Software | Name | Version | Classification |
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Blu-Ice | | data collectionMOSFLM | | data reductionAimless | 0.5.27data scalingCRANK2 | | phasing Coot | | model buildingREFMAC | 5.8.0238refinementPDB_EXTRACT | 3.24 | data extraction | | | | | | | | |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→37.74 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.756 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.126 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.2144 | 1924 | 4.9 % | RANDOM |
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Rwork | 0.1695 | - | - | - |
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obs | 0.1717 | 37320 | 98.99 % | - |
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å |
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Displacement parameters | Biso max: 144.96 Å2 / Biso mean: 47.465 Å2 / Biso min: 25.53 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 3.02 Å2 | -0 Å2 | 0 Å2 |
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2- | - | 0.76 Å2 | -0 Å2 |
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3- | - | - | -3.78 Å2 |
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Refinement step | Cycle: final / Resolution: 1.9→37.74 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 3113 | 0 | 68 | 276 | 3457 |
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Biso mean | - | - | 55.85 | 51.63 | - |
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Num. residues | - | - | - | - | 388 |
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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_d0.007 | 0.013 | 3244 | X-RAY DIFFRACTION | r_bond_other_d0.002 | 0.017 | 2989 | X-RAY DIFFRACTION | r_angle_refined_deg1.386 | 1.657 | 4380 | X-RAY DIFFRACTION | r_angle_other_deg1.267 | 1.588 | 6941 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg7.021 | 5 | 385 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg27.985 | 21.921 | 177 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg14.167 | 15 | 555 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg16.595 | 15 | 23 | X-RAY DIFFRACTION | r_chiral_restr0.066 | 0.2 | 414 | X-RAY DIFFRACTION | r_gen_planes_refined0.006 | 0.02 | 3570 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 698 | | | | | | | | | | | |
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.395 | 129 | - |
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Rwork | 0.343 | 2709 | - |
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all | - | 2838 | - |
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obs | - | - | 98.3 % |
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Refinement TLS params. | Method: refined / Origin x: 34.0167 Å / Origin y: 5.8281 Å / Origin z: 23.8975 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.0296 Å2 | 0.0162 Å2 | 0.0068 Å2 | - | 0.0426 Å2 | -0.0195 Å2 | - | - | 0.0207 Å2 |
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L | 0.1395 °2 | 0.151 °2 | -0.1426 °2 | - | 0.2939 °2 | -0.3941 °2 | - | - | 1.0592 °2 |
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S | 0.0222 Å ° | 0.0378 Å ° | -0.0299 Å ° | 0.0377 Å ° | -0.0141 Å ° | 0.0069 Å ° | 0.0599 Å ° | 0.1267 Å ° | -0.0081 Å ° |
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