Software | Name | Version | Classification |
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REFMAC | 5.2.0019refinementHKL-2000 | | data reductionSCALEPACK | | data scalingAMoRE | | phasing | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1GQU Resolution: 3.1→23 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.946 / SU B: 45.734 / SU ML: 0.75 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 5.02 / ESU R Free: 0.554 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.34585 | 115 | 10.5 % | RANDOM |
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Rwork | 0.3316 | - | - | - |
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obs | 0.33318 | 983 | 99.82 % | - |
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all | - | 985 | - | - |
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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: 50 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.32 Å2 | -0.16 Å2 | 0 Å2 |
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2- | - | -0.32 Å2 | 0 Å2 |
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3- | - | - | 0.48 Å2 |
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Refinement step | Cycle: LAST / Resolution: 3.1→23 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 0 | 243 | 0 | 0 | 243 |
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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_d0.008 | 0.021 | 272 | X-RAY DIFFRACTION | r_angle_refined_deg1.98 | 3 | 418 | X-RAY DIFFRACTION | r_chiral_restr0.087 | 0.2 | 47 | X-RAY DIFFRACTION | r_gen_planes_refined0.005 | 0.02 | 126 | X-RAY DIFFRACTION | r_nbd_refined0.248 | 0.2 | 119 | X-RAY DIFFRACTION | r_nbtor_refined0.314 | 0.2 | 152 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.298 | 0.2 | 1 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.236 | 0.2 | 27 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.137 | 0.2 | 9 | X-RAY DIFFRACTION | r_scbond_it0 | 3 | 389 | X-RAY DIFFRACTION | r_scangle_it0 | 4.5 | 418 | | | | | | | | | | | |
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LS refinement shell | Resolution: 3.1→3.181 Å / Total num. of bins used: 20
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.612 | 9 | - |
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Rwork | 0.541 | 62 | - |
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obs | - | - | 100 % |
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Refinement TLS params. | Method: refined / Origin x: 17.858 Å / Origin y: 6.857 Å / Origin z: 89.525 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.3179 Å2 | -0.0465 Å2 | -0.0543 Å2 | - | 0.4424 Å2 | 0.0078 Å2 | - | - | 0.2198 Å2 |
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L | 3.1157 °2 | 1.2362 °2 | -6.2853 °2 | - | 8.7648 °2 | -9.2344 °2 | - | - | 18.1706 °2 |
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S | -0.0855 Å ° | -0.0718 Å ° | 0.5401 Å ° | -0.733 Å ° | -0.6916 Å ° | -0.1924 Å ° | -0.5044 Å ° | 1.3114 Å ° | 0.777 Å ° |
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