Software Name Version Classification NB SCALEPACKdata scalingShow PHASER2.1.4phasingShow PHENIX1.7.3_928refinementShow PDB_EXTRACT3.11 data extractionShow Blu-Icedata collection DENZOdata reduction
Refinement Method to determine structure : MOLECULAR REPLACEMENT / Resolution : 2.201→19.853 Å / Occupancy max : 1 / Occupancy min : 0.65 / SU ML : 0.23 / σ(F) : 0 / Phase error : 22.34 / Stereochemistry target values : MLRfactor Num. reflection % reflection Selection details Rfree 0.2154 1645 5.08 % random Rwork 0.1763 - - - obs 0.1783 32403 95.4 % - all - 32403 - -
Solvent computation Shrinkage radii : 0.86 Å / VDW probe radii : 1.1 Å / Solvent model : FLAT BULK SOLVENT MODEL / Bsol : 33.118 Å2 / ksol : 0.341 e/Å3 Displacement parameters Biso max : 142.77 Å2 / Biso mean : 38.175 Å2 / Biso min : 4.26 Å2 Baniso -1 Baniso -2 Baniso -3 1- -0.9515 Å2 0 Å2 1.2053 Å2 2- - 1.3344 Å2 0 Å2 3- - - 0.1235 Å2
Refinement step Cycle : LAST / Resolution : 2.201→19.853 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 5014 0 30 189 5233
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.009 5154 X-RAY DIFFRACTION f_angle_d1.174 6970 X-RAY DIFFRACTION f_chiral_restr0.08 754 X-RAY DIFFRACTION f_plane_restr0.006 912 X-RAY DIFFRACTION f_dihedral_angle_d15.543 1906
Refine LS restraints NCS Ens-ID Dom-ID Auth asym-ID Number Refine-ID Type Rms dev position (Å)1 1 A2328 X-RAY DIFFRACTION POSITIONAL0.019 1 2 B2328 X-RAY DIFFRACTION POSITIONAL0.019
LS refinement shell Refine-ID : X-RAY DIFFRACTION / Total num. of bins used : 12
Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Num. reflection all % reflection obs (%)2.2014-2.2661 0.3174 76 0.224 1625 1701 60 2.2661-2.3391 0.2548 137 0.2333 2314 2451 88 2.3391-2.4226 0.303 140 0.2167 2627 2767 99 2.4226-2.5194 0.238 138 0.1983 2704 2842 100 2.5194-2.6338 0.2072 154 0.1846 2683 2837 100 2.6338-2.7723 0.2475 145 0.1862 2669 2814 100 2.7723-2.9455 0.2527 145 0.1915 2682 2827 100 2.9455-3.172 0.2325 150 0.1874 2669 2819 100 3.172-3.4897 0.2219 137 0.1855 2697 2834 100 3.4897-3.9911 0.1932 142 0.1675 2696 2838 100 3.9911-5.0149 0.1661 139 0.1355 2688 2827 100 5.0149-19.8541 0.1866 142 0.1608 2704 2846 99
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 40) 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 0.0023 -0.0028 0.0038 0.0055 -0.0009 0.0074 -0.0097 -0.0156 -0.0043 0.0167 -0.0076 -0.0134 0.0024 0.0142 -0.0323 0.0753 0.0586 -0.0367 0.2601 0.1743 0.0162 16.5915 25.8121 22.0843 2 0.041 0.0415 -0.0234 0.0387 -0.018 0.0631 -0.0598 -0.0589 -0.0551 0.0296 -0.0384 -0.0222 0.0286 0.0384 -0.2005 0.1507 0.0967 0.005 -0.0144 