Software Name Version Classification NB SCALEPACKdata scalingShow PHENIX1.7.3_928refinementShow PDB_EXTRACT3.1 data extractionShow
Refinement Method to determine structure : MOLECULAR REPLACEMENT / Resolution : 1.4→41.01 Å / Occupancy max : 1 / Occupancy min : 0.32 / SU ML : 0.2 / σ(F) : 1.34 / Phase error : 18.5 / Stereochemistry target values : MLRfactor Num. reflection % reflection Rfree 0.198 7379 10 % Rwork 0.175 - - obs 0.178 73824 96.3 %
Solvent computation Shrinkage radii : 0.73 Å / VDW probe radii : 1 Å / Solvent model : FLAT BULK SOLVENT MODEL / Bsol : 49.01 Å2 / ksol : 0.39 e/Å3 Displacement parameters Biso mean : 31.13 Å2 Baniso -1 Baniso -2 Baniso -3 1- 0 Å2 0 Å2 0 Å2 2- - 0 Å2 0 Å2 3- - - 0 Å2
Refinement step Cycle : LAST / Resolution : 1.4→41.01 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 2577 0 0 339 2916
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.005 2726 X-RAY DIFFRACTION f_angle_d1.001 3710 X-RAY DIFFRACTION f_dihedral_angle_d14.639 996 X-RAY DIFFRACTION f_chiral_restr0.131 390 X-RAY DIFFRACTION f_plane_restr0.004 488
LS refinement shell Show large table (7 x 30) Hide large table Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)1.4-1.4143 0.3757 218 0.3712 1986 X-RAY DIFFRACTION 87 1.4143-1.431 0.3865 234 0.3599 2145 X-RAY DIFFRACTION 94 1.431-1.4484 0.3097 242 0.3285 2160 X-RAY DIFFRACTION 94 1.4484-1.4668 0.3412 239 0.2976 2136 X-RAY DIFFRACTION 95 1.4668-1.4861 0.2794 241 0.2743 2143 X-RAY DIFFRACTION 95 1.4861-1.5064 0.2315 242 0.2555 2147 X-RAY DIFFRACTION 95 1.5064-1.5279 0.2357 241 0.2427 2193 X-RAY DIFFRACTION 95 1.5279-1.5507 0.2737 229 0.2193 2171 X-RAY DIFFRACTION 95 1.5507-1.575 0.1871 249 0.2185 2167 X-RAY DIFFRACTION 96 1.575-1.6008 0.243 247 0.2081 2185 X-RAY DIFFRACTION 96 1.6008-1.6284 0.2333 237 0.1895 2191 X-RAY DIFFRACTION 96 1.6284-1.658 0.1925 247 0.1796 2191 X-RAY DIFFRACTION 96 1.658-1.6899 0.1903 243 0.176 2192 X-RAY DIFFRACTION 96 1.6899-1.7244 0.1963 245 0.1769 2199 X-RAY DIFFRACTION 96 1.7244-1.7619 0.2115 247 0.1733 2229 X-RAY DIFFRACTION 97 1.7619-1.8029 0.204 246 0.175 2180 X-RAY DIFFRACTION 97 1.8029-1.848 0.1937 253 0.1734 2257 X-RAY DIFFRACTION 97 1.848-1.8979 0.1808 245 0.1671 2200 X-RAY DIFFRACTION 97 1.8979-1.9538 0.1788 252 0.1665 2252 X-RAY DIFFRACTION 97 1.9538-2.0168 0.181 250 0.1669 2233 X-RAY DIFFRACTION 98 2.0168-2.0889 0.1728 246 0.1606 2246 X-RAY DIFFRACTION 98 2.0889-2.1726 0.1915 247 0.1614 2240 X-RAY DIFFRACTION 98 2.1726-2.2714 0.1711 252 0.1529 2283 X-RAY DIFFRACTION 98 2.2714-2.3912 0.1652 251 0.1484 2266 X-RAY DIFFRACTION 98 2.3912-2.541 0.178 253 0.1569 2286 X-RAY DIFFRACTION 99 2.541-2.7371 0.2032 251 0.1626 2299 X-RAY DIFFRACTION 99 2.7371-3.0125 0.1983 257 0.1787 2297 X-RAY DIFFRACTION 99 3.0125-3.4482 0.1861 258 0.1675 2325 X-RAY DIFFRACTION 98 3.4482-4.3436 0.1675 256 0.1536 2305 X-RAY DIFFRACTION 97 4.3436-41.0262 0.2359 261 0.1936 2341 X-RAY DIFFRACTION 94
