sample in solution ▼ size (Rg, Dmax, volume) folding state, compactness overal shape ~30 A resolution oligomeric state quaternary structure flexible systems 0 0.1 0.2 0.3 0.4 q [A-1] 0.5 Experimental setup XRD vs SAXS XRD detector image diffarction spots SAXS detector image x-ray scattering Putnam et al. (2007) Quart. Rev, Biophys, 40(3), 191-285. Output structure XRD vs SAXS XRD - data reduction Set of diffraction images indexing » t ++ 4 4 ++ + * * +' +1 +* 44 44 + * * 4* ** 4 44* ť + ++ +- + + +4 4 * 4 + 444444 4 4. ' +.4» 44++ 4 %l 4 4 *W ■ . + + « +4 4 4 4 41 ^+ ,t 444 4 . + 4 4 t+ * 4-4 + 4 4-4 4 4 4 4 4 4 4 4. * 4'{ - fÍ' * 4 44 4 *k " Reduced data - intensities with h, k, 1 indices h k Orig. H Orig. K Orig. l M/ISYM BATCH 1 sigl FRACTIONCALC XDET YDET ROT LP FLAG 1 0 0 5 0 0 5 1 706 0,45 0,34 1,00 1243,:c 1285.20 c :: 0 2 0 0 6 0 0 6 1 710 11780.00 315.60 1,00 1260.90 1281,00 70.93 c 0 3 0 0 7 0 0 7 1 714 -0.17 0,52 1 00 1273,90 1276,90 71.36 C 01 0 4 0 0 13 0 0 13 740 0,54 0.98 1,00 1351,80 1252,00 73,93 o,ca 0 5 0 0 14 0 0 14 1 744 1.26 1,08 1,00 1364.80 1247.90 74,35 0,02 0 6 0 0 15 0 0 15 1 746 3.08 1,15 LOO 1377.80 1243.80 74.78 0.02 0 7 0 0 16 0 0 16 1 753 -0.53 1,18 1,00 1390.90 1239.70 75.21 0,02 0 fl :"i 0 17 0 0 17 757 -0,12 1,25 1,00 1403,90 1235,60 75,64 0,03 0 9 0 0 ls 0 0 18 l 761 157,10 5,16 1,00 1417,00 1231,50 76,07 0,c3 0 10 0 0 19 0 0 19 1 766 1.74 1.48 1,00 1430.10 1227.50 76.51 O.Cj 0 11 0 0 20 0 0 20 1 770 3.40 1,58 1,00 1443.20 1223.40 76.94 0.03 0 12 0 0 21 0 21 774 2,61 1,65 1,00 1456,30 1219,30 77,37 0,03 0 13 0 0 21 0 0 -21 2 595 -0.20 1,56 0,79 910,30 1393,30 59,46 0,03 0 14 0 0 22 0 0 22 1 779 13.00 2.00 1,00 1469.50 1215.30 77.80 0 q 3 0 15 0 : 22 0 0 -22 2 591 :o 20 1,68 1,00 897.20 1397.40 59.03 0.03 : 16 0 0 23 0 0 -23 2 587 6.14 1,68 1,00 884,00 1401,50 58,60 0 d4 0 17 0 0 j4 0 0 24 1 787 17610.00 472,70 1,00 1495,80 1207,20 78,67 C cm 0 18 Ü : 24 0 0 -24 2 il2 17080.00 458.50 1 ::j 870.90 1405.60 58.17 c : 19 0 0 25 0 0 25 792 1.56 1.95 1,00 1509.10 1203.20 79.10 c 0 20 0 0 25 0 0 25 2 578 -2,49 1,81 1,00 857,70 1409,60 57,73 0,04 0 21 0 0 26 0 0 26 1 796 1,20 2,02 0,89 1522,30 1199,20 79.54 G M 0 22 D D 26 0 0 -26 1 574 -: _■■ 1 _:} 844.40 1413.70 57.30 0.04 D 23 0 0 27 0 0 -27 2 569 -0.63 1,98 1,00 831,20 1417.70 56.87 0.04 0 24 0 0 0 0 -28 2 565 2,69 2,06 1,00 817,90 1421,80 56,43 0 04 0 25 0 0 29 0 0 -29 2 561 -0,08 2,09 1,00 804,70 1425,80 56,00 0,04 0 26 0 0 30 0 0 -30 2 556 3668.00 99,62 1,00 791.30 1429.80 55,56 0 27 0 0 31 0 0 -31 2 552 -0,04 2.20 1,00 778.00 1433.80 55.13 0.05 0 ?r 0 0 3 2 0 0 -32 2 547 0.5s 2,33 1,00 764.60 1437.70 54.69 0.05 0 indexing integration Space group determination Space group P 61 2 2 Space group confidence S (spacegroup is known) Cell 177.54 177.54 203.64 90 90 120 Resolution low 4ß.33 Resolution high 2.832 Number of lattices 1 Number of reflections 398868 Number of data sets 1 XRD - output s xrd intensities ~105 reflexions, reciprocal space, indices h, k, 1 Electron density map h k 1 Orig. H Orig. K Orig. L M/ISYM BATCH 1 SIGI FRACTIONCALC XDET YDET ROT LP FLAG 1 0 0 5 0 0 5 1 7013 0,45 0.34 1.00 1245 00 12 3:. 20 70.50 0 01 0 2 0 0 6 0 0 6 1 710 11780,00 315,60 1,00 1260,90 12 31. CO 70,93 0,01 ■EVJ 3 0 0 ? 0 0 7 1 714 -0,17 0,52 1,00 1273,90 1276,90 71,36 0,01 0 4 0 0 13 D D 13 740 0,54 0.9H LOO 1351,80 1252,00 73.93 ' i:. 0 5 0 D L4 0 0 14 l 744 1,26 1,08 1.00 1364,30 1247,90 74.35 0,02 0 e 0 0 IS 0 0 15 l 74E 3,08 1,15 1,00 1377,90 1243,30 74,78 0,02 0 7 □ □ Lb 0 0 16 l 753 -0,63 1,18 1,00 1390,90 1239,70 75,21 0,02 0 3 0 0 17 0 D 17 l 757 -0,12 1,25 1.00 1403,90 1235,60 75.64 0,03 0 g 0 0 23 0 0 18 l 751 157,10 5,16 1.00 1417,00 1231,50 76.07 0,03 0 ID 0 0 19 0 0 19 756 1,74 1,48 1,00 1430,10 1227,50 76,51 0,03 0 11 0 0 20 0 0 20 1 770 3,40 1,58 1,00 1443,20 1223,40 76,94 0,03 0 12 0 0 21 0 0 21 774 2,61 1,65 1.00 1456,30 1219,30 77.37 0,03 0 13 0 0 21 0 c -21 2 595 -0,20 1,56 0.79 910,30 1393,30 59.46 0.03 0 14 0 0 22 0 c 22 1 779 13,00 2,00 1.00 1469,50 1215,30 77.30 D 0 3 0 15 0 0 22 0 0 •22 2 591 i o 2:: L Gfl l, c: 897,20 1397,40 5»,c -: :i i:-; :i 16 0 0 23 0 0 •23 2 537 6.14 1,68 1.00 884,00 1401.50 58.60 D.04 0 17 0 0 .4 0 0 24 1 787 17610.00 472.70 1.00 1495,80 1207,20 78.67 U U4 0 19 0 : 24 0 0 -24 2 5S2 17080.00 458.50 i,c: 870,90 1405,60 53,27 0 04 0 19 0 0 25 0 0 25 1 792 1,56 1,96 1.00 1509.10 1203,20 79.10 n 04 0 20 0 0 25 0 0 -25 2 57B -2,49 1,81 1,00 857,70 1409,60 57.73 0,04 0 21 : : 26 0 0 26 1 796 1,20 2.02 0.89 1522,30 1199,20 79.54 D 04 0 22 0 : 26 0 0 -26 : 574 1,04 i l.o: 844,40 1413,70 57.:': ;i 04 0 23 0 0 27 0 D -27 2 569 -0,63 1,98 1,00 831,20 1417,70 56,87 D 04 0 24 0 0 28 0 0 -28 2 555 2,69 2,06 1,00 817,90 1421,80 56,43 0 04 0 25 0 0 29 0 D -29 2 551 -0,08 2,09 1.00 804,70 1425,80 56.00 D,04 0 26 0 D 3:1: 0 0 -30 2 556 3668,00 99,62 1.00 791.30 1429,30 55.56 0,05 0 27 0 0 31 0 0 -31 2 552 -0,04 2,20 1,00 778,00 1433,30 55,13 0,05 0 2a 0 0 J2 0 0 -32 2 547 0,58 2,33 1,00 764,50 1437,70 54,69 0,05 0 29 0 0 33 0 0 -33 543 0,79 2,38 1.00 