Software | Name | Version | Classification |
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SBC-Collect | | data collectionHKL-3000 | | data collectionHKL-3000 | | phasingMOLREP | | phasingBALBES | | phasingPHENIX | (phenix.refine: 1.5_2)refinementHKL-3000 | | data reductionHKL-3000 | | data scaling | | | | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2EMQ Resolution: 1.8→24.4 Å / SU ML: 0.23 / Isotropic thermal model: mixed / σ(F): 1.35 / Phase error: 21.8 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2376 | 622 | 4.92 % |
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Rwork | 0.1839 | - | - |
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obs | 0.1864 | 12640 | 98.2 % |
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all | - | 9287 | - |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.472 Å2 / ksol: 0.358 e/Å3 |
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Displacement parameters | Biso mean: 39.6 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 5.408 Å2 | -0 Å2 | -0 Å2 |
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2- | - | -0.3039 Å2 | 0 Å2 |
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3- | - | - | -5.1041 Å2 |
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Refinement step | Cycle: LAST / Resolution: 1.8→24.4 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 1225 | 0 | 48 | 103 | 1376 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.016 | 1295 | X-RAY DIFFRACTION | f_angle_d1.636 | 1758 | X-RAY DIFFRACTION | f_dihedral_angle_d20.051 | 490 | X-RAY DIFFRACTION | f_chiral_restr0.125 | 195 | X-RAY DIFFRACTION | f_plane_restr0.008 | 223 | | | | | |
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LS refinement shell | Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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1.8005-1.9816 | 0.2643 | 136 | 0.1997 | 2837 | X-RAY DIFFRACTION | 94 | 1.9816-2.2682 | 0.2424 | 177 | 0.1767 | 2970 | X-RAY DIFFRACTION | 100 | 2.2682-2.857 | 0.2756 | 158 | 0.1764 | 3051 | X-RAY DIFFRACTION | 100 | 2.857-24.4028 | 0.2114 | 151 | 0.1828 | 3160 | X-RAY DIFFRACTION | 99 |
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Refinement TLS params. | Method: refined / Origin x: 4.7088 Å / Origin y: 18.3059 Å / Origin z: 10.094 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.1013 Å2 | 0.0082 Å2 | -0.0037 Å2 | - | 0.075 Å2 | 0.0077 Å2 | - | - | 0.0762 Å2 |
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L | 1.0459 °2 | 0.4614 °2 | -0.5319 °2 | - | 1.6481 °2 | 0.7899 °2 | - | - | 1.9846 °2 |
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S | -0.1371 Å ° | 0.0472 Å ° | -0.0329 Å ° | 0.024 Å ° | 0.0089 Å ° | -0.0629 Å ° | 0.2603 Å ° | -0.0185 Å ° | 0.1177 Å ° |
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Refinement TLS group | Selection details: chain A |
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