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 16) 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 4.4128 1.9581 0.9061 3.081 -0.3795 0.4618 0.2184 -0.5604 -0.0902 0.1383 -0.5167 -0.1619 0.2342 0.0177 0.2549 0.2886 0.0556 0.101 0.3117 0.1031 0.2765 25.9309 1.7735 4.0535 2 3.7146 -1.3525 -0.0295 4.4711 -1.3585 3.1416 0.0013 0.3438 -0.2003 -0.5335 -0.102 0.1346 0.3856 -0.0964 0.0737 0.2185 0.0184 0.0426 0.1536 -0.0186 0.1479 12.2132 2.5848 -5.9708 3 2.7021 -0.2663 -1.0588 2.5899 -1.6972 4.3647 -0.0431 -0.0949 0.2306 0.1334 -0.2345 -0.5499 -0.0743 0.5466 0.2764 0.2173 0.0109 0.0149 0.2808 0.115 0.3088 23.0298 2.6837 6.5191 4 5.037 0.247 0.237 3.3679 -0.8736 3.0817 -0.1445 -0.5045 -0.484 0.2254 0.2644 0.4381 0.1365 -0.5014 0.0028 0.2231 0.0075 0.0635 0.2876 0.1166 0.3015 6.8061 -0.5901 9.308 5 2.5933 -0.9485 -0.0816 2.6952 -0.9515 2.23 -0.0743 -0.1662 -0.0455 0.0979 0.0876 0.0583 0.033 -0.1706 -0.0066 0.116 -0.0097 0.02 0.1502 0.0034 0.1287 6.7565 9.5187 3.7977 6 8.2822 0.0975 -2.7939 3.8155 -1.5457 6.9315 -0.046 -1.0666 0.4036 0.537 -0.0782 -0.5368 -0.5912 0.8499 0.2001 0.3376 -0.0278 -0.0685 0.5335 -0.0414 0.276 15.6674 17.8831 13.3151 7 3.9724 -0.446 -0.4513 2.9859 -1.4744 5.0808 -0.0329 0.145 0.5903 0.0215 -0.1301 -0.0766 -0.6488 0.1247 0.0348 0.1996 0.0116 0.0164 0.148 0.0182 0.2739 10.6656 24.2626 -0.7956 8 3.4146 -0.7265 -0.33 5.5407 1.058 3.9823 -0.1848 -0.1702 0.0467 0.2146 0.1264 0.5077 -0.1675 -0.3894 0.0581 0.2082 0.0094 0.0273 0.279 -0.0021 0.1752 -22.8189 13.9784 23.017 9 2.0664 -0.6595 -0.0405 3.0219 0.6213 1.8629 -0.1926 -0.4661 0.1557 0.1656 0.184 -0.0676 -0.2509 -0.025 0.0406 0.2693 0.0625 0.0285 0.2156 -0.0266 0.156 -15.2969 14.5101 27.4188 10 5.1024 -0.6765 -0.7693 4.9525 0.1093 6.1894 -0.1985 -0.0216 0.478 0.233 0.0296 -0.3881 -0.5606 0.3709 -0.028 0.2162 -0.0084 -0.0402 0.1901 0.0094 0.2283 -9.447 19.9602 17.3957 11 3.9938 1.2069 -0.2056 7.1166 1.1315 3.9331 -0.0853 0.5564 0.0074 -0.4398 0.2359 -0.3925 0.0077 0.5445 -0.0217 0.1889 0.0137 0.0162 0.2189 0.0203 0.1851 -8.1762 12.3587 8.455 12 2.0266 0.1287 0.0344 4.194 0.5633 2.7654 -0.1513 0.0826 0.0546 0.0665 0.144 0.2274 0.153 -0.2034 -0.03 0.1537 -0.0141 -0.008 0.163 0.0148 0.147 -15.3798 13.9728 9.611 13 6.2141 -2.5736 1.8405 3.5774 -1.3984 2.9614 0.0789 0.2708 -0.3471 -0.1163 -0.0175 0.0705 0.4643 0.0966 -0.039 0.1821 0.0147 0.0213 0.1229 -0.0061 0.1163 -10.5061 4.1188 17.951 14 2.0935 0.0177 0.4767 2.8389 -0.2315 1.7931 -0.1404 0.0452 -0.07 0.2445 0.1651 -0.2966 0.3835 0.4183 -0.0291 0.2445 0.0981 -0.0082 0.2243 -0.0193 0.1907 -0.1396 4.2528 24.7192 15 3.7137 2.0421 -2.2043 5.0265 -1.1178 2.2835 0.2759 -0.0343 0.7448 0.2926 -0.0656 -0.6306 -0.3526 0.6605 -0.2662 0.2978 0.0197 -0.0469 0.3216 -0.0449 0.3951 4.6059 16.0297 26.0974 16 4.4382 -2.0818 0.5099 4.305 -1.024 1.1258 -0.0772 -0.4155 -0.1587 0.5808 0.2219 -0.2102 0.1637 -0.0787 -0.191 0.3352 0.1477 -0.0916 0.2697 -0.0638 0.1734 1.8284 3.512 33.4119
Refinement TLS group Show large table (4 x 16) Hide large table ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 chain 'A' and (resseq 48:72)2 X-RAY DIFFRACTION 2 chain 'A' and (resseq 73:92)3 X-RAY DIFFRACTION 3 chain 'A' and (resseq 93:112)4 X-RAY DIFFRACTION 4 chain 'A' and (resseq 113:132)5 X-RAY DIFFRACTION 5 chain 'A' and (resseq 133:192)6 X-RAY DIFFRACTION 6 chain 'A' and (resseq 193:202)7 X-RAY DIFFRACTION 7 chain 'A' and (resseq 203:220)8 X-RAY DIFFRACTION 8 chain 'B' and (resseq 61:81)9 X-RAY DIFFRACTION 9 chain 'B' and (resseq 82:106)10 X-RAY DIFFRACTION 10 chain 'B' and (resseq 107:118)11 X-RAY DIFFRACTION 11 chain 'B' and (resseq 119:127)12 X-RAY DIFFRACTION 12 chain 'B' and (resseq 128:141)13 X-RAY DIFFRACTION 13 chain 'B' and (resseq 142:163)14 X-RAY DIFFRACTION 14 chain 'B' and (resseq 164:191)15 X-RAY DIFFRACTION 15 chain 'B' and (resseq 192:200)16 X-RAY DIFFRACTION 16 chain 'B' and (resseq 201:220)