751,20 144-1,70 54.25 0,05 0 30 0 D 34 0 0 -34 2 539 2,15 2.44 1.00 737,30 1445,70 53.32 0,05 0 31 0 0 35 0 D -35 2 534 1,52 2,54 1,00 724,30 1449,60 53,38 0,05 0 32 □ □ ib 0 0 ■36 2 530 531,30 16,14 1,00 710,90 1453,50 52,94 tl.lir, 0 33 0 0 37 0 0 -37 2 526 0,98 2,68 1.00 697,30 1457,40 52.50 D.0S 0 34 0 0 38 0 0 -38 2 521 -0,53 2,S5 1.00 663,30 1461,30 52.05 0,06 0 35 0 0 39 0 0 -39 2 517 -4,92 3,00 0.95 670,20 1465,10 51,61 0,06 0 36 0 0 45 0 0 -45 2 490 2,37 3,73 1,00 587,80 1487,90 48,93 0,07 0 Phase problem Fourier transform XRD - output s xrd intensities ~105 reflexions, reciprocal space, indices h, k, 1 Electron density map Atom coordinates h k 1 Orig. H Orig. K Orig. L M/ISYM BATCH 1 SIGI FRACTIONCALC XDET YDET ROT LP FLAG 1 0 0 5 0 0 5 1 7013 0,45 0.34 1.00 1245 00 12 3:. 20 70.50 0 01 0 2 0 0 6 0 0 6 1 710 11780,00 315,60 1,00 1260,90 12 31. CO 70,93 0,01 ■EVJ 3 0 0 ? 0 0 7 1 714 -0,17 0,52 1,00 1273,90 1276,90 71,36 0,01 0 4 0 0 13 D D 13 740 0,54 0.9H LOO 1351,80 1252,00 73.93 ' i:. 0 5 0 D L4 0 0 14 l 744 1,26 1,08 1.00 1364,30 1247,90 74.35 0,02 0 e 0 0 IS 0 0 15 l 74E 3,08 1,15 1,00 1377,90 1243,30 74,78 0,02 0 7 □ □ Lb 0 0 16 l 753 -0,63 1,18 1,00 1390,90 1239,70 75,21 0,02 0 3 0 0 17 0 D 17 l 757 -0,12 1,25 1.00 1403,90 1235,60 75.64 0,03 0 g 0 0 23 0 0 18 l 751 157,10 5,16 1.00 1417,00 1231,50 76.07 0,03 0 ID 0 0 19 0 0 19 756 1,74 1,48 1,00 1430,10 1227,50 76,51 0,03 0 11 0 0 20 0 0 20 1 770 3,40 1,58 1,00 1443,20 1223,40 76,94 0,03 0 12 0 0 21 0 0 21 774 2,61 1,65 1.00 1456,30 1219,30 77.37 0,03 0 13 0 0 21 0 c -21 2 595 -0,20 1,56 0.79 910,30 1393,30 59.46 0.03 0 14 0 0 22 0 c 22 1 779 13,00 2,00 1.00 1469,50 1215,30 77.30 D 0 3 0 15 0 0 22 0 0 •22 2 591 i o 2:: L Gfl l, c: 897,20 1397,40 5»,c -: :i i:-; :i 16 0 0 23 0 0 •23 2 537 6.14 1,68 1.00 884,00 1401.50 58.60 D.04 0 17 0 0 .4 0 0 24 1 787 17610.00 472.70 1.00 1495,80 1207,20 78.67 U U4 0 19 0 : 24 0 0 -24 2 5S2 17080.00 458.50 i,c: 870,90 1405,60 53,27 0 04 0 19 0 0 25 0 0 25 1 792 1,56 1,96 1.00 1509.10 1203,20 79.10 n 04 0 20 0 0 25 0 0 -25 2 57B -2,49 1,81 1,00 857,70 1409,60 57.73 0,04 0 21 : : 26 0 0 26 1 796 1,20 2.02 0.89 1522,30 1199,20 79.54 D 04 0 22 0 : 26 0 0 -26 : 574 1,04 i l.o: 844,40 1413,70 57.:': ;i 04 0 23 0 0 27 0 D -27 2 569 -0,63 1,98 1,00 831,20 1417,70 56,87 D 04 0 24 0 0 28 0 0 -28 2 555 2,69 2,06 1,00 817,90 1421,80 56,43 0 04 0 25 0 0 29 0 D -29 2 551 -0,08 2,09 1.00 804,70 1425,80 56.00 D,04 0 26 0 D 3:1: 0 0 -30 2 556 3668,00 99,62 1.00 791.30 1429,30 55.56 0,05 0 27 0 0 31 0 0 -31 2 552 -0,04 2,20 1,00 778,00 1433,30 55,13 0,05 0 2a 0 0 J2 0 0 -32 2 547 0,58 2,33 1,00 764,50 1437,70 54,69 0,05 0 29 0 0 33 0 0 -33 543 0,79 2,38 1.00 751,20 144-1,70 54.25 0,05 0 30 0 D 34 0 0 -34 2 539 2,15 2.44 1.00 737,30 1445,70 53.32 0,05 0 31 0 0 35 0 D -35 2 534 1,52 2,54 1,00 724,30 1449,60 53,38 0,05 0 32 □ □ ib 0 0 ■36 2 530 531,30 16,14 1,00 710,90 1453,50 52,94 tl.lir, 0 33 0 0 37 0 0 -37 2 526 0,98 2,68 1.00 697,30 1457,40 52.50 D.0S 0 34 0 0 38 0 0 -38 2 521 -0,53 2,S5 1.00 663,30 1461,30 52.05 0,06 0 35 0 0 39 0 0 -39 2 517 -4,92 3,00 0.95 670,20 1465,10 51,61 0,06 0 36 0 0 45 0 0 -45 2 490 2,37 3,73 1,00 587,80 1487,90 48,93 0,07 0 Phase problem Fourier transform XRD - output Structure with high resolution 3D coordinates, PDB format, in real space x, y, z HETATM 2968 C9A FNR HETATM 2969 N10 FNR HETATM 2970 CAA FNR HETATM 2971 Nl FNR HETATM 2972 C2 FNR HETATM 2973 02 FNR HETATM 2974 N3 FNR HETATM 2975 C4 FNR HETATM 2976 04 FNR HETATM 2977 C4A FNR HETATM 2978 N5 FNR HETATM 2979 C5A FNR HETATM 2980 C6 FNR HETATM 2981 C7 FNR HETATM 2982 C7M FNR HETATM 2983 C8 FNR HETATM 2984 C8M FNR HETATM 2985 C9 FNR HETATM 2986 CI FNR HETATM 2987 C2 FNR HETATM 2988 02' FNR HETATM 2989 C3 FNR HETATM 2990 03' FNR HETATM 2991 C41 FNR HETATM 2992 04' FNR HETATM 2993 C5 FNR HETATM 2994 05' FNR HETATM 2995 P FNR HETATM 2996 01P FNR HETATM 2997 02P FNR HETATM 2998 03P FNR B 201 18.093 -4.814 B 201 18.926 -4.246 B 201 20.263 -4.072 B 201 21.001 -3.377 B 201 22.260 -3.219 B 201 22.895 -2.495 B 201 22.832 -3.652 B 201 22.174 -4.394 B 201 22.762 -4.851 B 201 20.769 -4.664 B 201 19.988 -5.342 B 201 18.678 -5.408 B 201 17.856 -5.955 B 201 16.502 -5.982 B 201 15.729 -6.554 B 201 15.929 -5.414 B 201 14.454 -5.501 B 201 16.734 -4.854 B 201 18.395 -3.681 B 201 18.023 -2.264 B 201 19.202 -1.525 B 201 16.991 -1.922 B 201 15.809 -2.741 B 201 16.644 -0.457 B 201 15.924 -0.152 B 201 15.746 -0.178 B 201 15.556 1.235 B 201 14.156 1.902 B 201 14.298 3.344 B 201 13.020 1.211 B 201 14.088 1.723 66.786 1.00 7.49 C 67.742 1.00 7.31 N 67.478 1.00 7.09 C 68.290 1.00 7.03 N 68.029 1.00 7.67 C 68.786 1.00 8.20 0 66.907 1.00 7.06 N 65.997 1.00 6.83 C 64.973 1.00 6.36 0 66.266 1.00 6.92 C 65.408 1.00 7.47 N 65.569 1.00 7.59 C 64.611 1.00 7.52 c 64.805 1.00 7.90 c 63.669 1.00 8.29 c 65.987 1.00 8.03 c 66.238 1.00 8.78 c 66.964 1.00 7.60 c 68.980 1.00 7.22 c 68.917 1.00 7.07 c 69.187 1.00 6.83 0 69.974 1.00 7.10 c 69.803 1.00 7.23 0 69.874 1.00 7.17 c 71.082 1.00 7.78 0 68.686 1.00 6.50 c 68.495 1.00 