Software | Name | Version | Classification |
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CrystalClear | | data collectionPHENIX | | phasingCNS | | refinementPDB_EXTRACT | 3.14 | data extractionSOLVE | | phasingd*TREK | | data scaling | | | | | |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→100 Å / FOM work R set: 0.7962 / Cross valid method: FREE R-VALUE / σ(F): 0
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2646 | 726 | 10.8 % |
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Rwork | 0.2194 | 5968 | - |
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obs | - | 6694 | 99.6 % |
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Solvent computation | Bsol: 65.1243 Å2 |
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Displacement parameters | Biso max: 99.24 Å2 / Biso mean: 39.1932 Å2 / Biso min: 19.01 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.478 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 7.452 Å2 | 0 Å2 |
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3- | - | - | -7.93 Å2 |
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Refinement step | Cycle: final / Resolution: 2.3→100 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 0 | 916 | 102 | 138 | 1156 |
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Biso mean | - | - | 45.54 | 46.94 | - |
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Num. residues | - | - | - | - | 43 |
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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_d0.91 | | X-RAY DIFFRACTION | c_mcbond_it0 | 1.5 | X-RAY DIFFRACTION | c_scbond_it1.717 | 2 | X-RAY DIFFRACTION | c_mcangle_it0 | 2 | X-RAY DIFFRACTION | c_scangle_it2.442 | 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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2.3-2.38 | 0.4083 | 67 | 0.3967 | 589 | 656 | 100 | 2.38-2.48 | 0.5019 | 84 | 0.4463 | 566 | 650 | 100 | 2.48-2.59 | 0.4026 | 66 | 0.3508 | 597 | 663 | 100 | 2.59-2.73 | 0.3122 | 67 | 0.3121 | 580 | 647 | 100 | 2.73-2.9 | 0.3791 | 60 | 0.3008 | 600 | 660 | 100 | 2.9-3.12 | 0.3026 | 86 | 0.2213 | 583 | 669 | 100 | 3.12-3.44 | 0.2478 | 70 | 0.2099 | 598 | 668 | 99.7 | 3.44-3.93 | 0.2233 | 77 | 0.1821 | 593 | 670 | 99.6 | 3.93-4.96 | 0.2207 | 75 | 0.1545 | 612 | 687 | 100 | 4.96-100 | 0.2057 | 74 | 0.1904 | 650 | 724 | 97.3 |
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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.paramX-RAY DIFFRACTION | 4 | bru.paramX-RAY DIFFRACTION | 5 | get_xplor.param | | | |
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