Software Name Version Classification REFMAC5.2.0019refinement ADSCQuantumdata collection DENZOdata reduction SCALEPACKdata scaling REFMACphasing
Refinement Method to determine structure : FOURIER SYNTHESISStarting model : PDB ENTRY 2G8QResolution : 1.6→30 Å / Cor.coef. Fo :Fc : 0.958 / Cor.coef. Fo :Fc free : 0.944 / SU B : 3.013 / SU ML : 0.057 / TLS residual ADP flag : LIKELY RESIDUAL / Cross valid method : THROUGHOUT / σ(F) : 0 / ESU R : 0.099 / ESU R Free : 0.096 / Stereochemistry target values : MAXIMUM LIKELIHOOD / Details : HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONSRfactor Num. reflection % reflection Selection details Rfree 0.20937 1562 5 % RANDOM Rwork 0.17861 - - - obs 0.18016 29373 98.93 % - all - 31270 - -
Solvent computation Ion probe radii : 0.8 Å / Shrinkage radii : 0.8 Å / VDW probe radii : 1.4 Å / Solvent model : MASKDisplacement parameters Biso mean : 16.207 Å2 Baniso -1 Baniso -2 Baniso -3 1- -0.08 Å2 0 Å2 -0.03 Å2 2- - 0.48 Å2 0 Å2 3- - - -0.4 Å2
Refine analyze Free Obs Luzzati coordinate error 0.096 Å 0.099 Å
Refinement step Cycle : LAST / Resolution : 1.6→30 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 1902 0 48 369 2319
Refine LS restraints Show large table (5 x 17) Hide large table Refine-ID Type Dev ideal Dev ideal target Number X-RAY DIFFRACTION r_bond_refined_d0.008 0.021 1999 X-RAY DIFFRACTION r_angle_refined_deg1.443 1.951 2708 X-RAY DIFFRACTION r_dihedral_angle_1_deg5.593 5 246 X-RAY DIFFRACTION r_dihedral_angle_2_deg34.14 25.169 89 X-RAY DIFFRACTION r_dihedral_angle_3_deg10.404 15 339 X-RAY DIFFRACTION r_dihedral_angle_4_deg11.274 15 8 X-RAY DIFFRACTION r_chiral_restr0.145 0.2 298 X-RAY DIFFRACTION r_gen_planes_refined0.004 0.02 1505 X-RAY DIFFRACTION r_nbd_refined0.186 0.2 947 X-RAY DIFFRACTION r_nbtor_refined0.295 0.2 1374 X-RAY DIFFRACTION r_xyhbond_nbd_refined0.127 0.2 305 X-RAY DIFFRACTION r_symmetry_vdw_refined0.165 0.2 67 X-RAY DIFFRACTION r_symmetry_hbond_refined0.106 0.2 45 X-RAY DIFFRACTION r_mcbond_it0.513 1.5 1273 X-RAY DIFFRACTION r_mcangle_it0.879 2 2022 X-RAY DIFFRACTION r_scbond_it1.319 3 801 X-RAY DIFFRACTION r_scangle_it2.158 4.5 686
LS refinement shell Resolution : 1.6→1.641 Å / Total num. of bins used : 20 Rfactor Num. reflection % reflection Rfree 0.254 120 - Rwork 0.206 2120 - obs - - 97.82 %
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 19) 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 16.0026 2.4745 1.0572 15.0953 7.5705 10.2913 -0.0649 -0.0451 0.7748 -0.6494 0.3206 -0.3655 -1.7691 0.4812 -0.2557 0.2667 -0.0974 0.0794 -0.067 0.03 -0.0201 33.0819 15.1759 12.3871 2 3.5296 -0.6955 -0.0077 3.8318 1.0515 6.1276 0.1723 0.2198 0.0424 -0.1098 -0.032 -0.0573 -0.201 -0.1292 -0.1403 0.0546 0.0075 0.0242 0.0453 0.0426 0.0061 29.2271 5.7837 7.7378 3 3.1845 -0.2125 2.744 0.0142 -0.1831 2.3644 0.9789 0.4569 -0.3852 -0.2775 -0.2313 0.8536 -0.6267 -0.7451 -0.7476 0.513 -0.0768 0.0269 0.3059 -0.0798 0.1921 24.8214 -5.2553 -1.6926 4 3.4927 -0.4901 -2.344 0.8904 0.3491 2.9095 0.1008 0.2882 0.0765 -0.1654 0.0634 -0.1237 -0.1339 -0.0861 -0.1642 0.0363 -0.009 0.0118 0.0637 0.0106 0.0105 32.2213 2.1093 4.7363 5 4.1993 0.0597 0.6925 1.968 -0.6101 2.1543 -0.0306 -0.0319 -0.0719 0.1033 0.048 -0.0849 -0.0302 -0.1844 -0.0174 0.0494 -0.0013 -0.0001 0.0397 0.0081 0.0396 27.9791 -1.6206 24.0285 6 11.0821 1.5675 -5.5984 0.2988 -1.1595 4.5813 -0.2738 