6.21 0 68.939 1.00 5.78 p 68.517 1.00 5.61 0 68.280 1.00 5.79 0 70.433 1.00 6.03 0 SAXS - isotropic scattering -> radial averaging Image from detector Beam center position Radiály averaged data - SAXS curve 'subtractecLdata' q[A-] SAXS curve - txt file S I SD 0.0166627 0.973409 0.0105135 0.0181009 0.949327 0.00825875 0.019539 0.926431 0.00710475 0.0209772 0 903951 0 00601258 0.0224154 0 874771 0 00508973 0.0238536 0 852858 0 00497113 0.0252918 0 814447 0 00488254 0.0267299 0 786807 0 00621834 0.0281681 0 764362 0 00503159 0.0296063 0 728444 0 00473319 0.0310445 0 715133 0 00407554 0.0324826 0 689458 0 00290202 0.0339208 0 673741 0 00323363 0.035359 0.643885 0.00306539 0.0367972 0.62527 0.00308635 0.0382354 0.607309 0.00260789 0.0396735 0.577026 0.00250923 0.0411117 0.559098 0.00284009 0.0425499 0.539921 0.00270961 0.0439881 0.517847 0.00237405 0.0454262 0.498033 0.00242969 0.0468644 0.479202 0.00216011 0.0483026 0.46049 0.00254124 0.0497408 0.442897 0.00241848 0.051179 0.430697 0.00202251 0.0526171 0.410743 0.00230559 0.0540553 0.396025 0.00210054 0.0554935 0.380624 0.00223789 0.0569317 0.362036 0.00205874 0.0583698 0.351014 0.002059 0.059808 0.336265 0.00196403 0.0612462 0.324684 0.00208857 0.0626844 0.311476 0.00170515 0.0641225 0.299744 0.00185129 0.0655607 0.290324 0.00174539 0.0669989 0.276878 0.00176257 0.0684371 0.267973 0.00167985 0.0698753 0.255922 0.00181061 0.0713134 0.245727 0.00178832 SAXS - output Low resolution structure SAXS data 0 0.1 0.2 q [1/Ä] 0.3 Data-collection parameters Instrument BioSAXS-1000 (Rigaku) Wavelength [A] 1.5418 q range [A~-l] 0.0095 - 0.65 Exposure time [min] 60 Temperature [°C] 4 Concentration [mg ml^-1] 5.0 Structural parameters Rg [A] (from Guinier) 18.163 Rg [A] (from P(r) 18.85 Dmax [A] 62.21 Porod volume estimate [A~3] 15417 MW theoretical [kDa] 9.4 MW porod [kDa] 9.4 MW dammin [kDa] 10.5 SAXS - output Low resolution structure SAXS table SAXS data 0.2 q [1/A] reconstruction 0.3 Data-collection parameters Instrument BioSAXS-1000 (Rigaku) Wavelength [A] 1.5418 q range [A~-l] 0.0095 - 0.65 Exposure time [min] 60 Temperature [°C] 4 Concentration [mg ml^-1] 5.0 Structural parameters Rg [A] (from Guinier) 18.163 Rg [A] (from P(r) 18.85 Dmax [A] 62.21 Porod volume estimate [A~3] 15417 MW theoretical [kDa] 9.4 MW porod [kDa] 9.4 MW dammin [kDa] 10.5 Rigid body modeling 'experimental_data' 'coral_model_no-1' SAXS model fit 0.1 0.2 q [A ] 0.3 SAXS - output Low resolution structure ATOM 1 N ILE A 4 -36 .360 17 .558 21 .748 1 .00 20 .00 ATOM 2 CA ILE A 4 -36 .096 16 .392 22 .585 1 .00 20 .00 ATOM 3 C ILE A 4 -35 .687 16 .837 23 .988 1 .00 20 .00 ATOM 4 0 ILE A 4 -34 .781 17 .649 24 . 159 1 .00 20 .00 ATOM 5 CB ILE A 4 -35 .027 15 .488 21 .933 1 .00 20 .00 ATOM 6 CGI ILE A 4 -35 .563 14 .881 20 .645 1 .00 20 .00 ATOM 7 CG2 ILE A 4 -34 .584 14 .383 22 .884 1 .00 20 .00 ATOM 8 CD1 ILE A 4 -34 .500 14 .135 19 .847 1 .00 20 .00 ATOM 9 N GLY A 5 -36 .348 16 .278 25 .000 1 .00 20 .00 ATOM 10 CA GLY A 5 -36 . 166 16 .769 26 .356 1 .00 20 .00 ATOM 11 C GLY A 5 -34 .790 16 .441 26 .907 1 .00 20 .00 ATOM 12 0 GLY A 5 -34 .256 15 .350 26 .703 1 .00 20 .00 ATOM 13 N THR A 6 -34 .216 17 .399 27 .635 1 .00 20 .00 ATOM 14 CA THR A 6 -32 .917 17 .203 28 . 259 1 .00 20 .00 ATOM 15 C THR A 6 -33 .002 16 .952 29 .758 1 .00 20 .00 ATOM 16 0 THR A 6 -31 .999 16 .560 30 .359 1 .00 20 .00 ATOM 17 CB THR A 6 -32 .014 18 .421 28 .013 1 .00 20 .00 ATOM 18 CG2 THR A 6 -31 .912 18 .722 26 .539 1 .00 20 .00 ATOM 19 0G1 THR A 6 -32 .570 19 .559 28 .685 1 .00 20 .00 ATOM 20 N GLY A 7 -34 . 162 17 .186 30 .377 1 .00 20 .00 ATOM 21 CA GLY A 7 -34 .280 17 .005 31 .806 1 .00 20 .00 ATOM 22 C GLY A 7 -34 .519 15 .562 32 . 194 1 .00 20 .00 ATOM 23 0 GLY A 7 -34 .870 14 .716 31 .368 1 .00 20 .00 ATOM 24 N PHE A 8 -34 .320 15 .295 33 .486 1 .00 20 .00 ATOM 25 CA PHE A 8 -34 .561 13 .987 34 .094 1 .00 20 .00 ATOM 26 C PHE A 8 -35 .542 14 .179 35 .247 1 .00 20 .00 ATOM 27 0 PHE A 8 -35 . 138 14 .249 36 .417 1 .00 20 .00 SAXS - output Low resolution structure ATOM 1 N ILE A 4 -36 .360 17 .558 21 .748 1 .00 20 .00 ATOM 2 CA ILE A 4 -36 .096 16 .392 22 .585 1 .00 20 .00 ATOM 3 C ILE A 4 -35 .687 16 .837 23 .988 1 .00 20 .00 ATOM 4 0 ILE A 4 -34 .781 17 .649 24 . 159 1 .00 20 .00 ATOM 5 CB ILE A 4 -35 .027 15 .488 21 .933 1 .00 20 .00 ATOM 6 CGI ILE A 4 -35 .563 14 .881 20 .645 1 .00 20 .00 ATOM 7 CG2 ILE A 4 -34 .584 14 .383 22 .884 1 .00 20 .00 ATOM 8 CD1 ILE A 4 -34 .500 14 .135 19 .847 1 .00 20 .00 ATOM 9 N GLY A 5 -36 .348 16 .278 25 .000 1 .00 20 .00 ATOM 10 CA GLY A 5 -36 . 166 16 .769 26 .356 1 .00 20 .00 ATOM 11 C GLY A 5 -34 .790 16 .441 26 .907 1 .00 20 .00 ATOM 12 0 GLY A 5 -34 .256 15 .350 26 .703 1 .00 20 .00 ATOM 13 N THR A 6 -34 .216 17 .399 27 .635 1 .00 20 .00 ATOM 14 CA THR A 6 -32 .917 17 .203 28 . 259 1 .00 20 .00 ATOM 15 C THR A 6 -33 .002 16 .952 29 .758 1 .00 20 .00 ATOM 16 0 THR A 6 -31 .999 16 .560 30 .359 1 .00 20 .00 ATOM 17 CB THR A 6 -32 .014 18 .421 28 .013 1 .00 20 .00 ATOM 18 CG2 THR A 6 -31 .912 18 .722 26 .539 1 .00 20 .00 ATOM 19 0G1 THR A 6 -32 .570 19 .559 28 .685 1 .00 20 .00 ATOM 20 N GLY A 7 -34 . 