Software | Name | Version | Classification |
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MAR345dtb | | data collectionPHENIX | | model buildingPHENIX | (phenix.refine: 1.7.3_928)refinementXDS | | data reductionXDS | | data scalingPHENIX | | phasing | | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZGG Resolution: 1.8→18.917 Å / SU ML: 0.23 / σ(F): 2 / Phase error: 19.34 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.2013 | 1152 | 9.99 % | RANDOM |
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Rwork | 0.1785 | - | - | - |
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obs | 0.1808 | 11536 | 93.56 % | - |
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.762 Å2 / ksol: 0.367 e/Å3 |
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Displacement parameters | | Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 2.3965 Å2 | 0 Å2 | 0.9353 Å2 |
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2- | - | 1.3439 Å2 | -0 Å2 |
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3- | - | - | -2.4324 Å2 |
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Refinement step | Cycle: LAST / Resolution: 1.8→18.917 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 1178 | 0 | 3 | 184 | 1365 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.003 | 1217 | X-RAY DIFFRACTION | f_angle_d0.769 | 1642 | X-RAY DIFFRACTION | f_dihedral_angle_d13.565 | 463 | X-RAY DIFFRACTION | f_chiral_restr0.055 | 187 | X-RAY DIFFRACTION | f_plane_restr0.004 | 213 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | % reflection obs (%) |
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1.8-1.8819 | 0.3192 | 144 | 0.2696 | 1312 | 96 | 1.8819-1.981 | 0.2873 | 150 | 0.2193 | 1305 | 96 | 1.981-2.105 | 0.246 | 145 | 0.1914 | 1324 | 95 | 2.105-2.2673 | 0.2226 | 142 | 0.1772 | 1306 | 95 | 2.2673-2.495 | 0.1931 | 146 | 0.1814 | 1294 | 94 | 2.495-2.8549 | 0.2108 | 143 | 0.1786 | 1290 | 93 | 2.8549-3.5929 | 0.1755 | 143 | 0.1678 | 1289 | 92 | 3.5929-18.9179 | 0.1469 | 139 | 0.1502 | 1264 | 88 |
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Refinement TLS params. | Method: refined / Origin x: -12.4094 Å / Origin y: -8.0651 Å / Origin z: -7.9117 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.0596 Å2 | 0.0001 Å2 | -0.0068 Å2 | - | 0.0738 Å2 | 0.0094 Å2 | - | - | 0.0718 Å2 |
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L | 0.8255 °2 | -0.1247 °2 | -0.4198 °2 | - | 0.9841 °2 | 0.3251 °2 | - | - | 1.284 °2 |
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S | 0.0121 Å ° | 0.0127 Å ° | 0.0432 Å ° | 0.0218 Å ° | -0.0141 Å ° | -0.0319 Å ° | -0.0323 Å ° | 0.0406 Å ° | 0.0167 Å ° |
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Refinement TLS group | Selection details: CHAIN A |
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