0.1571 0.1167 6.2927 24.787 -0.7481 3 0.0193 0.0136 0.0087 0.0112 0.0036 0.0084 -0.002 0.0025 -0.0129 0.0015 -0.0005 0.0053 0.0113 -0.0117 -0.0017 0.2415 -0.1616 0.0568 0.2357 0.0272 0.2661 -4.3895 21.9121 4.5665 4 0.0005 0.0005 -0.0007 0.0019 0.0015 0.0043 -0.0037 -0.01 -0.0157 0.0165 -0.0227 -0.0001 0.0355 0 -0.0463 0.3083 -0.1315 0.0763 0.1318 0.2149 0.3073 5.2893 12.9213 12.175 5 0.0597 0.0467 -0.0769 0.0346 -0.0587 0.097 -0.0487 -0.0692 -0.048 -0.0357 -0.0033 -0.0018 -0.008 0.0343 -0.0919 0.1191 0.0552 0.0153 0.035 0.1556 0.0233 10.1408 25.9348 8.6432 6 0.02 -0.0113 0.0001 0.0465 -0.0345 0.0295 -0.0001 -0.0116 -0.0117 0.0041 0.0028 0.0096 -0.0007 -0.0036 0.011 0.2117 -0.0026 0.1462 0.2905 0.0903 0.2064 1.6635 23.6988 16.7268 7 0.0454 -0.009 0.0161 0.0131 0.0154 0.0347 -0.0074 -0.0542 -0.0549 0.0424 0.0058 0.0161 0.062 0 0.0049 0.1001 -0.0172 0.062 0.1301 0.112 0.0639 12.908 31.4381 4.1521 8 0.0006 0.0008 0.0014 0.0008 0.0016 0.003 -0.0059 0.0138 -0.0076 -0.0037 -0.01 0.0003 -0.0021 0.0057 -0.0001 0.3202 -0.0018 0.0357 0.274 0.048 0.2994 15.9347 47.7391 -7.2602 9 0.0453 0.0017 -0.0067 0.0129 -0.0014 0.001 -0.0029 -0.051 0.0398 0.0106 0.0064 -0.0176 -0.0343 0.0196 0.0119 0.0736 -0.0396 -0.0034 0.0996 -0.0433 0.0936 17.3908 44.1687 5.7748 10 0.0049 -0.0062 0.0076 0.0063 -0.0089 0.0097 0.0059 -0.0217 -0.0061 -0.0031 0.0096 0.0124 -0.0074 -0.0371 0.0395 -0.0078 0.0306 0.0131 0.1551 0.0062 -0.03 13.839 34.4465 8.9251 11 0.0005 -0.0017 -0.0006 0.011 0.0059 0.0047 0.0059 0.0088 0.0147 -0.004 -0.0028 0.0008 0 0.0054 0 0.1717 0.0658 0.0628 0.2132 0.0093 0.1553 26.6557 33.4861 -9.812 12 0.0098 0.0071 0.013 0.0257 0.0103 0.0221 -0.0328 -0.0126 0.0514 -0.0201 -0.0046 0.0065 -0.0149 0.0131 -0.0209 -0.0189 -0.048 -0.0489 0.2159 -0.0339 0.0977 24.3514 38.5188 4.8686 13 0.0393 0.0302 0.011 0.0244 0.0071 0.0418 0.006 -0.0418 -0.069 -0.0296 -0.0108 -0.0003 0.0428 0.0447 -0.0518 -0.029 0.1525 -0.0619 0.1971 0.0856 0.0945 30.2485 26.0215 0.4874 14 0.0172 -0.0324 -0.0035 0.0614 0.0186 0.0203 -0.0229 0.0015 -0.0375 -0.0162 -0.0336 0.022 0.0425 0.0449 -0.1569 0.0885 0.1739 0.0083 0.1797 0.164 0.2376 26.3546 18.4854 0.0234 15 0.0019 0.0034 -0.0029 0.0111 -0.008 0.0061 -0.0031 0.0049 -0.0097 -0.0014 -0.0045 -0.0131 0.0101 0.0027 -0.0011 0.4024 0.1822 0.0715 0.2136 0.0066 0.5154 26.9921 8.1274 -2.8574 16 0.0436 -0.0256 0.0227 0.0147 -0.0125 0.0128 0.0166 -0.0008 -0.0267 0.0107 0.0036 -0.0027 0.0025 0.0104 0.0152 0.2382 0.2588 -0.091 0.3129 0.1951 0.3782 34.0616 13.529 8.0598 17 0.0364 -0.0131 -0.0095 0.0186 0.0062 0.0019 -0.0385 0.0145 -0.0612 0.0114 -0.0405 -0.037 0.0271 