162 17 .186 30 .377 1 .00 20 .00 ATOM 21 CA GLY A 7 -34 .280 17 .005 31 .806 1 .00 20 .00 ATOM 22 C GLY A 7 -34 .519 15 .562 32 . 194 1 .00 20 .00 ATOM 23 0 GLY A 7 -34 .870 14 .716 31 .368 1 .00 20 .00 ATOM 24 N PHE A 8 -34 .320 15 .295 33 .486 1 .00 20 .00 ATOM 25 CA PHE A 8 -34 .561 13 .987 34 .094 1 .00 20 .00 ATOM 26 C PHE A 8 -35 .542 14 .179 35 .247 1 .00 20 .00 ATOM 27 0 PHE A 8 -35 . 138 14 .249 36 .417 1 .00 20 .00 ATOM 1 CA ASP 1 0 .778 -0 .275 -0 .227 1 .00 20 .00 ATOM 2 CA ASP 1 -7 .972 1 .475 12 . 148 1 .00 20 .00 ATOM 3 CA ASP 1 9 .528 -5 .525 -12 .601 1 .00 20 .00 ATOM 4 CA ASP 1 13 .028 -5 .525 -12 .601 1 .00 20 .00 ATOM 5 CA ASP 1 -0 .972 15 .475 7 . 198 1 .00 20 .00 ATOM 6 CA ASP 1 11 .278 6 .725 14 .623 1 .00 20 .00 ATOM 7 CA ASP 1 9 .528 8 .475 12 . 148 1 .00 20 .00 ATOM 8 CA ASP 1 -14 .972 1 .475 -2 .701 1 .00 20 .00 ATOM 9 CA ASP 1 -6 .222 -0 .275 14 .623 1 .00 20 .00 ATOM 10 CA ASP 2 11 .278 -3 .775 -15 .076 1 .00 20 .00 ATOM 11 CA ASP 2 2 .528 -2 .025 2 .248 1 .00 20 .00 ATOM 12 CA ASP 2 2 .528 15 .475 7 . 198 1 .00 20 .00 ATOM 13 CA ASP 2 -6 .222 3 .225 14 .623 1 .00 20 .00 ATOM 14 CA ASP 2 11 .278 13 .725 -5 . 176 1 .00 20 .00 ATOM 15 CA ASP 2 0 .778 17 .225 4 .723 1 .00 20 .00 ATOM 16 CA ASP 2 -14 .972 4 .975 -2 .701 1 .00 20 .00 ATOM 17 CA ASP 2 -16 .721 3 .225 -0 .227 1 .00 20 .00 ATOM 18 CA ASP 2 7 .778 -3 .775 -15 .076 1 .00 20 .00 ATOM 19 CA ASP 2 16 .529 4 .975 -2 .701 1 .00 20 .00 ATOM 20 CA ASP 3 0 .778 13 .725 4 .723 1 .00 20 .00 ATOM 21 CA ASP 3 -7 .972 1 .475 17 .098 1 .00 20 .00 ATOM 22 CA ASP 3 7 .778 6 .725 14 .623 1 .00 20 .00 ATOM 23 CA ASP 3 -2 .722 13 .725 4 .723 1 .00 20 .00 ATOM 24 CA ASP 3 11 .278 -7 .275 -15 .076 1 .00 20 .00 ATOM 25 CA ASP 3 9 .528 -9 .025 -12 .601 1 .00 20 .00 ATOM 26 CA ASP 3 -13 .222 3 .225 -0 .227 1 .00 20 .00 SAXS curve - averaged data - SAXS data SAXS profil scattering vector, momentum transfer: s = q [nm } Á"1] SAXS - application Sample: solution of proteins, nucleic acids, and complexes 1. size 2. shape 3. homogenous vs. aggregated sample 4. folded vs. flexible protein 5. oligomeric state (mixtures) 6. interaction, quarternary structure 7. modeling of flexible systems SAXS - advantages 1. sample preparation 2. in solution - close to ^natural conditions" 3. usefull before and after molecular structure is known 4. time consumption 5. not limited by size or flexibility (almost) SAXS - disadvantages 1. low resolution 2. non unambiguous interpretation SAXS - resolution 1. Bragg * s = 0.006 Ä"1 ~ d = 1000 Ä = 0.6 Ä-1 ~ d = 10 Á 2. Efective low resolution structure" 20—30 A SAXS - experiment - home source 1 ■ - rotating anode - point focus - colimation: 2D Kratky - Pilatus 100K - temperature range -30 to +65°C SAXS - experiment - home source Data-collection parameters Instrument BioSAXS-1000 (Rigaku) Wavelength [A] 1.5418 q range [A^-l] 0.0095 - 0.65 Exposure time [min] 60 Temperature [°C] 4 Concentration [mg ml^-1] 5.0 Structural parameters Rg [A] (from Guinier) Rg [A] (from P(r) Dmax [A] Porod volume estimate [A~3] MW theoretical [kDa] 9.4 MW porod [kDa] MW dammin [kDa] SAXS - experiment - sample Sample quality: - pure as possible - monodisperse - free of aggregation SAXS - experiment - sample Sample quality: - pure as possible - monodisperse - free of aggregation Quality control: - native gels - DLS kDa 66 45 36 29 24 20 B 14 buffer 1 buffer 2 SAXS - experiment - sample Sample quality: - pure as possible - monodisperse - free of aggregation Quality control: - native gels - DLS kDa 66 45 36 29 24 20 B mtiMtNJ 14 buffer 1 buffer 2 Sample volume and concentration: - -25 microL - concentration series 10; 5; 2.5 mg/ml Forward scattering intensity is proportional to size (number of electrons): 15 kDa protein needs 2.0 mg/ml 300 kDa protein ............... 0.1 mg/ml => Aggregates ruins meaningful data interpretation SAXS - subtraction SAXS - buffer Buffer requirements: - identical to last step of purification (dialysis) - salt < 1 M - glycerol < 5% v/v - detergents < CMC Matching buffer = no oversubtraction or undersubtraction 'sample.dat' 'buffer.dat' q [A"1] SAXS - buffer Buffer requirements: - identical to last step of purification (dialysis) - salt < 1 M - glycerol < 5% v/v - detergents < CMC Matching buffer = no oversubtraction or undersubtraction SAXS - buffer Buffer requirements: - identical to last step of purification (dialys - salt < 1 M - glycerol < 5% v/v - detergents < CMC Matching buffer = no over- or under-subtraction 'sample.dat' 0 0.1 0.2 0.3 0.4 0.5 q [A"1] SAXS - buffer Buffer requirement:s: - identical to last step of purification (dialysis) - salt < 1 M - glycerol < 5% v/v - detergents < CMC Matching buffer = no over- or under-subtraction SAXS - buffer Buffer requirements: - identical to last step of purification (dialysis) - salt < 1 M - glycerol < 5% v/v - detergents < CMC Matching buffer = no over- or under-subtraction 0.1 0.2 0.3 'sample.dat' 'buffer.dat' 'over_buffer.dat' 'under_buffer.dat' 