Software | Name | Version | Classification |
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Blu-Ice | | data collectionHKL-2000 | | data processingSCALEPACK | | data scalingPHENIX | 1.10.1-2155 | model buildingPHENIX | 1.10.1-2155 | refinement | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XEW Resolution: 2.097→29.576 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.07 Details: The force field of Chro unit used in the refinement of CoII(Chro)2-DNA complex structure was generated using the atomic resolution crystal structure of NiII(Chro)2.
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2457 | 1230 | 9.77 % |
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Rwork | 0.2253 | - | - |
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obs | 0.2275 | 12596 | 98.45 % |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å |
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Displacement parameters | Biso max: 123.08 Å2 / Biso mean: 55.6101 Å2 / Biso min: 30.93 Å2 |
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Refinement step | Cycle: final / Resolution: 2.097→29.576 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 0 | 480 | 169 | 50 | 699 |
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Biso mean | - | - | 43.95 | 57.27 | - |
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Num. residues | - | - | - | - | 24 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.004 | 714 | X-RAY DIFFRACTION | f_angle_d0.764 | 1056 | X-RAY DIFFRACTION | f_chiral_restr0.039 | 136 | X-RAY DIFFRACTION | f_plane_restr0.004 | 30 | X-RAY DIFFRACTION | f_dihedral_angle_d28.767 | 316 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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2.0967-2.1806 | 0.3429 | 123 | 0.28 | 1155 | 1278 | 92 | 2.1806-2.2798 | 0.3864 | 145 | 0.2878 | 1312 | 1457 | 99 | 2.2798-2.4 | 0.3077 | 140 | 0.3005 | 1246 | 1386 | 100 | 2.4-2.5503 | 0.2934 | 132 | 0.2897 | 1271 | 1403 | 99 | 2.5503-2.747 | 0.3933 | 140 | 0.2963 | 1286 | 1426 | 100 | 2.747-3.0232 | 0.2815 | 132 | 0.3165 | 1297 | 1429 | 100 | 3.0232-3.4601 | 0.2217 | 140 | 0.2029 | 1275 | 1415 | 99 | 3.4601-4.3572 | 0.2396 | 134 | 0.2024 | 1260 | 1394 | 99 | 4.3572-29.5794 | 0.1946 | 144 | 0.1866 | 1264 | 1408 | 98 |
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