Software | Name | Version | Classification |
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HKL-2000 | | data collectionPHENIX | | model buildingPHENIX | (phenix.refine: 1.5_2)refinementXDS | | data reductionXDS | | data scalingPHENIX | | phasing | | | | | | |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→19.977 Å / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.8977 / SU ML: 0.17 / σ(F): 2 / Phase error: 16.98 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.1912 | 1998 | 2.26 % |
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Rwork | 0.1603 | - | - |
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obs | 0.161 | 88570 | 99.48 % |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.912 Å2 / ksol: 0.377 e/Å3 |
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Displacement parameters | Biso max: 91.51 Å2 / Biso mean: 29.0305 Å2 / Biso min: 9.89 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -3.1344 Å2 | -0 Å2 | 0 Å2 |
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2- | - | -1.4519 Å2 | -0 Å2 |
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3- | - | - | 4.5864 Å2 |
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Refinement step | Cycle: LAST / Resolution: 1.7→19.977 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 5680 | 0 | 20 | 588 | 6288 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.009 | 5852 | X-RAY DIFFRACTION | f_angle_d1.164 | 7944 | X-RAY DIFFRACTION | f_chiral_restr0.08 | 891 | X-RAY DIFFRACTION | f_plane_restr0.005 | 1032 | X-RAY DIFFRACTION | f_dihedral_angle_d14.888 | 2022 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.7-1.7425 | 0.2307 | 153 | 0.1659 | 6141 | 6294 | 100 | 1.7425-1.7896 | 0.227 | 131 | 0.1664 | 6137 | 6268 | 100 | 1.7896-1.8422 | 0.2145 | 149 | 0.1576 | 6127 | 6276 | 100 | 1.8422-1.9016 | 0.2059 | 134 | 0.1517 | 6161 | 6295 | 100 | 1.9016-1.9695 | 0.1818 | 150 | 0.1519 | 6166 | 6316 | 100 | 1.9695-2.0483 | 0.1891 | 135 | 0.1446 | 6170 | 6305 | 100 | 2.0483-2.1414 | 0.1596 | 140 | 0.148 | 6179 | 6319 | 100 | 2.1414-2.2542 | 0.184 | 142 | 0.1486 | 6189 | 6331 | 100 | 2.2542-2.3952 | 0.1839 | 148 | 0.1561 | 6172 | 6320 | 100 | 2.3952-2.5798 | 0.1912 | 145 | 0.1659 | 6227 | 6372 | 100 | 2.5798-2.8387 | 0.2407 | 146 | 0.1679 | 6216 | 6362 | 100 | 2.8387-3.248 | 0.182 | 144 | 0.1708 | 6256 | 6400 | 100 | 3.248-4.0864 | 0.1744 | 144 | 0.1471 | 6314 | 6458 | 100 | 4.0864-19.9779 | 0.174 | 137 | 0.1624 | 6117 | 6254 | 93 |
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Refinement TLS params. | Method: refined / Origin x: 57.4739 Å / Origin y: 37.4782 Å / Origin z: 82.6439 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.1089 Å2 | -0.0016 Å2 | 0.0094 Å2 | - | 0.0865 Å2 | 0.0079 Å2 | - | - | 0.0714 Å2 |
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L | 1.2007 °2 | -0.2084 °2 | -0.0785 °2 | - | 0.6574 °2 | 0.0319 °2 | - | - | 0.672 °2 |
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S | 0.0071 Å ° | 0.0317 Å ° | -0.0541 Å ° | 0.0396 Å ° | -0.0102 Å ° | 0.0486 Å ° | -0.0272 Å ° | 0.0075 Å ° | -0 Å ° |
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Refinement TLS group | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | ( CHAIN A AND ( RESID 2:183 OR RESID 184:184 OR RESID 185:185 OR RESID 186:588 ) ) OR ( CHAIN C AND ( RESID 2:183 OR RESID 184:184 OR RESID 185:185 OR RESID 186:581 ) ) OR ( CHAIN B AND ( RESID 2:183 OR RESID 184:184 OR RESID 185:185 OR RESID 186:583 ) ) OR ( CHAIN D AND ( RESID 184:184 OR RESID 2:182 OR RESID 185:185 OR RESID 186:587 ) )A2 - 183 | 2 | X-RAY DIFFRACTION | 1 | ( CHAIN A AND ( RESID 2:183 OR RESID 184:184 OR RESID 185:185 OR RESID 186:588 ) ) OR ( CHAIN C AND ( RESID 2:183 OR RESID 184:184 OR RESID 185:185 OR RESID 186:581 ) ) OR ( CHAIN B AND ( RESID 2:183 OR | | |
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