0.4 q[A-1] 0.5 Subtracted SAXS data Guinier plot analysis of very low angle slope of decay proportional to size (Rg) Rg = radius of gyration aggregation/repulsion detection q \\ M / ' \ i cm > 3 —R2 2 ln[l(q)]-ln[l(0)]exp(— Valid in: 0.001 0 AT5A5 software + Group members - ATSAS software Download BUNCH CORAL CRYSOL CRYSON DAM AVER DAMMIF DAMMIN DATtools EOM GASBQR GLOBSYMM GNOM MASSHA MIXTURE MONSA OLIGOMER PEAK PRIMUS SASFLOW 5A5REF SREFLEX SUPCOMB Manuals + Web services ±1 Facilities + Courses Contact us Biological Small Angle Scattering Data analysis software ATSAS 2.8.0 A program suite lor small-angle scattering data analysis from biological macromolecules Data processing PRIMUS - manipulations with experimental ID SAS data GNOM - indirect transform program that evaluates the particle distance distribution function p(r) Data manipulation and anaryais tools - AUTORG. ALMERGE. DATGNOM. DATPOROD etc. Ab initio methods DAMMIN - ab initio shape determination using a dummy atom model DAMMIF - rapid shape determination GAS-BOR - reconstruction of a protein structure by a chain-like ensemble of dummy residues MONSA - shape determination using a multiphase dummy atom model Rigid body modelling SASREF - modelling of multisubunit complexes BUNCH - modelling of multidomain proteins against multiple data sets CORAL - modelling of multidomain protein complexes against multiple data sets MASSHA - interactive modelling of atomic structures and shape analysis GLOBSYMM - rigid body modelling of symmetric oligomers Mixtures and flexible systems OLIGOMER - volume fractions of mixtures with known scattering intensities from the components MIXTURE - modelling of rnulticornponent systems EOM - Ensemble Optimization Method for flexible proteins SREFLEX - flexible refinement of high-resolution models combining SAXS and NMA PDB oriented tools CRYSOL - X-ray scattering patterns from known hires structures CRYSON - neutron scattering patterns from known hi-res structures SUPCQMB - superimposes one 3D structure onto another DAM AVER - align ab initio models, select the most typical one Manuals If you use ATSAS please cite: Petoukhov, M.V., Franke, D., Shkumatov, A.V., Tria, G., Kikhney, A.G., Gajda, M., Gcrba, C, Mertens, H.D.T., Konarev, P.V. and Svergun, D.I, (2012) New developments in the ATSAS r-^gir-.v package for small-angle scattering data analysis 1 Appl. Cryst. 45, 342-350 International Union of Crystallography DPI SAXS Small Angle X-ray Scattering Initiative for Europe:: Forum J] Login 0 Register View unanswered posts. | View active topics Board index Forum General <§> Announcements Courses and workshops, new software releases @ SAS Hardware/Instrumentation Detectors, sample changers, home sources, nanomanipulation tools, add-ons [Raman spectrometer. HPLC}. gas phase scattering etc. @ SAS Experiment Design Planyoui small angle X-ray oi neutron scattering measurements @ Literature Books and reviews on small angle scattering. Discussions and criticism on recent SAXS papers. @ Feedback Suggestions for new topics to discuss, questions an the use of the Forum ATSAS <§> FAQ Frequently Asked Questions about ATSAS small-angle scattering analysis program package @ ATSAS Package in General ATSAS for Linux and Mac, general installation issues, ATSAS online etc. Primary Data Processing 1 nteractrve and automated data processing tools [PRIMUS, GNOM. AUTORG}. Scattering from simple bodies (BODIES), peak analysis (PEAK), data plotting (SASPLOT) etc. @ AO Initio Shape Determination Ab initio modelling: DAMMIF. DAMMIN. GASEOR. MONSA @ Rigid Body Modelling Interactive modelling [MASSHA, SASpy) and global minimization programs [SASREF, BUNCH, CORAL, GLOBSYMM} @ Mixtures and Flexible Systems Linear {OLIGOMER), and non-linear (MIXTURE) analysis, singular value decomposition (SVDPLOT), addition of missing fragments [BUNCH, COPAL), analysts af flexible systems (EOWRAN models (SREFLEX) Working with Models Calculation of SAXS and SANS profiles (CRYSOL. CRYSON). superposition of models (SUPCCMB. DAMAVER, DAMCLUST). database DARA Other Software @ SAXS & SANS Software Small angle scattering software (except ATSAS) mod I ?c: October E. 2015 De ?re &II I: care coc <. es | The learn Pnj*rrl inrlr=--, ATSAS software lUCtTuJlTJi UM £ KYI-TALL CK. ■.. ^- ■¥ G Ö " Secure | https://www.embl-hamburg.de/biosan5/software.htrnl EMBL •I1 Home > AT5A5 software + Group members - ATSAS software Download BUNCH CORAL CRYSOL CRYSON DAM AVER DAMMIF DAMMIN DATtools EOM GASBOR GLOBSYMM GNOM MASSHA MIXTURE MONSA OLIGOMER PEAK PRIMUS SASFLOW 5A5REF SREFLEX SUPCOMB Manuals + Web services + Facilities + Courses Contact us Biological Small Angle Scattering Small Angle X-Ray and Neutron Scattering from Solutions of Biological M acromol ecu les Data analysis software ATSAS 2.8.0 A program suite lor small-angle scattering data analysis from biological Data processing PRIMUS ■ manipulations with experimental ID SAS data GNOM - ind irect transform prog rarn that evaluates the particle distance distribution functio Data