Software | Name | Version | Classification |
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REFMAC | 5.2.0005refinementDENZO | | data reduction CCP4 | (SCALA)data scalingDM | | phasing | | | | | |
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Refinement | Method to determine structure: SAD / Resolution: 2→49.94 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.326 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.24753 | 1198 | 5.1 % | RANDOM |
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Rwork | 0.21706 | - | - | - |
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obs | 0.21866 | 22474 | 99.04 % | - |
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all | - | 37807 | - | - |
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK |
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Displacement parameters | Biso mean: 25.866 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.8 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 1.36 Å2 | 0 Å2 |
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3- | - | - | -0.56 Å2 |
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Refine analyze | Luzzati sigma a obs: 0.287 Å |
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Refinement step | Cycle: LAST / Resolution: 2→49.94 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 1822 | 0 | 23 | 224 | 2069 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Dev ideal target | Number |
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X-RAY DIFFRACTION | r_bond_refined_d0.018 | 0.021 | 1886 | X-RAY DIFFRACTION | r_bond_other_d | | | X-RAY DIFFRACTION | r_angle_refined_deg1.623 | 1.914 | 2545 | X-RAY DIFFRACTION | r_angle_other_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.613 | 5 | 227 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg35.749 | 23.229 | 96 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg16.898 | 15 | 307 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg27.359 | 15 | 16 | X-RAY DIFFRACTION | r_chiral_restr0.116 | 0.2 | 278 | X-RAY DIFFRACTION | r_gen_planes_refined0.007 | 0.02 | 1430 | X-RAY DIFFRACTION | r_gen_planes_other | | | X-RAY DIFFRACTION | r_nbd_refined0.264 | 0.2 | 964 | X-RAY DIFFRACTION | r_nbd_other | | | X-RAY DIFFRACTION | r_nbtor_refined0.306 | 0.2 | 1269 | X-RAY DIFFRACTION | r_nbtor_other | | | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.201 | 0.2 | 173 | X-RAY DIFFRACTION | r_xyhbond_nbd_other | | | X-RAY DIFFRACTION | r_metal_ion_refined | | | X-RAY DIFFRACTION | r_metal_ion_other | | | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.313 | 0.2 | 66 | X-RAY DIFFRACTION | r_symmetry_vdw_other | | | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.323 | 0.2 | 27 | X-RAY DIFFRACTION | r_symmetry_hbond_other | | | X-RAY DIFFRACTION | r_symmetry_metal_ion_refined | | | X-RAY DIFFRACTION | r_symmetry_metal_ion_other | | | X-RAY DIFFRACTION | r_mcbond_it1.185 | 1.5 | 1139 | X-RAY DIFFRACTION | r_mcbond_other | | | X-RAY DIFFRACTION | r_mcangle_it2.09 | 2 | 1828 | X-RAY DIFFRACTION | r_scbond_it3.24 | 3 | 771 | X-RAY DIFFRACTION | r_scangle_it5.161 | 4.5 | 717 | X-RAY DIFFRACTION | r_rigid_bond_restr5.556 | 3 | 1930 | X-RAY DIFFRACTION | r_sphericity_free5.576 | 3 | 96 | X-RAY DIFFRACTION | r_sphericity_bonded2.784 | 3 | 1867 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.29 | 95 | - |
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Rwork | 0.208 | 1605 | - |
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obs | - | - | 98.61 % |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION 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) |
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1 | 66.6985 | -12.419 | -16.9838 | 20.6816 | 7.31 | 5.2612 | 0.4529 | 0.1412 | 0.111 | -0.5653 | -0.3719 | -1.023 | -0.7719 | 0.8635 | -0.0811 | 0.0998 | -0.052 | -0.0411 | 0.07 | 0.0437 | -0.0038 | 42.264 | 42.299 | 4.666 | 2 | 4.5699 | 0.6862 | 1.3746 | 13.5072 | -1.6265 | 0.6641 | 0.2587 | -0.5391 | 0.0787 | 0.3911 | -0.3728 | 0.2268 | 0.0608 | 0.1535 | 0.1141 | 0.0527 | -0.0714 | 0.0101 | 0.0066 | -0.0021 | 0.0297 | 35.071 | 42.888 | 12.917 | 3 | 7.5713 | -8.7181 | 2.4529 | 34.6456 | -3.3807 | 7.9349 | 0.3618 | -0.0006 | -0.0197 | 0.3241 | -0.3551 | -0.4462 | -0.3304 | 0.7676 | -0.0066 | 0.0002 | -0.1515 | -0.009 | 0.0677 | 0.0342 | -0.0459 | 42.326 | 39.038 | 17.965 | 4 | 7.2414 | -0.6322 | 0.2037 | 1.0158 | 2.1379 | 4.8431 | 0.1583 | -0.0969 | -0.1258 | -0.161 | -0.1873 | -0.1506 | -0.3062 | 0.3865 | 0.029 | 0.0528 | -0.0456 | -0.0298 | 0.0626 | 0.0741 | 0.0199 | 40.512 | 34.372 | 16.528 | 5 | 2.1087 | 1.6302 | -1.6011 | 3.4881 | 1.737 | 5.1878 | 0.1835 | 0.0228 | 0.007 | 0.1273 | -0.2726 | -0.2048 | 0.246 | 0.2519 | 0.0891 | 0.0428 | 0.0321 | -0.0338 | 0.028 | 0.0077 | 0.0685 | 36.992 | 25.519 | 13.355 | 6 | 0.5875 | 1.2649 | -1.1619 | 2.7237 | -2.5019 | 2.2982 | 0.0517 | 0.0694 | -0.0177 | 0.1604 | -0.2368 | 0.0572 | 0.2619 | 0.0038 | 0.1851 | 0.066 | -0.0293 | 0.0125 | 0.0025 | 0.0072 | 0.0564 | 31.872 | 21.31 | 11.534 | 7 | 0.5021 | -0.6584 | -0.6519 | 3.4273 | -1.0116 | 5.5113 | -0.0411 | 0.0336 | 0.3028 | -0.0741 | 0.0717 | 0.2088 | 0.061 | -0.6644 | -0.0306 | 0.0174 | -0.052 | 0.0074 | 0.0455 | -0.0137 | 0.0749 | 24.549 | 25.911 | 5.095 | 8 | 1.4466 | 0.4414 | -3.9525 | 3.2928 | -1.6015 | 10.8491 | -0.0227 | 0.071 | 0.0326 | -0.2282 | 0.0907 | 0.2658 | -0.0438 | -1.0607 | -0.068 | 0.0766 | -0.0008 | -0.0342 | 0.0311 | -0.0073 | 0.0385 | 27.016 | 28.816 | 0.394 | 9 | 0.0444 | 0.1869 | 0.0468 | 2.1057 | 1.4776 | 1.2923 | 0.0976 | -0.289 | -0.0739 | 0.039 | -0.3126 | 0.0124 | 0.3443 | -0.4149 | 0.215 | 0.0351 | -0.0416 | -0.0282 | 0.0573 | 0.0065 | 0.0396 | 28.374 | 30.224 | 15.702 | 10 | 1.4303 | 0.413 | -1.8162 | 4.6947 | -1.193 | 2.4038 | 0.1299 | -0.6311 | -0.0728 | -0.075 | -0.2954 | 0.1018 | -0.5011 | 0.366 | 0.1655 | 0.0644 | -0.0815 | 0.0009 | 0.0844 | 0.0165 | 0.0273 | 36.062 | 33.32 | 25.436 | 11 | 24.6781 | 11.5251 | 9.9916 | 23.8533 | -6.2872 | 28.3564 | -0.4135 | 0.0068 | 0.7006 | 2.4546 | 0.2961 | 0.6139 | -1.896 | -1.0002 | 0.1174 | 0.1967 | -0.0304 | 0.0104 | -0.0856 | -0.0134 | 0.0119 | 33.917 | 38.663 | 25.823 | 12 | 5.6933 | -3.8271 | 9.3279 | 12.493 | -15.1958 | 23.3133 | 0.1168 | 0.4767 | -0.5245 | 0.0665 | -0.1613 | -0.1253 | 0.6639 | 0.2274 | 0.0445 | 0.1389 | -0.0664 | 0.0145 | -0.0956 | -0.0375 | 0.09 | 25.711 | 16.715 | 8.731 | 13 | 15.6865 | -2.5225 | -9.5465 | 6.1138 | 0.4778 | 6.0057 | -0.4083 | 0.4533 | -0.4872 | 0.0726 | -0.0164 | -0.0318 | 0.7067 | -0.5093 | 0.4247 | 0.1133 | -0.0307 | 0.0098 | -0.0674 | -0.0089 | 0.0131 | 29.541 | 15.35 | 2.364 | 14 | 1.3916 | 0.5228 | 0.2265 | 4.2438 | 2.9759 | 2.1016 | -0.1235 | -0.2541 | -0.0289 | -0.2755 | 0.1021 | -0.042 | 0.3696 | 0.4576 | 0.0214 | 0.1113 | 0.0478 | 0.0344 | -0.0014 | 0.0134 | 0.0348 | 35.89 | 18.435 | 1.735 | 15 | 1.1686 | 2.6481 | 3.2814 | 16.7914 | 6.7108 | 9.2629 | -0.195 | 0.1118 | -0.0802 | -0.4048 | 0.2366 | -0.2463 | -0.0881 | 0.4827 | -0.0416 | 0.003 | 0.0163 | 0.0201 | 0.082 | 0.0232 | 0.0383 | 39.111 | 27.826 | 5.314 | 16 | 0.3056 | 1.7267 | -0.8867 | 9.7556 | -5.0099 | 2.5728 | -0.2868 | -0.2354 | 0.0361 | -0.201 | 0.0621 | -0.0691 | -0.4056 | 0.1163 | 0.2247 | 0.0755 | -0.0152 | 0.0007 | 0.0075 | 0.0179 | 0.0198 | 38.818 | 34.651 | 6.543 | 17 | 7.0132 | -6.2957 | -6.2517 | 6.1043 | 3.4712 | 15.6955 | 0.3766 | 0.0738 | -0.2262 | 0.0119 | -0.2046 | 0.05 | -0.6189 | -0.6475 | -0.172 | 0.0358 | -0.06 | -0.0033 | 0.0078 | 0.001 | 0.0294 | 30.62 | 37.923 | 10.213 | 18 | 0.2321 | -1.1125 | 1.8038 | 5.3329 | -8.6461 | 14.0178 | -0.082 | 0.1488 | 0.2347 | 0.4027 | 0.4914 | -0.0558 | -0.2975 | -0.5681 | -0.4093 | 0.0389 | -0.0399 | -0.0238 | 0.0494 | -0.0014 | 0.0569 | 27.9 | 34.757 | 15.807 | 19 | 0.8626 | -0.2738 | 0.9362 | 0.0869 | -0.2972 | 1.0161 | 0.0177 | -0.13 | -0.0639 | -0.2635 | -0.1222 | 0.2723 | -0.0718 | 0.1346 | 0.1045 | 0.1 | 0.0198 | -0.0029 | 0.0017 | 0.0051 | 0.0583 | 30.775 | 31.304 | 0.767 | 20 | 4.1317 | -1.319 | -5.0989 | 11.981 | -3.1935 | 8.3034 | -0.1369 | 0.123 | 0.0552 | -0.3521 | 0.025 | -0.5525 | 0.0912 | -0.7337 | 0.1119 | 0.1492 | 0.0182 | 0.0149 | -0.0252 | -0.012 | 0.0456 | 34.402 | 22.042 | -7.063 | 21 | 12.1368 | 13.0162 | -4.0231 | 36.7388 | -21.1478 | 29.3734 | -0.279 | 1.3704 | 0.2111 | 0.4865 | 0.1037 | 0.1129 | 0.5647 | -1.8588 | 0.1753 | 0.0216 | 0.0141 | 0.0392 | 0.049 | -0.0989 | -0.0372 | 29.008 | 20.766 | -8.479 | 22 | 19.8592 | -9.051 | 4.1246 | 8.3335 | 3.9251 | 8.8637 | 0.5808 | -1.0592 | 0.0332 | -0.5895 | -0.4868 | 0.5008 | 0.0753 | -0.8959 | -0.094 | -0.001 | -0.1139 | -0.0362 | 0.2172 | 0.0011 | -0.0135 | 5.059 | 21.358 | 16.898 | 23 | 11.9469 | -0.9631 | 4.4935 | 4.1768 | 6.1807 | 12.1337 | 0.0934 | -0.03 | -0.3558 | 0.0095 | -0.2817 | 0.0516 | 0.7919 | -0.4852 | 0.1883 | 0.0559 | -0.2033 | -0.0302 | 0.0285 | 0.0468 | 0.0183 | 7.934 | 11.734 | 14.663 | 24 | 8.4684 | 5.5898 | 1.158 | 6.6993 | 1.3277 | 0.3373 | 0.3069 | -0.14 | 0.0566 | 0.0007 | -0.0435 | 0.0266 | -0.1139 | -0.2038 | -0.2634 | 0.0572 | -0.1462 | -0.0339 | 0.0347 | 0.0509 | 0.0173 | 12.645 | 13.372 | 16.987 | 25 | 20.7508 | 7.1728 | 6.8738 | 3.7431 | 5.3843 | 9.4381 | -0.0956 | 0.0617 | -0.9306 | 0.003 | 0.2857 | -0.2781 | 0.6941 | -0.0749 | -0.1901 | 0.0695 | -0.0967 | -0.0343 | -0.0021 | 0.0737 | 0.0957 | 21.041 | 15.868 | 21.899 | 26 | 5.9769 | 0.7688 | -1.3389 | 3.3375 | -1.2974 | 0.8391 | 0.3064 | -0.0645 | -0.0481 | 0.2261 | -0.2106 | -0.1387 | 0.2113 | -0.2089 | -0.0959 | 0.029 | -0.0731 | -0.0192 | 0.0461 | 0.046 | 0.0252 | 25.751 | 20.328 | 23.833 | 27 | 6.515 | -2.4778 | -2.6265 | 16.3382 | 9.1729 | 8.9589 | 0.3323 | -0.2964 | 0.2643 | -0.2767 | -0.0464 | -0.1236 | -0.3799 | -0.1877 | -0.2859 | 0.0104 | -0.0396 | 0.0077 | 0.0511 | 0.01 | 0.0039 | 22.508 | 30.042 | 26.699 | 28 | 4.0031 | 0.9781 | 0.8583 | 2.0407 | -2.9945 | 5.8823 | 0.2246 | -0.4585 | 0.287 | 0.3259 | -0.0733 | -0.1653 | -0.0344 | -0.9338 | -0.1514 | -0.0073 | -0.052 | 0.0295 | 0.1843 | -0.0336 | -0.0025 | 17.48 | 30.318 | 30.189 | 29 | 0.7096 | 1.0606 | 2.2145 | 1.5852 | 3.3097 | 6.9105 | -0.1339 | -0.1651 | -0.1952 | -0.1894 | 0.1993 | 0.0501 | -0.2152 | 0.0451 | -0.0654 | 0.0666 | -0.0737 | 0.0196 | 0.0413 | 0.0188 | 0.035 | 19.849 | 23.881 | 16.039 | 30 | 17.5293 | -0.8955 | -8.0579 | 0.0495 | 0.1709 | 18.955 | -0.0279 | 0.1045 | -0.6786 | -0.2911 | 0.2134 | 0.0126 | 0.7704 | -0.019 | -0.1856 | 0.1579 | -0.2026 | -0.0202 | 0.0301 | 0.0005 | 0.0314 | 16.577 | 14.581 | 8.074 | 31 | 32.649 | 5.1501 | -7.3707 | 22.8514 | 9.0747 | 13.806 | 0.0607 | 2.128 | 1.0441 | -0.9468 | -0.2584 | -0.1073 | -0.137 | 0.4194 | 0.1977 | 0.0929 | -0.2337 | -0.135 | 0.1001 | 0.1638 | -0.0485 | 12.842 | 18.259 | 5.124 | 32 | 31.7921 | 1.1206 | -1.2984 | 8.0744 | 7.942 | 9.4747 | -0.4435 | -0.007 | -1.6548 | 0.0229 | 0.6014 | -0.2882 | 0.7921 | 0.623 | -0.1578 | 0.0427 | -0.0198 | -0.0319 | 0.0186 | 0.0652 | 0.0921 | 34.43 | 21.889 | 23.632 | 33 | 9.0177 | -4.2132 | 0.8463 | 2.2181 | 0.2052 | 1.5248 | 0.0218 | -0.2209 | 0.5019 | 0.1306 | -0.0472 | 0.0504 | 0.2588 | -0.4177 | 0.0255 | 0.0234 | -0.0466 | -0.0087 | 0.0774 | 0.008 | 0.0264 | 28.74 | 28.683 | 29.994 | 34 | 4.9994 | 0.9331 | 4.9378 | 14.6007 | 2.4128 | 5.0311 | 0.3592 | -0.4681 | -0.1511 | 0.0586 | 0.0587 | -0.1089 | 0.5565 | -0.5089 | -0.4179 | 0.0757 | -0.0757 | -0.0252 | 0.0477 | 0.0373 | -0.015 | 28.472 | 21.496 | 36.258 | 35 | 8.3699 | 1.5612 | 7.3018 | 4.0375 | 3.7519 | 7.8946 | 0.2123 | -0.3728 | -0.2286 | 0.0458 | -0.0736 | -0.03 | 0.2643 | -0.3224 | -0.1387 | 0.0349 | -0.1399 | -0.0319 | 0.0925 | 0.0867 | -0.0177 | 23.587 | 19.73 | 33.35 | 36 | 20.7349 | -6.0705 | -5.1057 | 2.9727 | 4.9901 | 11.477 | 0.4568 | -1.3263 | -0.4701 | -0.0232 | -0.4291 | -0.0317 | 0.1376 | -0.1565 | -0.0276 | 0.0519 | -0.2335 | -0.0347 | 0.2007 | 0.1049 | -0.0077 | 14.453 | 17.909 | 29.126 | 37 | 3.8499 | -0.5534 | 0.9151 | 0.1103 | -0.0658 | 0.3581 | 0.1258 | -0.6198 | -0.092 | -0.0254 | 0.0288 | 0.0399 | 0.3152 | -0.7588 | -0.1546 | -0.0069 | -0.0932 | 0.0098 | 0.1671 | 0.0236 | 0.023 | 8.946 | 19.526 | 24.841 | 38 | 10.6858 | -7.8298 | -6.6559 | 6.3711 | 9.0924 | 32.1739 | 1.0683 | 0.493 | 0.884 | -0.374 | -0.0932 | -0.1075 | -1.7663 | 0.8118 | -0.975 | 0.0025 | -0.0608 | -0.0084 | 0.207 | -0.0007 | -0.0308 | 13.36 | 26.609 | 12.748 |
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Refinement TLS group | ID | Refine-ID | Refine TLS-ID | Auth asym-ID | Label asym-ID | Auth seq-ID | Label seq-ID |
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1 | X-RAY DIFFRACTION | 1 | AA6 - 51 | 6 - 10 | 2 | X-RAY DIFFRACTION | 2 | AA52 - 56 | 11 - 15 | 3 | X-RAY DIFFRACTION | 3 | AA57 - 61 | 16 - 20 | 4 | X-RAY DIFFRACTION | 4 | AA62 - 66 | 21 - 25 | 5 | X-RAY DIFFRACTION | 5 | AA67 - 72 | 26 - 31 | 6 | X-RAY DIFFRACTION | 6 | AA73 - 77 | 32 - 36 | 7 | X-RAY DIFFRACTION | 7 | AA78 - 84 | 37 - 43 | 8 | X-RAY DIFFRACTION | 8 | AA85 - 90 | 44 - 49 | 9 | X-RAY DIFFRACTION | 9 | AA91 - 95 | 50 - 54 | 10 | X-RAY DIFFRACTION | 10 | AA96 - 100 | 55 - 59 | 11 | X-RAY DIFFRACTION | 11 | AA101 - 105 | 60 - 64 | 12 | X-RAY DIFFRACTION | 12 | BB7 - 54 | 7 - 13 | 13 | X-RAY DIFFRACTION | 13 | BB55 - 60 | 14 - 19 | 14 | X-RAY DIFFRACTION | 14 | BB61 - 66 | 20 - 25 | 15 | X-RAY DIFFRACTION | 15 | BB67 - 72 | 26 - 31 | 16 | X-RAY DIFFRACTION | 16 | BB73 - 77 | 32 - 36 | 17 | X-RAY DIFFRACTION | 17 | BB78 - 84 | 37 - 43 | 18 | X-RAY DIFFRACTION | 18 | BB85 - 90 | 44 - 49 | 19 | X-RAY DIFFRACTION | 19 | BB91 - 95 | 50 - 54 | 20 | X-RAY DIFFRACTION | 20 | BB96 - 100 | 55 - 59 | 21 | X-RAY DIFFRACTION | 21 | BB101 - 105 | 60 - 64 | 22 | X-RAY DIFFRACTION | 22 | CC51 - 56 | 10 - 15 | 23 | X-RAY DIFFRACTION | 23 | CC57 - 61 | 16 - 20 | 24 | X-RAY DIFFRACTION | 24 | CC62 - 66 | 21 - 25 | 25 | X-RAY DIFFRACTION | 25 | CC67 - 72 | 26 - 31 | 26 | X-RAY DIFFRACTION | 26 | CC73 - 77 | 32 - 36 | 27 | X-RAY DIFFRACTION | 27 | CC78 - 84 | 37 - 43 | 28 | X-RAY DIFFRACTION | 28 | CC85 - 90 | 44 - 49 | 29 | X-RAY DIFFRACTION | 29 | CC91 - 95 | 50 - 54 | 30 | X-RAY DIFFRACTION | 30 | CC96 - 100 | 55 - 59 | 31 | X-RAY DIFFRACTION | 31 | CC101 - 105 | 60 - 64 | 32 | X-RAY DIFFRACTION | 32 | DD6 - 51 | 6 - 10 | 33 | X-RAY DIFFRACTION | 33 | DD52 - 56 | 11 - 15 | 34 | X-RAY DIFFRACTION | 34 | DD57 - 61 | 16 - 20 | 35 | X-RAY DIFFRACTION | 35 | DD62 - 67 | 21 - 26 | |
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