Software | Name | Version | Classification |
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MAR345dtb | | data collectionAMoRE | | phasingREFMAC | 5.2.0019refinementAUTOMAR | | data reductionSCALEPACK | | data scaling | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1P4Y Resolution: 2.94→19.81 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.956 / SU B: 18.845 / SU ML: 0.321 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.456 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.23946 | 56 | 5 % | RANDOM |
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Rwork | 0.21517 | - | - | - |
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all | 0.2251 | 1129 | - | - |
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obs | 0.2166 | 1073 | 93.15 % | - |
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK |
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Displacement parameters | Biso mean: 51.104 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 1.15 Å2 | 0 Å2 | 0.71 Å2 |
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2- | - | -0.97 Å2 | 0 Å2 |
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3- | - | - | 0.46 Å2 |
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Refine analyze | Luzzati coordinate error obs: 0.493 Å |
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Refinement step | Cycle: LAST / Resolution: 2.94→19.81 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 0 | 404 | 0 | 10 | 414 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target | Number |
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X-RAY DIFFRACTION | r_bond_refined_d0.019 | 0.021 | 452 | X-RAY DIFFRACTION | r_angle_refined_deg3.158 | 3 | 694 | X-RAY DIFFRACTION | r_chiral_restr0.112 | 0.2 | 78 | X-RAY DIFFRACTION | r_gen_planes_refined0.011 | 0.02 | 210 | X-RAY DIFFRACTION | r_nbd_refined0.274 | 0.2 | 115 | X-RAY DIFFRACTION | r_nbtor_refined0.35 | 0.2 | 250 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.151 | 0.2 | 9 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.187 | 0.2 | 44 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.26 | 0.2 | 9 | X-RAY DIFFRACTION | r_scbond_it5.115 | 3 | 666 | X-RAY DIFFRACTION | r_scangle_it4.326 | 4.5 | 694 | | | | | | | | | | | |
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LS refinement shell | Resolution: 2.942→3.017 Å / Rfactor Rfree error: 0.456 / Total num. of bins used: 20
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.799 | 4 | - |
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Rwork | 0.534 | 71 | - |
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obs | - | 71 | 97.4 % |
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