Software | Name | Version | Classification |
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CrystalClear | | data collectionPHENIX | | phasingCNS | | refinementPDB_EXTRACT | 3.14 | data extractiond*TREK | | data reductiond*TREK | | data scaling | | | | | |
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Refinement | Resolution: 2→44.3 Å / FOM work R set: 0.7803 / Cross valid method: FREE R-VALUE / σ(F): 0
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.27 | 878 | 10.6 % |
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Rwork | 0.2457 | 7372 | - |
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obs | - | 8250 | 99.2 % |
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Solvent computation | Bsol: 74.1715 Å2 |
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Displacement parameters | Biso max: 87.75 Å2 / Biso mean: 43.0773 Å2 / Biso min: 18.53 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.647 Å2 | 0 Å2 | 7.145 Å2 |
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2- | - | -1.206 Å2 | 0 Å2 |
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3- | - | - | 0.559 Å2 |
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Refinement step | Cycle: final / Resolution: 2→44.3 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 0 | 931 | 4 | 125 | 1060 |
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Biso mean | - | - | 38.34 | 47.78 | - |
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Num. residues | - | - | - | - | 44 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target |
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X-RAY DIFFRACTION | c_bond_d0.004 | | X-RAY DIFFRACTION | c_angle_d0.786 | | X-RAY DIFFRACTION | c_mcbond_it0 | 1.5 | X-RAY DIFFRACTION | c_scbond_it1.553 | 2 | X-RAY DIFFRACTION | c_mcangle_it0 | 2 | X-RAY DIFFRACTION | c_scangle_it2.067 | 2.5 | | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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2-2.07 | 0.392 | 86 | 0.3517 | 718 | 804 | 97.5 | 2.07-2.15 | 0.2915 | 81 | 0.3131 | 730 | 811 | 100 | 2.15-2.25 | 0.3142 | 93 | 0.3025 | 739 | 832 | 100 | 2.25-2.37 | 0.306 | 97 | 0.2846 | 713 | 810 | 99.9 | 2.37-2.52 | 0.2995 | 97 | 0.2807 | 728 | 825 | 100 | 2.52-2.71 | 0.2697 | 93 | 0.2797 | 750 | 843 | 100 | 2.71-2.99 | 0.3254 | 84 | 0.2909 | 727 | 811 | 100 | 2.99-3.42 | 0.3067 | 85 | 0.2146 | 753 | 838 | 99.8 | 3.42-4.31 | 0.1654 | 76 | 0.1803 | 758 | 834 | 99 | 4.31-44.3 | 0.2765 | 86 | 0.2462 | 756 | 842 | 95.9 |
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Xplor file | Refine-ID | Serial no | Param file |
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X-RAY DIFFRACTION | 1 | dna-rna_free.param | X-RAY DIFFRACTION | 2 | CNS_TOPPAR:water_rep.paramX-RAY DIFFRACTION | 3 | CNS_TOPPAR:ion.param | |
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