Software | Name | Version | Classification |
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PHENIX | 1.17.1_3660refinementPDB_EXTRACT | 3.27 | data extractionXDS | | data reductionXSCALE | | data scalingSHARP | | phasing | | | | | |
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Refinement | Method to determine structure: SAD / Resolution: 2.69→43.56 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.41 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2584 | 695 | 5.42 % |
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Rwork | 0.2153 | 21278 | - |
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obs | 0.2177 | 22498 | 99.96 % |
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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: 166.51 Å2 / Biso mean: 66.8739 Å2 / Biso min: 36.12 Å2 |
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Refinement step | Cycle: final / Resolution: 2.69→43.56 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 2549 | 0 | 0 | 10 | 2559 |
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Biso mean | - | - | - | 59.2 | - |
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Num. residues | - | - | - | - | 321 |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 % Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all |
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2.69-2.8 | 0.3932 | 133 | 0.3308 | 2357 | 2490 | 2.8-2.93 | 0.3522 | 111 | 0.3041 | 2396 | 2507 | 2.93-3.08 | 0.3961 | 137 | 0.2724 | 2376 | 2513 | 3.08-3.28 | 0.2541 | 147 | 0.2424 | 2337 | 2484 | 3.28-3.53 | 0.2504 | 136 | 0.2448 | 2362 | 2498 | 3.53-3.88 | 0.2699 | 128 | 0.2043 | 2383 | 2511 | 3.88-4.44 | 0.215 | 144 | 0.181 | 2334 | 2478 | 4.45-5.59 | 0.2115 | 129 | 0.176 | 2376 | 2505 | 5.6-43.56 | 0.2588 | 155 | 0.2061 | 2357 | 2512 |
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Refinement TLS params. | Method: refined / Origin x: 2.3292 Å / Origin y: 15.9678 Å / Origin z: -9.8295 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.4969 Å2 | 0.07 Å2 | -0.1025 Å2 | - | 0.5312 Å2 | -0.1291 Å2 | - | - | 0.4018 Å2 |
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L | 1.5399 °2 | -1.7761 °2 | -1.1668 °2 | - | 4.3456 °2 | 1.8438 °2 | - | - | 0.9919 °2 |
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S | -0.1237 Å ° | -0.0248 Å ° | 0.0209 Å ° | 0.3427 Å ° | -0.0094 Å ° | 0.3586 Å ° | 0.1781 Å ° | -0.0103 Å ° | 0.121 Å ° |
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Refinement TLS group | Selection details: Chain A |
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