0.0286 -0.1297 0.1753 -0.0453 0.0405 -0.0318 0.0519 0.2244 8.081 16.0992 -4.3003 18 0.0063 -0.0068 -0.0023 0.0173 -0.0003 0.0022 0.0023 -0.0021 -0.027 -0.0186 -0.021 0.0279 0.0086 0.0088 -0.0289 0.3974 0.0217 0.0532 0.0683 0.095 0.5622 16.1487 6.8809 2.5007 19 0.0011 -0.0013 0.0011 0.0029 0.0029 0.0093 -0.0105 -0.0016 -0.0107 0.0014 -0.0212 -0.0061 0.0059 0.0007 -0 0.5896 0.2095 -0.1089 0.4205 0.1512 0.6046 29.9289 2.7832 12.9796 20 0.0042 -0.0071 0.0039 0.0138 -0.0093 0.0052 -0.0096 -0.0175 -0.022 0.0075 -0.0101 -0.0161 0.0314 0.0219 -0.0322 0.1919 0.1162 -0.0111 0.3315 0.2922 0.2216 26.1342 17.7301 16.3345 21 0.0112 -0.0065 -0.0031 0.0159 0.0031 0.0003 0.0093 0.0036 0.0028 -0.0142 -0.0042 0.0301 -0.0034 -0.0148 -0.0022 0.0261 0.1363 -0.0584 0.2883 0.0916 0.0931 -20.304 44.3726 -18.8243 22 0.0366 -0.0044 0.0002 0.0111 0.0193 0.0277 0.0497 0.02 0.0286 -0.0129 -0.001 0.0134 -0.0465 -0.0493 0.0678 0.0878 0.1654 0.0061 -0.072 0.1033 0.1145 1.3528 45.4114 -6.2427 23 0.0031 0.0064 0.0061 0.017 0.0052 0.023 0.0072 -0.0123 0.0094 0.0068 0.0021 0.0082 -0.0147 0.0016 0.0054 0.2925 0.0611 0.0522 0.2405 -0.1605 0.2468 -5.0278 48.302 3.8354 24 0.0039 -0.002 -0.0007 0.0033 -0.0022 0.0044 0.0048 -0.0103 0.0183 -0.0008 -0.0053 0.0145 -0.0183 -0.0037 -0.0043 0.3246 0.2238 0.0642 0.1423 -0.1074 0.3618 -11.607 57.282 -6.5787 25 0.0983 -0.0481 -0.0703 0.0469 0.0324 0.0513 0.0271 0.0221 0.0042 0.0084 0.0098 -0.0124 -0.0561 -0.0828 0.0869 0.0005 0.172 -0.0403 0.0089 0.0644 0.0808 -7.592 44.2605 -11.0287 26 0.0235 -0.0218 0.0056 0.0253 -0.0132 0.0132 0 -0.0056 -0.0001 0.0094 0.0009 0.0056 -0.0127 -0.0103 -0.0001 0.1443 0.077 0.1238 0.2464 0.0009 0.1738 -16.5051 46.5017 -3.4278 27 0.0343 0.002 0.0217 0.0246 -0.0196 0.0404 -0.001 0.0094 0.0961 0.003 -0.0015 0.0398 -0.0701 -0.0545 -0.0057 0.0733 0.1006 0.0299 0.1082 0.0115 0.1202 -2.8373 38.7532 -13.3252 28 0.0085 0.0018 -0.0034 0.0007 -0.0016 0.0046 0.0077 0.0013 -0.0058 0.0034 -0.0026 -0.0054 -0.0026 0.0131 0 0.2803 0.0365 0.0579 0.2813 -0.016 0.3478 8.8216 22.4552 -15.1445 29 0.0002 0.0001 -0.0001 0.0109 -0.0135 0.0264 -0.0078 0.0249 -0.0323 -0.0333 -0.001 0.0011 0.0255 -0.045 -0.0104 0.1059 -0.0358 -0.0025 0.0989 -0.06 0.0805 -3.9972 26.0245 -17.9329 30 0.0088 -0.0095 0.0052 0.0098 -0.0082 0.0075 -0.0088 -0.0358 -0.008 0.0108 -0.0086 0.0044 -0.0046 -0.0395 -0.0441 -0.0152 0.0142 0.0255 0.188 0.0251 0.0077 -7.4977 35.747 -14.7291 31 0.0041 0.0049 0.0012 0.0108 0.0016 0.0014 -0.0202 0.0064 -0.0072 0.0028 -0.0158 -0.0023 0.0241 0.0049 -0.0001 0.1183 0.0094 0.0731 0.2152 0.0592 0.2001 12.4535 36.7002 -25.5614 32 0.0105 0.0038 