manipulation and analysis tools - AUTORG. ALMERGE. DATGNOM. DATPOROD et Ab initio methods DAMMIN - ab initio shape determination using a dummy atom model DAMMIF - rapid shape determination GASBQR - reconstruction of a protein structure by a chain-like ensemble of dummy residul MDNSA - shape determination using a multiphase dummy atom model Rigid body modelling SASREF - modelling of multisubunit complexes BUNCH - modelling of multidomain proteins against multiple data sets CORAL - modelling ol multidomain protein complexes against multiple data sets MASSHA - interactive modelling of atomic structures and shape analysis GLOBSYMM - rigid body modelling of symmetric oligomers Mixtures and flexible systems OLIGOMER - volume fractions of mixtures with known scattering intensities from the components MIXTURE - modelling of rnulticornponent systems EOM - Ensemble Optimization Method for flexible proteins SREFLEX - flexible refinement of high-resolution models combining SAXS and NMA PDB oriented tools CRYSOL - X-ray scattering patterns from known hires structures CRYSON - neutron scattering patterns from known hi-res structures SUPCQMB - superimposes one 3D structure onto another DAM AVER - align ab initio models, select the most typical one Manuals If you use ATSAS please cite: Petoukhov, M.V., Franke, D., Shkumatov, A.V., Tria, G., Kikhney, A.G., Gajda, M., Gcrba, C, Mertens, H.D.T., Konarev, P.V. and Svergun, D.I, (2012) New developments in the ATSAS jycciK-.v package for small-angle scattering data analysis 1 Appl. Cryst. 45, 342-350 International Union of CrystalIngraphy DOJ M FÜR MOLEKULARBIOLOGIE [DE] | https://www.saxier.org/fcrum/ SAXS Small Angle X-ray Scattering Initiative for Europe:: Forum ip.iarian toob add-o-is (Rair&r s|:;c:-on-?:;r. HP.Ci. caz ph&isE scattering etc. ns and criticism on recent SAXS papers. e j&eof the Forjm scattering analysis program package ATSAS Package in General ATSAS for Linux arid Mac, general installation issues, ATSAS online etc. (§> Primary Data Processing 1 nteractive and a n to mated data processing tools [PRIMUS, GNOM, AUTORG). Scattering fiom simple bodies (BODIES), peak analysis (PEAK), data plotting (SASPLOT) etc. @ AO Initio Shape Determination Ab initio modelling: DAMMIF. DAMMIN. GASEOR. MONSA @ Rigid Body Modelling Interactive modelling [MASSHA, SASpy) and global minimization programs [SASREF, BUNCH, CORAL, GLOBSYMM} @ Mixtures and Flexible Systems Linear {OLIGOMER), and non-linear (MIXTURE) analysis, singular value decomposition (SVDPLOT), addition of missing fragments [BUNCH, COPAL), analysts of flexible systems (EOMrRAN models (SREFLEX) <§> Working with Models Calculation of SAXS and SANS profiles (CRYSOL. CRYSON). superposition of models (SUPCCMB. DAMAVER, DAMCLUST). database DARA Other Software @ SAXS & SANS Software Small angle scattering software (except ATSAS) mod I ec: October E. 2015 De ?re ^|| |; care cqc <. es | The learn Finn rrl inrlr=.-, SAXS - theoretical scattering CRYSOL — evaluation of solution scattering of known atomic structure — fitting to experimental data — validation tool 0 0.1 0.2 q[A"1] 0.3 https://www.embl-hamburg.de/biosaxs/reprints/crysol_1995.pdf SAXS - theoretical scattering CRYSOL — evaluation of solution scattering of known atomic structure — fitting to experimental data — validation tool https://www.embl-hamburg.de/biosaxs/reprints/crysol_1995.pdf SAXS - theoretical scattering CRYSOL https://www.embl-hamburg.de/biosaxs/reprints/crysol_1995.pdf SAXS - theoretical scattering CRYSOL l{q)=(\Aa{q)-psAs{q)^PbAb{q)\2 2_J_y JexP(Rk)-C-Icalc(qk,r0bp) 2 ±y n k=l 'theoretical' 'in_vacuo' solvent_scattering' 'bo rd e Mayer' 'experimental' 0.1 0.2 q [A ] 0.3 https://wvwv.embl-hamburg.de/biosaxs/reprints/crysol_1995.pdf SAXS - modeling final model (ab initio, rigid body) Ab initio modeling dummy residues - GASBOR — low resolution shape reconstruction — dummy residues: spheres with electron density as average 7AA resudue — distance constrain 3.8 A as approx. Ca-Ca position — fixed number of dummy residues (protein sequence) initial model final model 0 01 — simulated annealing method to minimize goal function: f(x) = x2+^aP(x) — penalties: bond length, hidtogram distances, peripherial, discontiguity Ab initio modeling dummy residues - GASBOR initial model Ab initio modeling dummy atoms - DAMMIN low resolution shape reconstruction dummy atoms - densely packed spheres (beads) search volume ~ Dmax, radius of beads « Dmax two phases: solute (protein) and solvent (water) Ab initio modeling dummy atoms - DAMMIN — low resolution shape reconstruction - dummy atoms - densely packed spheres (beads) — search volume ~ Dmax, radius of beads « Dmax - two phases: solute (protein) and solvent (water) 'initial_model' 'experimental' 0 0.1 q[A"1] 0.2 Ab initio modeling dummy atoms - DAMMIN - low resolution shape reconstruction - dummy atoms — densely packed spheres (beads) - search volume ~ Dmax, radius of beads « Dmax - two phases: solute (protein) and solvent (water) 'initial_model' 'experimental' Afo