Software | Name | Version | Classification |
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MLPHARE | | phasingCNS | 0.9 | refinementbioteX | | data reductionSCALEPACK | | data scaling | | | |
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Refinement | Method to determine structure: MIR / Resolution: 1.7→18.22 Å / Rfactor Rfree error: 0.007 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: bulk solvent correction
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.237 | 1007 | 5.4 % | RANDOM |
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Rwork | 0.19 | - | - | - |
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all | - | 19959 | - | - |
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obs | - | 18697 | 93.8 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.4512 Å2 / ksol: 0.394983 e/Å3 |
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Displacement parameters | Biso mean: 18 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 2.65 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 2.77 Å2 | 0 Å2 |
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3- | - | - | -5.42 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.25 Å | 0.19 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.22 Å | 0.17 Å |
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Refinement step | Cycle: LAST / Resolution: 1.7→18.22 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 1389 | 0 | 27 | 183 | 1599 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.0128 | | X-RAY DIFFRACTION | c_angle_deg1.697 | | X-RAY DIFFRACTION | c_dihedral_angle_d24.4 | | X-RAY DIFFRACTION | c_improper_angle_d1.26 | | X-RAY DIFFRACTION | c_mcbond_it1.43 | 1.5 | X-RAY DIFFRACTION | c_mcangle_it1.97 | 2 | X-RAY DIFFRACTION | c_scbond_it2.39 | 2 | X-RAY DIFFRACTION | c_scangle_it3.47 | 2.5 | | | | | | | | |
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LS refinement shell | Resolution: 1.7→1.76 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 10
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.389 | 106 | 5.9 % |
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Rwork | 0.369 | 1676 | - |
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obs | - | - | 91.8 % |
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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 | dna-rna_rep.param | dna-rna.top | X-RAY DIFFRACTION | 3 | water_rep.paramwater.topX-RAY DIFFRACTION | 4 | ion.paramion.topX-RAY DIFFRACTION | 5 | mysam.parmysam.top | | | | | | | |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement |
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Refinement | *PLUS Highest resolution: 1.7 Å / σ(F): 0 / % reflection Rfree: 5.4 % / Rfactor obs: 0.191 / Rfactor Rwork: 0.19 |
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Solvent computation | *PLUS |
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Displacement parameters | *PLUS Biso mean: 18 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_dihedral_angle_d | | X-RAY DIFFRACTION | c_dihedral_angle_deg24.4 | | X-RAY DIFFRACTION | c_improper_angle_d | | X-RAY DIFFRACTION | c_improper_angle_deg1.26 | | 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: 0.389 / % reflection Rfree: 5.9 % / Rfactor Rwork: 0.369 |
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