Software | Name | Version | Classification |
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MD2 | diffractometer software from EMBL (with LS-CAT developed extensions) | data collection CCP4 | | model buildingMOLREP | | phasingREFMAC | 5.6.0117refinementHKL-2000 | | data reductionHKL-2000 | | data scaling CCP4 | | phasing | | | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3EY2 Resolution: 1.59→29.875 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.552 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(I): 5 / ESU R: 0.155 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.25331 | 486 | 7.6 % | RANDOM |
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Rwork | 0.18193 | - | - | - |
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obs | 0.18694 | 5930 | 99.6 % | - |
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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: 20.104 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.38 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 0.24 Å2 | 0 Å2 |
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3- | - | - | 0.14 Å2 |
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Refinement step | Cycle: LAST / Resolution: 1.59→29.875 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 0 | 408 | 2 | 52 | 462 |
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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_d0.005 | 0.012 | 456 | X-RAY DIFFRACTION | r_angle_refined_deg1.365 | 1.517 | 700 | X-RAY DIFFRACTION | r_chiral_restr0.077 | 0.2 | 64 | X-RAY DIFFRACTION | r_gen_planes_refined0.01 | 0.02 | 218 | X-RAY DIFFRACTION | r_rigid_bond_restr3.22 | 3 | 456 | X-RAY DIFFRACTION | r_sphericity_free22.969 | 5 | 24 | X-RAY DIFFRACTION | r_sphericity_bonded11.461 | 5 | 442 | | | | | | | |
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LS refinement shell | Resolution: 1.59→1.636 Å / Total num. of bins used: 20
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.241 | 25 | - |
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Rwork | 0.146 | 363 | - |
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obs | - | - | 94.87 % |
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