Software | Name | Version | Classification |
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SBC-Collect | | data collectionSHELXD | | phasingMLPHARE | | phasingDM | | model buildingARP | | model buildingWARP | | model buildingHKL-3000 | | phasingPHENIX | (phenix.refine: 1.5_2)refinementHKL-3000 | | data reductionHKL-3000 | | data scalingDM | | phasing | | | | | | | | | | | |
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Refinement | Method to determine structure: SAD / Resolution: 1.582→34.324 Å / SU ML: 0.17 / σ(F): 0.07 / σ(I): 0 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.2036 | 1661 | 5.06 % | random |
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Rwork | 0.1761 | - | - | - |
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all | 0.1776 | 32797 | - | - |
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obs | 0.1776 | 32797 | 93.64 % | - |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.919 Å2 / ksol: 0.352 e/Å3 |
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Displacement parameters | | Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -1.814 Å2 | 0 Å2 | 1.7299 Å2 |
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2- | - | 9.2903 Å2 | 0 Å2 |
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3- | - | - | -7.4763 Å2 |
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Refinement step | Cycle: LAST / Resolution: 1.582→34.324 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2157 | 0 | 3 | 222 | 2382 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.006 | 2292 | X-RAY DIFFRACTION | f_angle_d0.942 | 3131 | X-RAY DIFFRACTION | f_dihedral_angle_d15.156 | 867 | X-RAY DIFFRACTION | f_chiral_restr0.066 | 371 | X-RAY DIFFRACTION | f_plane_restr0.005 | 408 | | | | | |
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LS refinement shell | Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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1.5817-1.6382 | 0.2513 | 158 | 0.2474 | 2734 | X-RAY DIFFRACTION | 83 | 1.6382-1.7038 | 0.2339 | 182 | 0.2125 | 2895 | X-RAY DIFFRACTION | 88 | 1.7038-1.7814 | 0.2439 | 152 | 0.2029 | 3032 | X-RAY DIFFRACTION | 92 | 1.7814-1.8753 | 0.2348 | 158 | 0.1878 | 3141 | X-RAY DIFFRACTION | 94 | 1.8753-1.9928 | 0.2104 | 173 | 0.1775 | 3180 | X-RAY DIFFRACTION | 97 | 1.9928-2.1466 | 0.2113 | 162 | 0.1714 | 3237 | X-RAY DIFFRACTION | 97 | 2.1466-2.3626 | 0.1934 | 177 | 0.1705 | 3246 | X-RAY DIFFRACTION | 98 | 2.3626-2.7043 | 0.2341 | 155 | 0.1828 | 3239 | X-RAY DIFFRACTION | 97 | 2.7043-3.4067 | 0.2172 | 175 | 0.1784 | 3251 | X-RAY DIFFRACTION | 97 | 3.4067-34.3318 | 0.1611 | 169 | 0.1545 | 3181 | X-RAY DIFFRACTION | 94 |
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Refinement TLS params. | Method: refined / Origin x: 9.7683 Å / Origin y: 4.8838 Å / Origin z: 33.3832 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.1269 Å2 | 0.0037 Å2 | -0.0068 Å2 | - | 0.1047 Å2 | 0.0018 Å2 | - | - | 0.1099 Å2 |
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L | 1.3859 °2 | 0.1106 °2 | -0.3252 °2 | - | 0.3914 °2 | 0.0533 °2 | - | - | 1.0114 °2 |
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S | -0.0103 Å ° | 0.0308 Å ° | -0.0104 Å ° | 0.0499 Å ° | 0.0121 Å ° | 0.0032 Å ° | 0.056 Å ° | -0.0981 Å ° | 0.0015 Å ° |
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Refinement TLS group | Selection details: chain A |
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