Software | Name | Version | Classification |
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HKL-2000 | | data reductionPHENIX | (phenix.refine: dev_1624)refinementPDB_EXTRACT | 3.15 | data extractionHKL-2000 | | data scalingPHENIX | | phasing | | | | | |
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Refinement | Method to determine structure: SAD / Resolution: 3.3→47.206 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.28 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2381 | 1990 | 3.04 % |
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Rwork | 0.1748 | - | - |
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obs | 0.1767 | 65439 | 99.78 % |
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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: 230.84 Å2 / Biso mean: 70.6692 Å2 / Biso min: 30.42 Å2 |
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Refinement step | Cycle: final / Resolution: 3.3→47.206 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 18711 | 0 | 84 | 93 | 18888 |
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Biso mean | - | - | 96.95 | 47.67 | - |
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Num. residues | - | - | - | - | 2255 |
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Refine LS restraints NCS | Ens-ID | Dom-ID | Auth asym-ID | Number | Refine-ID | Rms | Type |
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1 | 1 | A2864 | X-RAY DIFFRACTION | 8.643 | TORSIONAL1 | 2 | D2864 | X-RAY DIFFRACTION | 8.643 | TORSIONAL2 | 1 | B3650 | X-RAY DIFFRACTION | 8.643 | TORSIONAL2 | 2 | E3650 | X-RAY DIFFRACTION | 8.643 | TORSIONAL3 | 1 | C3878 | X-RAY DIFFRACTION | 8.643 | TORSIONAL3 | 2 | F3878 | X-RAY DIFFRACTION | 8.643 | TORSIONAL | | | | | | | | | | | |
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Refinement TLS params. | Method: refined / Origin x: 97.2875 Å / Origin y: 5.5196 Å / Origin z: 142.3371 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.4694 Å2 | -0.0628 Å2 | -0.0428 Å2 | - | 0.2737 Å2 | 0.0404 Å2 | - | - | 0.4333 Å2 |
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L | 0.9007 °2 | -0.2234 °2 | -0.0187 °2 | - | 0.2059 °2 | -0.029 °2 | - | - | 0.0616 °2 |
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S | 0.1172 Å ° | -0.0152 Å ° | -0.136 Å ° | -0.0318 Å ° | -0.099 Å ° | 0.0076 Å ° | -0.0033 Å ° | 0.0113 Å ° | -0.0209 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 | ( CHAIN A AND ( RESID 2:312 OR RESID 401:404 OR RESID 501:507 ) ) OR ( CHAIN C AND ( RESID 1:435 OR RESID 501:504 OR RESID 601:622 ) ) OR ( CHAIN B AND ( RESID 1:394 OR RESID 401:404 OR RESID 501:518 ) ) OR ( CHAIN E AND ( RESID 2:394 OR RESID 401:402 OR RESID 501:517 ) ) OR ( CHAIN D AND ( RESID 2:312 OR RESID 401:402 OR RESID 501:509 ) ) OR ( CHAIN F AND ( RESID 1:435 OR RESID 501:503 OR RESID 601:620 ) )A2 - 312 | 2 | X-RAY DIFFRACTION | 1 | ( CHAIN A AND ( RESID 2:312 OR RESID 401:404 OR RESID 501:507 ) ) OR ( CHAIN C AND ( RESID 1:435 OR RESID 501:504 OR RESID 601:622 ) ) OR ( CHAIN | | |
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