Software | Name | Version | Classification |
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MOSFLM | | data reductionSCALA | | data scalingMOLREP | | phasingPHENIX | 1.6.4_486refinement | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6AMK Resolution: 3.09→101.116 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.12 / Phase error: 36.2
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2813 | 3686 | 6.36 % |
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Rwork | 0.2101 | - | - |
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obs | 0.2146 | 57925 | 98.16 % |
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Bsol: 93.417 Å2 / ksol: 0.305 e/Å3 |
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Displacement parameters | Biso max: 593.78 Å2 / Biso mean: 148.38 Å2 / Biso min: 58.44 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 0 Å2 | 0 Å2 |
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3- | - | - | 0 Å2 |
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Refinement step | Cycle: final / Resolution: 3.09→101.116 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 4674 | 4059 | 0 | 0 | 8733 |
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Num. residues | - | - | - | - | 800 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.003 | 9319 | X-RAY DIFFRACTION | f_angle_d0.838 | 13476 | X-RAY DIFFRACTION | f_chiral_restr0.042 | 1548 | X-RAY DIFFRACTION | f_plane_restr0.003 | 1008 | X-RAY DIFFRACTION | f_dihedral_angle_d24.515 | 3795 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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3.09-3.2005 | 0.4201 | 366 | 0.3936 | 5423 | 5789 | 98 | 3.2005-3.3286 | 0.429 | 378 | 0.3849 | 5531 | 5909 | 100 | 3.3286-3.4801 | 0.3814 | 374 | 0.355 | 5504 | 5878 | 100 | 3.4801-3.6636 | 0.3651 | 376 | 0.2955 | 5471 | 5847 | 100 | 3.6636-3.8931 | 0.3709 | 377 | 0.2688 | 5504 | 5881 | 99 | 3.8931-4.1937 | 0.3073 | 371 | 0.2139 | 5486 | 5857 | 99 | 4.1937-4.6158 | 0.2745 | 377 | 0.1901 | 5404 | 5781 | 98 | 4.6158-5.2837 | 0.2646 | 356 | 0.1801 | 5423 | 5779 | 98 | 5.2837-6.6567 | 0.3144 | 361 | 0.2041 | 5333 | 5694 | 96 | 6.6567-101.1698 | 0.1957 | 350 | 0.152 | 5160 | 5510 | 93 |
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Refinement TLS params. | Method: refined / Origin x: 9.5108 Å / Origin y: -30.2892 Å / Origin z: -16.5929 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.7577 Å2 | 0.0722 Å2 | -0.0153 Å2 | - | 0.6983 Å2 | 0.0121 Å2 | - | - | 0.6552 Å2 |
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L | 1.712 °2 | 1.6605 °2 | 0.1721 °2 | - | 1.6666 °2 | 0.0249 °2 | - | - | 0.0522 °2 |
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S | 0.0032 Å ° | -0.1035 Å ° | -0.0586 Å ° | -0.0689 Å ° | -0.0621 Å ° | -0.0127 Å ° | -0.0663 Å ° | 0.0125 Å ° | -0 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 | allA9 - 62 | 2 | X-RAY DIFFRACTION | 1 | allB8 - 62 | 3 | X-RAY DIFFRACTION | 1 | allG9 - 62 | 4 | X-RAY DIFFRACTION | 1 | allH9 - 63 | 5 | X-RAY DIFFRACTION | 1 | allK9 - 62 | 6 | X-RAY DIFFRACTION | 1 | allL9 - 62 | 7 | X-RAY DIFFRACTION | 1 | allY6 - 62 | 8 | X-RAY DIFFRACTION | 1 | allC9 - 62 | 9 | X-RAY DIFFRACTION | 1 | allD9 - 62 | 10 | X-RAY DIFFRACTION | 1 | allO9 - 63 | 11 | X-RAY DIFFRACTION | 1 | allP7 - 62 | 12 | X-RAY DIFFRACTION | 1 | allN71 - 169 | 13 | X-RAY DIFFRACTION | 1 | allR11 - 109 | | | | | | | | | | | | | | | | | | | | | | | | | | |
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