Software | Name | Version | Classification |
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REFMAC | 5.8.0158refinementPDB_EXTRACT | 3.1 | data extractionXDS | | data reductionSCALA | | data scalingPHASER | | phasing | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KSI Resolution: 2.23→48.18 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.2586 | 5386 | 5 % | RANDOM |
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Rwork | 0.2259 | 102334 | - | - |
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obs | 0.2275 | 107720 | 99.76 % | - |
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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 max: 131.5 Å2 / Biso mean: 47.0476 Å2 / Biso min: 14.3 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 1.02 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 1.02 Å2 | 0 Å2 |
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3- | - | - | -2.04 Å2 |
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Refinement step | Cycle: LAST / Resolution: 2.23→48.18 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 6040 | 0 | 164 | 60 | 6264 |
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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_d0.025 | 0.019 | 6355 | X-RAY DIFFRACTION | r_bond_other_d0 | 0.02 | 5761 | X-RAY DIFFRACTION | r_angle_refined_deg2.603 | 1.95 | 8577 | X-RAY DIFFRACTION | r_angle_other_deg3.928 | 3 | 13402 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.749 | 5 | 762 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg36.107 | 24.145 | 304 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg20.697 | 15 | 992 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg23.951 | 15 | 30 | X-RAY DIFFRACTION | r_chiral_restr0.237 | 0.2 | 886 | X-RAY DIFFRACTION | r_gen_planes_refined0.014 | 0.021 | 7080 | X-RAY DIFFRACTION | r_gen_planes_other0.023 | 0.02 | 1334 | X-RAY DIFFRACTION | r_mcbond_it3.299 | 4.434 | 3054 | X-RAY DIFFRACTION | r_mcbond_other3.29 | 4.433 | 3053 | X-RAY DIFFRACTION | r_mcangle_it4.787 | 6.63 | 3814 | | | | | | | | | | | | | | |
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LS refinement shell | Resolution: 2.23→2.288 Å / Total num. of bins used: 20
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.427 | 382 | - |
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Rwork | 0.42 | 7260 | - |
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all | - | 7642 | - |
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obs | - | - | 97.02 % |
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Refinement TLS params. | L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION ID | Origin x (Å) | Origin y (Å) | Origin z (Å) |
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1 | 16.864 | 26.654 | -11.562 | 2 | 64.335 | 36.394 | -24.218 | 3 | 36.959 | 34.885 | -28.32 | 4 | 43.93 | 28.553 | -7.859 | 5 | 41.008 | 32.606 | -16.54 | 6 | 37.183 | 31.67 | -27.497 | 7 | 44.28 | 37.805 | -28.421 | 8 | 32.375 | 32.449 | -17.303 | 9 | 39.792 | 32.46 | -19.925 |
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Refinement TLS group | ID | Refine-ID | Refine TLS-ID | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | A4 - 385 | 2 | X-RAY DIFFRACTION | 2 | B4 - 385 | 3 | X-RAY DIFFRACTION | 3 | A401 | 4 | X-RAY DIFFRACTION | 3 | B401 | 5 | X-RAY DIFFRACTION | 4 | A402 | 6 | X-RAY DIFFRACTION | 4 | B402 | 7 | X-RAY DIFFRACTION | 5 | A403 | 8 | X-RAY DIFFRACTION | 5 | B403 | 9 | X-RAY DIFFRACTION | 6 | A404 - 405 | 10 | X-RAY DIFFRACTION | 6 | B404 - 405 | 11 | X-RAY DIFFRACTION | 7 | B406 | 12 | X-RAY DIFFRACTION | 8 | A501 - 534 | 13 | X-RAY DIFFRACTION | 8 | B501 - 526 | 14 | X-RAY DIFFRACTION | 9 | A406 | 15 | X-RAY DIFFRACTION | 9 | B407 | | | | | | | | | | | | | | | |
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