Software Name Version Classification NB SCALEPACKdata scalingShow SHARPphasingShow RESOLVEphasingShow PHENIX1.6.1_357refinementShow PDB_EXTRACT3.1 data extractionShow MAR345dtbdata collection DENZOdata reduction
Refinement Method to determine structure : SIRAS / Resolution : 2.03→29.741 Å / Occupancy max : 1 / Occupancy min : 0.21 / SU ML : 0.26 / Isotropic thermal model : Isotropic / Cross valid method : THROUGHOUT / σ(F) : 1.33 / σ(I) : 0 / Stereochemistry target values : MLRfactor Num. reflection % reflection Selection details Rfree 0.22 2511 5.06 % RANDOM Rwork 0.1843 - - - obs 0.1861 49601 98.86 % - all - 49970 - -
Solvent computation Shrinkage radii : 0.8 Å / VDW probe radii : 1 Å / Solvent model : FLAT BULK SOLVENT MODEL / Bsol : 63.224 Å2 / ksol : 0.366 e/Å3 Displacement parameters Biso max : 163.72 Å2 / Biso mean : 48.5881 Å2 / Biso min : 21.77 Å2 Baniso -1 Baniso -2 Baniso -3 1- 2.8092 Å2 -0 Å2 0.167 Å2 2- - -7.4496 Å2 0 Å2 3- - - 4.6404 Å2
Refine analyze Free Obs Luzzati coordinate error 0.28 Å 0.276 Å Luzzati d res low - 8 Å Luzzati sigma a 0.26 Å 0.29 Å
Refinement step Cycle : LAST / Resolution : 2.03→29.741 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 4494 0 6 397 4897
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.005 4654 X-RAY DIFFRACTION f_angle_d0.843 6328 X-RAY DIFFRACTION f_chiral_restr0.058 721 X-RAY DIFFRACTION f_plane_restr0.003 825 X-RAY DIFFRACTION f_dihedral_angle_d12.288 1712
LS refinement shell Refine-ID : X-RAY DIFFRACTION / Total num. of bins used : 18
Show large table (7 x 18) Hide large table Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Num. reflection all % reflection obs (%)2.03-2.0641 0.2648 124 0.2183 2564 2688 97 2.0641-2.1063 0.2354 137 0.2097 2653 2790 100 2.1063-2.1521 0.2489 137 0.2114 2645 2782 100 2.1521-2.2021 0.3301 144 0.271 2567 2711 98 2.2021-2.2572 0.4162 133 0.3774 2563 2696 97 2.2572-2.3182 0.357 153 0.3371 2400 2553 93 2.3182-2.3863 0.2379 146 0.2085 2660 2806 100 2.3863-2.4633 0.2044 160 0.1802 2614 2774 100 2.4633-2.5513 0.2419 135 0.1731 2665 2800 100 2.5513-2.6534 0.2322 132 0.1825 2607 2739 100 2.6534-2.7741 0.2139 142 0.1798 2643 2785 100 2.7741-2.9202 0.1951 146 0.1802 2676 2822 100 2.9202-3.103 0.2043 142 0.1712 2618 2760 100 3.103-3.3423 0.2078 137 0.1687 2640 2777 100 3.3423-3.6781 0.1898 135 0.155 2670 2805 100 3.6781-4.2091 0.1865 137 0.145 2640 2777 100 4.2091-5.2981 0.1703 141 0.1361 2671 2812 100 5.2981-29.7439 0.1929 130 0.1699 2594 2724 96
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 5) Hide large table ID L11 (°2 )L12 (°2 )L13 (°2 )L22 (°2 )L23 (°2 )L33 (°2 )S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2 )T12 (Å2 )T13 (Å2 )T22 (Å2 )T23 (Å2 )T33 (Å2 )Origin x (Å)Origin y (Å)Origin z (Å)1 0.8501 0.2846 -0.1441 0.7928 0.1314 0.5495 0.1801 -0.1487 0.2192 0.2031 -0.1633 0.2718 0.2284 -0.0059 0.0096 0.4559 -0.1828 0.1337 0.4027 -0.1009 0.5558 8.3482 30.0029 48.7892 2 2.0646 1.4644 0.9863 1.2357 0.7949 2.0085 -0.5969 0.1573 1.0189 -0.7967 0.1961 -0.3214 -1.3013 0.3381 0.299 0.6964 -0.2116 0.0063 0.3882 0.0312 1.0428 31.3175 12.9573 23.8109 3 1.2859 -0.1947 0.075 1.6125 0.4036 1.2711 0.1263 -0.033 -0.0132 0.0147 -0.1269 -0.2357 -0.0268 0.0314 -0.0057 0.2908 -0.0252 0.0014 0.2891 0.0325 0.2669 10.0695 -6.6652 24.6897 4 0.8533 0.0893 -0.1727 0.1995 0.389 0.98 0.071 0.2482 0.1588 -0.3882 0.0856 0.09 -0.3279 0.0138 -0.1331 0.6295 -0.0742 -0.0468 0.4126 -0.0135 0.5332 15.192 26.4949 30.1611 5 1.3469 -0.0258 0.4313 0.9244 0.8982 1.1308 0.1739 0.0338 0.2726 -0.2552 -0.2816 0.2374 -0.1217 -0.2516 0.1216 0.3966 -0.0872 -0.021 0.3638 -0.0971 0.568 6.1569 26.0726 38.2521
Refinement TLS group ID Refine-ID Refine TLS-ID Selection details Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 chain A and (resid 1:76)A1 - 76 2 X-RAY DIFFRACTION 2 chain A and (resid 77:85 or resid 300:356)A77 - 85 3 X-RAY DIFFRACTION 2 chain A and (resid 77:85 or resid 300:356)A300 - 356 4 X-RAY DIFFRACTION 3 chain A and (resid 86:195 or resid 224:299 or resid 357:378 or resid 406:615)A86 - 195 5 X-RAY DIFFRACTION 3 chain A and (resid 86:195 or resid 224:299 or resid 357:378 or resid 406:615)A224 - 299 6 X-RAY DIFFRACTION 3 chain A and (resid 86:195 or resid 224:299 or resid 357:378 or resid 406:615)A357 - 378 7 X-RAY DIFFRACTION 3 chain A and (resid 86:195 or resid 224:299 or resid 357:378 or resid 406:615)A406 - 615 8 X-RAY DIFFRACTION 4 chain A and (resid 379:405)A