initio multi-phase modeling dummy atoms - MONSA - low resolution shape reconstruction - dummy atoms - densely packed spheres (beads) - search volume ~ Dmax, radius of beads « Dmax - up to 4 phases: protein-protein complexes, protein::nucleic acid complexes Ab Initio multi-phase modeling dummy atoms - MONSA - low resolution shape reconstruction - dummy atoms - densely packed spheres (beads) - search volume ~ Dmax, radius of beads « Dmax - up to 4 phases: protein-protein complexes, protein::nucleic acid complexes Ab initio modeling refinement - mutiple runs of ab initio reconstruction give different results - refinement: alignment, averaging, clustering, most typical model - dummy atoms/res. with highest , occupancy11 used as starting structure lecommendat ion NSD File Include 0. .735 dammif3 .pdb Include 0. .739 dammif1 .pdb Include 0. .739 dammif8 .pdb Include 0. .740 dammif4 .pdb Include 0. .750 dammif9 .pdb Include 0. .752 dammif7 .pdb Include 0. .754 dammif l1 O.pdb Include 0. .756 dammif6 .pdb Include 0. .756 dammif2 .pdb Discard 0. .851 dammif5 .pdb damaver damfilt damstart Rigid body modeling CORAL — Complexes with Random Loops — translation and rotation search — library of random loops composed of dummy residues (5—100AA) — contact constrains, if known — penalties: clashes, shift, contacts complex Rigid bodies - atomic structures Rigid body modeling CORAL — Complexes with Random Loops — translation and rotation search — library of random loops composed of dummy residues (5—100AA) — contact constrains, if known — penalties: clashes, shift, contacts complex Rigid bodies - atomic structures Simulated annealing Aim: find vector of M variables minimizing a function f (x) 1. start from random configuration x at high temperature T 2. make a small random modification of configuration x -* and compute the difference A=f (x11) -F (x) ^ 3. if A>0, accept it with probability e"A/T § 4. make another step from previous configuration g> if previous step was rejected or from new configuration, if was accepted 5. repeat 2-4 many times, then decrease the temperature 6. continue the cooling until no improvement is observed o Flexible systems Conformational polydispersity Fully or partialy unstructured chains - conformational polydispersity - fully/partialy unstructured chains - ensemble modeling (selection) -multidomain proteins with flexible linkers, IDPs 0 0.1 0.2 Ensemble modeling KOM POOL EOM ALGORITHM CCHROMOSOMES RANDOM SELECTIO 15 20 25 30 35 40 45 L L k_ L. □ E EjUTISf^ □ □ □ QUANTITATIVE STRUCTURAL INFORMATION STRUCTURAL ANALYSIS <-► R EOM RUNS V L. □ □ L. □ □ □ □ DECONVOLUTION 15 20 25 30 35 40 45 Rg(A) https://www.embl-hamburg.de/biosaxs/eorri.htiTil Ensemble modeling KOM ensemble representation of possible flexibility model conformations not necessarily exists in solution 05 Rg and Dmax distribution of pool and selected ensemble i -1.5 -2 -2.5 ........I...... 0.05 prof iles_004_1 .fit 37% 33% 21% 19% SEC-SAXS EMBL :; Biological *!*;• Small Angle Scattering Home > ATSAS software ±1 Group members - ATSAS software Download BUNCH CORAL CRYSOL CRYSON DAMAVER DAMMIF DAMMIN DATtools EOM GASBOR GLOBS YMM GNOM MASSHA MIXTURE MONSA OLIGOMER PEAK PRIMUS SASFLOW SASREF SREFLEX SUPCOMB Manuals + Web services + Facilities + Courses Contact us Data analysis software ATSAS 2.8.0 A program suite for small-angle scattering data analysis from biological macromolecules Data processing PRIMUS - manipulations with experimental ID SAS data GNOM - indirect transform program that evaluates the panicle distance distribution function p(r) Data manipulation and analysis tools - AUTORG, ALMERGE. DATGNOM. DATPOROD etc. Ab initio methods DAMMIN - ab initio shape determination using a dummy atom model DAMMIF - rapid shape determination GASBOR - reconstruction of a procein structure by a chain-like ensemble of dummy residues MDNSA - shape determination using a multiphase dummy atom model Rigid body modelling SASREF - modelling of multisubunit complexes BUNCH - modelling of multidomain proteins against multiple data sets CORAL - modelling of multidomain procein complexes against multiple data sets MASS HA - interactive modelling of atomic structures and shape analysis GLOBS YMM - rigid body modelling of symmetric oligomers Mixtures and flexible systems OLIGOMER - volume fractions of mixtures with known scattering intensities from the components MIXTURE - modelling of multicomponent systems EOM - Ensemble Optimization Method for flexible proteins SREFLEX - flexible refinement of high-resolution models combining SAXS and NMA PDB oriented tools CRYSOL - X-ray scattering patterns from known hi-res structures CRYSON - neutron scattering patterns from known hi-res structures SUPCOMB - superimposes one 3D structure onto another DAM AVER - align ab initio models, select the most typical one Manuals If you use ATSAS please cite: Petoukhov, M.V, Franke, D., Shkumatov, A.V, Tria, G., Kikhney, A.G., Gajda, M., Gorba, C, Mertens, H.D.T, Konarev, P.V. and Svergun, D.I. (2012) New developments in