_deg1.2 | | X-RAY DIFFRACTION | c_dihedral_angle_d23.3 | | X-RAY DIFFRACTION | c_improper_angle_d0.63 | | X-RAY DIFFRACTION | c_mcbond_it3.44 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it3.51 | 2 | X-RAY DIFFRACTION | c_scbond_it1.82 | 2 | X-RAY DIFFRACTION | c_scangle_it2.84 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.266 | 234 | 10.4 % |
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Rwork | 0.25 | 2022 | - |
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obs | - | - | 99.8 % |
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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.PARAM | X-RAY DIFFRACTION | 3 | GDP_F.PARAM | X-RAY DIFFRACTION | 4 | WATER_REP.PARA | | | | | |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement |
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Refinement | *PLUS σ(F): 3 / % reflection Rfree: 10.1 % / Rfactor obs: 0.214 |
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Solvent computation | *PLUS |
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Displacement parameters | *PLUS Biso mean: 34.3 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_deg23.3 | | X-RAY DIFFRACTION | c_improper_angle_d | | X-RAY DIFFRACTION | c_improper_angle_deg0.63 | | 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: 0.266 / % reflection Rfree: 10.4 % / Rfactor Rwork: 0.25 |
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