Software | Name | Version | Classification |
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PHENIX | 1.13 | refinementPDB_EXTRACT | 3.24 | data extractionXDS | | data reductionXSCALE | | data scalingAimless | | data scalingHKL2Map | | phasing | | | | | |
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Refinement | Method to determine structure: SAD / Resolution: 1.47→23.8 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.86 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.1992 | 610 | 4.81 % |
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Rwork | 0.1921 | 12073 | - |
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obs | 0.1924 | 12683 | 98.04 % |
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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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Displacement parameters | Biso max: 91.76 Å2 / Biso mean: 33.7619 Å2 / Biso min: 19.85 Å2 |
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Refinement step | Cycle: final / Resolution: 1.47→23.8 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 0 | 580 | 25 | 67 | 672 |
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Biso mean | - | - | 50.68 | 39.21 | - |
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Num. residues | - | - | - | - | 28 |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | % reflection obs (%) |
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1.47-1.6179 | 0.3471 | 121 | 0.2829 | 2917 | 94 | 1.6179-1.852 | 0.2591 | 156 | 0.2065 | 3023 | 99 | 1.852-2.333 | 0.2218 | 179 | 0.2147 | 3043 | 100 | 2.333-23.8 | 0.1736 | 154 | 0.1772 | 3090 | 99 |
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Refinement TLS params. | Method: refined / Origin x: -3.603 Å / Origin y: -7.6468 Å / Origin z: -7.6421 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.2338 Å2 | -0.0152 Å2 | -0.0058 Å2 | - | 0.2214 Å2 | -0.0077 Å2 | - | - | 0.2398 Å2 |
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L | 1.7307 °2 | -0.6688 °2 | -0.6631 °2 | - | 1.4693 °2 | -0.101 °2 | - | - | 2.0666 °2 |
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S | -0.0404 Å ° | 0.1328 Å ° | -0.1068 Å ° | -0.0897 Å ° | 0.0395 Å ° | 0.0078 Å ° | -0.0505 Å ° | 0.048 Å ° | -0.0005 Å ° |
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Refinement TLS group | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | allA1 - 14 | 2 | X-RAY DIFFRACTION | 1 | allB1 - 14 | 3 | X-RAY DIFFRACTION | 1 | allC1 - 3 | 4 | X-RAY DIFFRACTION | 1 | allD1 | 5 | X-RAY DIFFRACTION | 1 | allE101 - 103 | 6 | X-RAY DIFFRACTION | 1 | allS1 - 68 | | | | | | | | | | | | |
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