0.2381 -0.4013 -0.1508 0.1297 -0.181 0.4579 0.0819 0.1442 0.0555 -0.0178 0.0316 0.0278 -0.0642 0.0202 38.4471 -4.457 2.0132 7 8.7673 3.746 -7.2497 1.7212 -3.5303 7.5461 -0.5403 0.2825 -0.5866 -0.3055 0.2212 -0.2717 0.8436 -0.2914 0.3191 0.0773 -0.0658 0.0354 0.0142 -0.093 0.0285 30.6375 -8.6454 4.2754 8 1.9469 0.0803 -0.2254 2.9302 0.5895 2.5215 -0.0063 0.0302 0.0567 -0.0394 0.0605 -0.0301 -0.0287 -0.1923 -0.0542 0.0472 0.001 -0.0047 0.0381 0.0153 0.0414 29.0377 2.6315 18.8657 9 9.2118 -0.1451 -3.8616 10.5689 8.077 11.3515 -0.1368 0.1741 -0.889 0.5707 0.2847 -0.4421 1.2399 0.5839 -0.1479 0.0776 0.0778 -0.0305 0.0108 -0.0775 0.0676 19.0932 -11.2401 31.9007 10 6.0909 0.7311 1.7081 1.7117 0.1042 5.3292 -0.1758 0.4025 -0.0544 -0.0224 0.2757 0.0226 -0.0745 0.103 -0.0999 0.0146 -0.0302 0.0166 0.0628 -0.0015 0.0162 14.2706 -2.5286 29.5727 11 5.637 6.298 -0.6855 14.4224 -0.3584 0.1058 -0.8955 1.6635 2.5075 -1.9048 0.0276 -0.1427 -0.6074 0.7948 0.8678 0.2336 -0.0537 -0.0662 0.1067 0.1436 0.0035 11.3583 10.4669 22.6442 12 3.7882 -3.7634 0.6187 16.9594 2.1642 0.6852 -0.3624 0.9614 0.2425 -1.0734 0.1982 -0.121 -0.3508 0.2992 0.1642 0.1167 -0.1497 -0.0549 0.1956 0.087 -0.1067 8.2185 1.9464 18.3808 13 14.8036 7.0092 7.7555 13.3612 6.1341 4.6666 0.0365 0.3612 -1.1003 -0.5279 -0.0024 -0.1615 0.115 0.1798 -0.0342 0.0209 -0.071 0.0458 0.1206 -0.0686 -0.0062 9.4905 -8.0511 20.3843 14 1.6296 0.4162 1.0477 1.097 1.2379 1.6241 -0.1326 0.1737 0.0808 -0.1762 0.0772 0.0345 -0.1339 0.0543 0.0554 0.0409 -0.0244 -0.0043 0.0177 0.0067 0.059 12.4687 2.5168 33.2096 15 6.6522 5.7209 0.8999 9.2285 1.7999 0.3661 -0.1678 -0.2329 -0.1945 0.0449 0.0362 0.2118 0.0966 -0.0934 0.1316 0.0332 -0.0028 0.0216 0.038 0.0282 0.0753 6.8807 -3.1217 46.7845 16 0.6835 0.5556 -0.0146 0.972 0.6337 0.8802 -0.1178 0.0074 0.0992 -0.1399 0.0105 0.1507 -0.0914 -0.068 0.1073 0.042 -0.0025 -0.0327 0.0038 0.0067 0.0721 9.2015 5.6985 39.5634 17 1.7822 -0.3776 2.3721 3.7954 3.0433 6.5411 -0.0641 0.5246 -0.2679 -0.4224 -0.1344 0.2675 -0.2267 0.0352 0.1985 0.0267 -0.03 -0.0178 0.0701 -0.0592 0.0039 -1.3399 -4.8203 17.6775 18 0.4318 0.825 1.2012 1.7849 1.9927 5.1649 -0.2926 0.0837 0.2386 -0.3652 -0.0091 0.3159 -0.552 -0.2046 0.3017 0.0659 -0.0085 -0.096 -0.0106 0.0237 0.0605 3.6034 7.24 29.3106 19 5.4393 -1.487 1.116 2.2246 -0.514 2.6347 -0.0421 0.0516 -0.1236 -0.0665 0.0119 0.1164 0.0773 0.0111 0.0302 0.057 -0.0166 0.0066 0.0121 -0.0013 0.0646 12.7731 -2.9149 40.2902
Refinement TLS group Show large table (7 x 19) Hide large table ID Refine-ID Refine TLS-ID Auth asym-ID Label asym-ID Auth seq-ID Label seq-ID 1 X-RAY DIFFRACTION 1 AA1 - 6 1 - 6 2 X-RAY DIFFRACTION 2 AA7 - 16 7 - 16 3 X-RAY DIFFRACTION 3 AA17 - 23 17 - 23 4 X-RAY DIFFRACTION 4 AA24 - 57 24 - 57 5 X-RAY DIFFRACTION 5 AA58 - 77 58 - 77 6 X-RAY DIFFRACTION 6 AA78 - 96 78 - 96 7 X-RAY DIFFRACTION 7 AA97 - 104 97 - 104 8 X-RAY DIFFRACTION 8 AA105 - 124 105 - 124 9 X-RAY DIFFRACTION 9 BB1 - 6 1 - 6 10 X-RAY DIFFRACTION 10 BB7 - 14 7 - 14 11 X-RAY DIFFRACTION 11 BB15 - 23 15 - 23 12 X-RAY DIFFRACTION 12 BB24 - 31 24 - 31 13 X-RAY DIFFRACTION 13 BB32 - 39 32 - 39 14 X-RAY DIFFRACTION 14 BB40 - 59 40 - 59 15 X-RAY DIFFRACTION 15 BB60 - 70 60 - 70 16 X-RAY DIFFRACTION 16 BB71 - 83 71 - 83 17 X-RAY DIFFRACTION 17 BB84 - 96 84 - 96 18 X-RAY DIFFRACTION 18 BB97 - 106 97 - 106 19 X-RAY DIFFRACTION 19 BB107 - 124 107 - 124