Software | Name | Version | Classification |
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PHENIX | (phenix.refine: 1.9_1692)refinementXDS | | data reductionXSCALE | | data scalingPHENIX | | phasing | | | | |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→34.315 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.47 / Phase error: 25.95 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.2352 | 787 | 4.71 % | Random |
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Rwork | 0.1953 | - | - | - |
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obs | 0.1973 | 16718 | 99.93 % | - |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL |
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Refinement step | Cycle: LAST / Resolution: 2.5→34.315 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 1044 | 0 | 20 | 31 | 1095 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.012 | 1065 | X-RAY DIFFRACTION | f_angle_d1.275 | 1411 | X-RAY DIFFRACTION | f_dihedral_angle_d17.189 | 440 | X-RAY DIFFRACTION | f_chiral_restr0.053 | 158 | X-RAY DIFFRACTION | f_plane_restr0.006 | 183 | | | | | |
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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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2.5002-2.6567 | 0.2701 | 109 | 0.255 | 2651 | X-RAY DIFFRACTION | 100 | 2.6567-2.8618 | 0.2964 | 143 | 0.2311 | 2659 | X-RAY DIFFRACTION | 100 | 2.8618-3.1496 | 0.2605 | 139 | 0.22 | 2648 | X-RAY DIFFRACTION | 100 | 3.1496-3.6049 | 0.2707 | 121 | 0.2057 | 2667 | X-RAY DIFFRACTION | 100 | 3.6049-4.5402 | 0.2229 | 132 | 0.1702 | 2667 | X-RAY DIFFRACTION | 100 | 4.5402-34.318 | 0.2049 | 143 | 0.1831 | 2639 | X-RAY DIFFRACTION | 100 |
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Refinement TLS params. | Method: refined / Origin x: 71.3112 Å / Origin y: -8.0539 Å / Origin z: 3.9062 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.7042 Å2 | 0.1281 Å2 | -0.0007 Å2 | - | 0.3975 Å2 | 0.0776 Å2 | - | - | 0.5048 Å2 |
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L | 1.2608 °2 | -1.9849 °2 | 0.4097 °2 | - | 5.6933 °2 | -0.9965 °2 | - | - | 0.4455 °2 |
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S | 0.0137 Å ° | -0.1544 Å ° | -0.3698 Å ° | -0.4709 Å ° | 0.0961 Å ° | -0.1191 Å ° | 0.4826 Å ° | 0.1735 Å ° | -0.1445 Å ° |
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Refinement TLS group | Selection details: chain 'A' or chain 'B' |
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