Software | Name | Version | Classification |
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PHENIX | 1.14_3247refinementDENZO | | data reductionHKL-2000 | | data scalingPDB_EXTRACT | 3.27 | data extractionPHASER | | phasing | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2NS2 Resolution: 2.7→40.363 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 34.46 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2859 | 666 | 4.74 % |
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Rwork | 0.2537 | 13396 | - |
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obs | 0.2553 | 14062 | 99.34 % |
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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: 234.11 Å2 / Biso mean: 100.4159 Å2 / Biso min: 35.4 Å2 |
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Refinement step | Cycle: final / Resolution: 2.7→40.363 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 3168 | 0 | 20 | 13 | 3201 |
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Biso mean | - | - | 145.13 | 60.83 | - |
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Num. residues | - | - | - | - | 389 |
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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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2.7-2.8968 | 0.3791 | 142 | 0.3069 | 2578 | 98 | 2.8968-3.1882 | 0.3375 | 101 | 0.2911 | 2672 | 100 | 3.1882-3.6493 | 0.3357 | 141 | 0.2664 | 2637 | 100 | 3.6493-4.5967 | 0.2829 | 140 | 0.2283 | 2696 | 100 | 4.5967-40.363 | 0.2448 | 142 | 0.2493 | 2813 | 99 |
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Refinement TLS params. | Method: refined / Origin x: -0.525 Å / Origin y: 9.626 Å / Origin z: -6.152 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.4864 Å2 | 0.0116 Å2 | -0.0385 Å2 | - | 0.5391 Å2 | 0.0449 Å2 | - | - | 0.4996 Å2 |
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L | 1.4971 °2 | -0.3793 °2 | 0.4297 °2 | - | 3.0495 °2 | -0.2184 °2 | - | - | 1.5537 °2 |
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S | -0.11 Å ° | -0.1311 Å ° | 0.223 Å ° | -0.1067 Å ° | 0.1735 Å ° | 0.4227 Å ° | -0.2181 Å ° | -0.2558 Å ° | -0.0786 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 48:261 OR RESID 301:310 ) ) OR ( CHAIN B AND RESID 228:232 ) OR ( CHAIN C AND ( RESID 48:262 OR RESID 301:303 ) ) OR ( CHAIN D AND RESID 229:230 )A48 - 261 | 2 | X-RAY DIFFRACTION | 1 | ( CHAIN A AND ( RESID 48:261 OR RESID 301:310 ) ) OR ( CHAIN B AND RESID 228:232 ) OR ( CHAIN C AND ( RESID 48:262 OR RESID 301:303 ) ) OR ( CHAIN D AND RESID 229:230 )A301 - 310 | 3 | X-RAY DIFFRACTION | 1 | ( CHAIN A AND ( RESID 48:261 OR RESID 301:310 ) ) OR ( CHAIN B AND RESID 228:232 ) OR ( CHAIN C AND ( RESID 48:262 OR RESID 301:303 ) ) OR ( CHAIN D AND RESID 229:230 )B228 - 232 | 4 | X-RAY DIFFRACTION | 1 | ( CHAIN A AND ( RESID 48:261 OR RESID 301:310 ) ) | | | | | | |
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