0.0096 0.0106 0.0023 0.0115 0.0118 0.0167 -0.0017 0.0006 0.0019 -0.0169 0.0361 -0.019 -0.001 0.1046 -0.0134 -0.0234 0.2084 -0.05 -0.0357 -2.385 31.668 -24.7681 33 0.0376 -0.0039 0.0099 0.0142 0.0157 0.0268 -0.0002 0.0612 0.0332 -0.0029 -0.0126 -0.0241 -0.0375 -0.0227 -0.0162 0.098 0.0624 -0.0383 0.2002 0.1782 -0.0384 2.5746 44.1585 -30.1981 34 0.0087 -0.0023 0.0062 0.0177 -0.0119 0.0091 0.0141 0.0369 0.0512 0.0276 -0.0058 -0.0088 -0.0317 -0.0041 0.0884 0.2379 0.1549 0.0089 0.1914 0.192 0.1123 2.6276 51.705 -26.3241 35 0.002 -0.0014 0.001 0.0112 -0.0023 0.0016 0.0015 0.004 0.0067 -0.0155 -0.0029 -0.0038 -0.0078 0.0034 -0.0049 0.4668 0.014 0.0911 0.2164 0.191 0.3829 5.5659 62.0538 -26.6353 36 0.0027 -0.0043 0.0075 0.0088 -0.0156 0.027 -0.0063 0.0123 -0.0008 0.0001 -0.0012 0.0128 -0.025 -0.0005 -0.0048 0.3436 0.17 -0.0539 0.2735 0.2882 0.2132 -4.5762 56.6439 -34.7805 37 0.0011 -0.0014 -0.0092 0.0182 -0.0051 0.0402 0.0302 0.0154 0.0397 -0.0184 -0.0082 -0.0078 -0.0492 0.0172 0.0412 0.23 0.058 0.0455 -0.0487 -0.0202 0.2304 5.0913 54.116 -7.6362 38 0.0026 -0.0067 0.0051 0.0132 -0.0098 0.0081 -0.0021 0.0083 0.0231 0.0089 -0.0175 -0.0009 -0.0327 -0.0002 -0.0051 0.4682 0.0918 0.0622 0.0322 0.021 0.4119 -0.8812 63.3402 -16.4056 39 0.0008 -0.0011 0.0006 0.0015 -0.0011 0.0006 0.0141 -0.0034 0.0071 -0.0014 -0.0004 -0.0011 -0.0073 0.0021 -0 0.6318 0.1595 -0.0623 0.3903 0.2151 0.5716 -9.8906 67.3922 -31.1823 40 0.0029 -0.0058 0.0036 0.01 -0.0066 0.0034 0.0125 0.0136 0.0293 -0.0116 -0.0007 0.0045 -0.0133 -0.0178 0.0147 0.2019 0.2382 -0.0142 0.2963 0.1252 0.2067 -13.6129 52.4498 -27.7333
Refinement TLS group Show large table (6 x 40) Hide large table ID Refine-ID Refine TLS-ID Selection details Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 (chain A and resid 3:19)A3 - 19 2 X-RAY DIFFRACTION 2 (chain A and resid 20:41)A20 - 41 3 X-RAY DIFFRACTION 3 (chain A and resid 42:47)A42 - 47 4 X-RAY DIFFRACTION 4 (chain A and resid 48:61)A48 - 61 5 X-RAY DIFFRACTION 5 (chain A and resid 62:81)A62 - 81 6 X-RAY DIFFRACTION 6 (chain A and resid 82:87)A82 - 87 7 X-RAY DIFFRACTION 7 (chain A and resid 88:109)A88 - 109 8 X-RAY DIFFRACTION 8 (chain A and resid 110:114)A110 - 114 9 X-RAY DIFFRACTION 9 (chain A and resid 115:131)A115 - 131 10 X-RAY DIFFRACTION 10 (chain A and resid 132:149)A132 - 149 11 X-RAY DIFFRACTION 11 (chain A and resid 150:155)A150 - 155 12 X-RAY DIFFRACTION 12 (chain A and resid 156:175)A156 - 175 13 X-RAY DIFFRACTION 13 (chain A and resid 176:217)A176 - 217 14 X-RAY DIFFRACTION 14 (chain A and resid 218:240)A218 - 240 15 X-RAY DIFFRACTION 15 (chain A and