Software | Name | Version | Classification |
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CrystalClear | | data collectionPHASER | | phasingPHENIX | (phenix.refine: 1.5_2)refinementd*TREK | | data reductiond*TREK | | data scaling | | | | | |
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Refinement | Method to determine structure : MOLECULAR REPLACEMENT Starting model: PDB entry: 1dwr Resolution: 1.6→21.85 Å / SU ML: 0.28 / Isotropic thermal model: isotropic / σ(F): 1.35 / Phase error: 24 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.2475 | 799 | 5.02 % |
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Rwork | 0.1929 | - | - |
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obs | 0.1957 | 15921 | 97.96 % |
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all | - | 15927 | - |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.034 Å2 / ksol: 0.392 e/Å3 |
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Displacement parameters | | Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.0031 Å2 | 0 Å2 | 0.1154 Å2 |
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2- | - | 0.2379 Å2 | 0 Å2 |
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3- | - | - | -0.2347 Å2 |
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Refinement step | Cycle: LAST / Resolution: 1.6→21.85 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 1185 | 0 | 62 | 97 | 1344 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.007 | 1283 | X-RAY DIFFRACTION | f_angle_d0.993 | 1735 | X-RAY DIFFRACTION | f_dihedral_angle_d16.78 | 457 | X-RAY DIFFRACTION | f_chiral_restr0.062 | 178 | X-RAY DIFFRACTION | f_plane_restr0.004 | 213 | | | | | |
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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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1.6-1.7002 | 0.325 | 127 | 0.2664 | 2433 | X-RAY DIFFRACTION | 96 | 1.7002-1.8314 | 0.2833 | 139 | 0.2267 | 2454 | X-RAY DIFFRACTION | 97 | 1.8314-2.0156 | 0.2856 | 126 | 0.193 | 2490 | X-RAY DIFFRACTION | 97 | 2.0156-2.307 | 0.2684 | 119 | 0.1743 | 2546 | X-RAY DIFFRACTION | 98 | 2.307-2.9055 | 0.2714 | 143 | 0.185 | 2564 | X-RAY DIFFRACTION | 100 | 2.9055-21.8568 | 0.1825 | 145 | 0.1626 | 2635 | X-RAY DIFFRACTION | 100 |
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