the ATSAS program package for small-angle scattering data analysis SASBDB Sign in 1 Register Search Small Angle Scattering Biological Data Bank advanced search E.g. SASDBF4, Lyz, Nucleic Acids Res Home Browse Submit data About SASBDB Help Curated repository for small angle scattering data and models Small angle scattering [SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm. SASBDB is a fully searchable curated repository of freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data. Recent depositions: SASBDB currently contains: 1262 experimental data sets 1892 node s 428 experimental ds:a sea on hold 565 models on hold SASDGB6 - Resistance to inhibitors of Cholinesterase 8 homolog A (RicSA) miniGi complex Sample: Resistance to inhibitors of Cholinesterase 8 homolog A monomer, 56 kDa Bos taurus protein MiniGi monomer, 25 kDa synthetic construct protein Buffer: 20 mM Tris, 150 mM KCl, 5 % glycerol, 1 mM TCEP. pH: 8 Experiment: SAXS data collected at BioCAT IBID, Advanced Photon Source (APS), Argonne National Laboratory on 2018 Oct 27 Large-scale conformational rearrangement of the «5-helix of Get subunits in complex with the guanine nucleotide exchange factor RicSA. J Biol Cfiem [2019) Srivastava D. Artemyev NO RgGuiniEr 3.2 nm DmaI 10.7 nm SASDG7S - Inhibitor of aptv ě% Flexible Tethering of ASPP F SASDGJ4 - Human alplia- i Sinn I,! Structural Analysis of Pathcq- SASDFB6 - The periplasmk SASDDR3 - Yeast IRMA Ni #51 SASDFLS - Plasnnodi' Protease-associ ated Structure of tRNA melhyltran Structural studies oftfie Hspj ' Browse the contents according to: Organism Macromolecule type Model type Dissemination type To cite SASBDB refer to: Valentini E, Kikhney AG, Previtali G. Jeffries CM, Suergun Dl. SASBDB, a repository for biological small-angle scattering data, rtucieic Acids Res. 2015 Jan 2fl;43:D357-63. '■ SASBDB 2014-2M9 Combination of SAXS and Protein Painting Discloses the Three-Dimensional Organization of the Bacterial Cysteine Synthase Complex, a Potential Target for Enhancers of Antibiotic Action Rosa B. Marchetti M, Paredi G, Amenitsch H, Franko N, Benoni R, Giabbai B, De Marino M, Mozzarelli A, Renda L, Storici P. Campanini B, Bettati S. International Journal of Molecular Sciences 20(20):5219 (2019) DOI SASDGW6 - Serine acetyltransferase Serine acetyltransferase log i(s) 1.91*10' ^^experimental 189 kDa yyyexpected 177 kDa ypwod 280 in Vs In l(s) (sRg)^l(S)/l(0) P(0 ■■ ■■.....I t r I ." p" " vi s, nm -i Fits and models log l(s) - \" ■ L I 1' 1 i i ■ ■ 0 s, nm" Synchrotron SAXS data from solutions of serine acetyltransferase in 20 mM sodium phosphate, 85 mM NaCf, 2 mM EDTA, 10 mM 2-MCE, pH 7.5 were collected on the Austrian SAXS oeamline 5.2L beam line at the ELETTRA - Sincrotrone Trieste storage ring {Trieste, Italy) using a Dectris / Pila(us3 1M detector at a wavelength of A = 0.154 nrn (l(s) vs s, where s = 4nsin9A, and 26 is the scattering angle}. Solute concentrations Tanging between 0.5 and 1.5 mg/ml were measured al 20°C. 12 successive 10 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged: the scattering of the solvent-blank was subtracted. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve. Serine acetyltransferase (CysE) Mol. type Protein Organism Escherichia coli K-12 Ol ig. state Hexamer Mon. MW 29.4 fcDa UniProt P0A9D4 [2-273) Sequence FASTA Structure and dynamics of the RNAPII CTDsome with Rttl03. Jasnovidova O, Klumpler T, Kubicek K, Kalynych S, Plevka P, Stefl R. Proc Natl Acad SciUSA 114(42):11133-11138 (2017) Europe PMC Download files ■ SASDCZ2 - Yeast CTDsome: transcription termination factor Rttl03p/C-terminal domain of DNA-directed RNA polymerase II subunit RPB1 (Rttl03 1-246-phospho-mimetic complex) Regulator of Tyl transposition protein 103 DNA-directed RNA polymerase II subunit RPB1 0 1 2 3 4 5 6 log l(s) s, nnr SAXS data from solutions of Rttl03 1-246-phospho-mimetic complex in 25 ooM KH2P04. 300 mM KCI, 10 mM p-mercaptoethanol. pH 6.5 were collected using a BioSAXS-1000 inslnjrnent at CEITEC (Brno. Czech Republic) equipped with a Pilatus 10OK detector at a sample-detector distance of 0.5 m and at a wavelength of X = 0.154 nm (l(s) vs s, where s = 4nsinSrt and 26 is the scattering angle). Five successive 3600 second frames were collected at a sample temperature of 4"C. The data were normalized to the intensity of the transmitted beam and radially averaged and the corresponding scattering from the solvent-blank was subtracted to produce the scattering profile displayed in this entry. Regulator of Tyl transposition protein 103 Mol. type Protein Organism Saccfraromyces cerevisiae (strain ATCC 204508 / 3288c) Ol ig. state Dimer Men. MW 28.6 kDa bioSAXS - summary With good quality SAXS data: 1. model independent: integral structural parameters: Rg, Dmax, Vporod agregation, folding/flexibility overal shape aib initio 2. model dependent: validation of molecular structures (XRD, MMR, molecular dynamics, docking) oligomeric state, mixtures quaternary structere missing parts in XRD structures study of flexible systems