Software | Name | Version | Classification |
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PHENIX | dev_2363refinementDENZO | | data reductionSCALEPACK | | data scalingMOLREP | | phasingPDB_EXTRACT | 3.2 | data extraction | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HI5 Resolution: 1.65→28.373 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.57 / Phase error: 23.58 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.203 | 2300 | 5 % |
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Rwork | 0.1645 | 43702 | - |
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obs | 0.1664 | 46002 | 95.42 % |
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL |
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Displacement parameters | Biso max: 180.55 Å2 / Biso mean: 45.3153 Å2 / Biso min: 18.53 Å2 |
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Refinement step | Cycle: final / Resolution: 1.65→28.373 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 3424 | 0 | 56 | 316 | 3796 |
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Biso mean | - | - | 57.17 | 41.93 | - |
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Num. residues | - | - | - | - | 445 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.007 | 3550 | X-RAY DIFFRACTION | f_angle_d0.876 | 4834 | X-RAY DIFFRACTION | f_chiral_restr0.053 | 535 | X-RAY DIFFRACTION | f_plane_restr0.005 | 610 | X-RAY DIFFRACTION | f_dihedral_angle_d13.603 | 2110 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.65-1.6859 | 0.3097 | 112 | 0.2883 | 2124 | 2236 | 74 | 1.6859-1.7251 | 0.3128 | 142 | 0.2664 | 2690 | 2832 | 94 | 1.7251-1.7682 | 0.284 | 144 | 0.2441 | 2734 | 2878 | 95 | 1.7682-1.816 | 0.2638 | 143 | 0.214 | 2733 | 2876 | 96 | 1.816-1.8695 | 0.2971 | 144 | 0.2087 | 2737 | 2881 | 96 | 1.8695-1.9298 | 0.2206 | 144 | 0.2024 | 2735 | 2879 | 96 | 1.9298-1.9988 | 0.2563 | 144 | 0.1928 | 2759 | 2903 | 97 | 1.9988-2.0788 | 0.2279 | 146 | 0.1871 | 2764 | 2910 | 96 | 2.0788-2.1733 | 0.2326 | 145 | 0.1816 | 2757 | 2902 | 97 | 2.1733-2.2879 | 0.2291 | 147 | 0.1709 | 2778 | 2925 | 97 | 2.2879-2.4311 | 0.226 | 148 | 0.1763 | 2817 | 2965 | 98 | 2.4311-2.6187 | 0.2295 | 146 | 0.1779 | 2770 | 2916 | 98 | 2.6187-2.882 | 0.2363 | 148 | 0.1704 | 2811 | 2959 | 98 | 2.882-3.2985 | 0.1778 | 148 | 0.1663 | 2830 | 2978 | 99 | 3.2985-4.1537 | 0.1783 | 150 | 0.1393 | 2838 | 2988 | 99 | 4.1537-28.3776 | 0.1595 | 149 | 0.1369 | 2825 | 2974 | 99 |
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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 | 2.6392 | 0.2309 | 1.5899 | 3.1329 | 1.7486 | 5.3876 | 0.0819 | -0.0272 | -0.2301 | 0.752 | 0.0138 | -0.1642 | 1.244 | 0.3022 | -0.1379 | 0.625 | 0.1591 | 0.0291 | 0.3568 | 0.0478 | 0.289 | 6.922 | -3.742 | 19.182 | 2 | 6.6821 | 1.1791 | -1.9173 | 6.0043 | -0.346 | 5.52 | -0.203 | -0.033 | 0.0506 | -0.0462 | 0.0821 | 0.4925 | 0.436 | -0.2599 | 0.1204 | 0.2777 | 0.0633 | 0.0156 | 0.1715 | -0.0272 | 0.248 | -1.548 | 5.226 | 17.811 | 3 | 4.9875 | -4.6039 | 6.1181 | 6.8526 | -4.3617 | 8.6985 | -0.0252 | -0.222 | -0.5198 | 0.426 | 0.0849 | 0.3496 | 0.3827 | 0.0536 | -0.0532 | 0.4604 | 0.0978 | 0.0108 | 0.2284 | 0.0287 | 0.2395 | 2.538 | -4.278 | 23.158 | 4 | 1.4834 | 0.5328 | 0.4021 | 1.6244 | 0.9529 | 1.9545 | -0.2975 | -0.2732 | 0.055 | 0.449 | -0.0448 | 0.3268 | 0.6339 | -0.2041 | -0.1107 | 0.3263 | -0.0001 | 0.1013 | 0.2869 | -0.0025 | 0.2799 | 0.263 | -2.702 | 11.774 | 5 | 2.2832 | -0.239 | -1.0977 | 3.0097 | 1.6606 | 7.2875 | 0.1626 | 0.0448 | -0.0845 | 0.0313 | -0.0692 | -0.0016 | -0.002 | -0.0615 | -0.0617 | 0.1442 | -0.0496 | 0.01 | 0.1415 | -0.0127 | 0.2191 | 0.091 | -15.998 | -17.31 | 6 | 3.1795 | 0.3524 | -2.1767 | 2.9593 | 1.0738 | 7.3499 | 0.227 | -0.0524 | 0.1416 | 0.0736 | -0.0168 | -0.0146 | -0.1974 | 0.1183 | -0.1831 | 0.1414 | -0.0133 | 0.0004 | 0.1766 | 0.009 | 0.268 | 1.403 | -12.195 | -14.674 | 7 | 4.688 | 1.3337 | -2.1198 | 3.4619 | -0.7102 | 4.5767 | -0.0276 | 0.2592 | -0.3363 | 0.1307 | -0.1192 | 0.0962 | 0.8295 | -0.076 | 0.1665 | 0.3299 | -0.0159 | 0.0063 | 0.1685 | -0.0411 | 0.3202 | -1.332 | -24.281 | -18.196 | 8 | 7.2523 | -0.5577 | -4.7051 | 3.3259 | 0.518 | 4.9469 | -0.0073 | 0.4099 | 0.5588 | -0.3354 | 0.2101 | 0.066 | -0.5178 | -0.3679 | -0.2315 | 0.3151 | -0.048 | -0.0448 | 0.2671 | 0.044 | 0.2134 | 5.863 | 16.924 | -1.974 | 9 | 4.7833 | -0.2269 | -1.6158 | 5.8624 | 1.9085 | 5.101 | -0.0609 | -0.2613 | 0.4736 | 0.0133 | 0.138 | 0.1766 | -0.5858 | 0.1583 | -0.0822 | 0.2374 | -0.0151 | -0.0308 | 0.1938 | -0.0145 | 0.2199 | 7.257 | 19.76 | 9.44 | 10 | 8.9765 | 4.2179 | 2.0077 | 6.7809 | 3.0072 | 5.3395 | -0.2236 | 0.0892 | -0.4629 | -0.5288 | 0.5067 | -0.4023 | 0.1451 | 0.594 | -0.3323 | 0.2261 | 0.0518 | -0.0012 | 0.3246 | 0.032 | 0.1761 | 13.14 | 8.771 | 7.245 | 11 | 1.6935 | 1.8241 | 1.4126 | 4.6011 | 1.3325 | 3.2845 | -0.1627 | -0.2086 | 0.2146 | 0.0179 | 0.5605 | -1.0312 | 0.0081 | 1.4214 | -0.3096 | 0.2137 | -0.0781 | -0.0255 | 0.6305 | -0.0949 | 0.4288 | 19.78 | 17.69 | 9.672 | 12 | 2.2973 | 0.6883 | -0.3161 | 2.3718 | 0.8281 | 4.854 | -0.2084 | -0.1023 | 0.2996 | -0.1365 | 0.2058 | -0.0581 | -0.3508 | 0.5498 | -0.04 | 0.2222 | -0.0027 | -0.0352 | 0.2421 | 0.0057 | 0.2609 | 9.981 | 16.566 | 8.056 | 13 | 1.5337 | -0.7284 | 0.8628 | 0.6184 | 0.8247 | 6.1035 | 0.0205 | 0.1296 | 0.0268 | -0.837 | 0.2135 | -0.0903 | -0.1217 | 0.476 | 0.1196 | 0.5982 | -0.1499 | 0.0015 | 0.2553 | 0.0591 | 0.2647 | 9.157 | 9.215 | -14.893 | 14 | 9.0881 | 0.8715 | -0.7688 | 3.6596 | 0.7095 | 4.2292 | 0.1712 | 0.0718 | -1.1307 | 0.0858 | -0.264 | 0.1692 | -0.0592 | -0.5438 | 0.1089 | 0.3697 | 0.0394 | -0.0815 | 0.3609 | -0.0202 | 0.3627 | -9.802 | -14.084 | -24.821 | 15 | 3.2614 | 1.2554 | 0.1676 | 3.3999 | 0.2481 | 3.2376 | -0.2035 | 0.0935 | 0.2992 | -0.3764 | -0.0461 | 0.5998 | -0.5473 | -0.3724 | 0.1144 | 0.2752 | 0.0422 | -0.0447 | 0.2189 | -0.0261 | 0.2909 | -7.027 | -2.533 | -18.523 | 16 | 3.0969 | 1.2064 | 0.7084 | 8.1793 | 2.5256 | 1.0299 | -0.1428 | 0.44 | 0.3064 | -1.1186 | -0.2937 | 0.2478 | -0.8632 | -0.095 | 0.3908 | 0.5801 | 0.0286 | -0.1771 | 0.4321 | 0.0611 | 0.3553 | -8.859 | -4.694 | -29.305 |
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Refinement TLS group | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | ( CHAIN L AND RESID 1:32 )L1 - 32 | 2 | X-RAY DIFFRACTION | 2 | ( CHAIN L AND RESID 33:61 )L33 - 61 | 3 | X-RAY DIFFRACTION | 3 | ( CHAIN L AND RESID 62:75 )L62 - 75 | 4 | X-RAY DIFFRACTION | 4 | ( CHAIN L AND RESID 76:113 )L76 - 113 | 5 | X-RAY DIFFRACTION | 5 | ( CHAIN L AND RESID 114:155 )L114 - 155 | 6 | X-RAY DIFFRACTION | 6 | ( CHAIN L AND RESID 156:188 )L156 - 188 | 7 | X-RAY DIFFRACTION | 7 | ( CHAIN L AND RESID 189:214 )L189 - 214 | 8 | X-RAY DIFFRACTION | 8 | ( CHAIN H AND RESID 1:17 )H1 - 17 | 9 | X-RAY DIFFRACTION | 9 | ( CHAIN H AND RESID 18:39 )H18 - 39 | 10 | X-RAY DIFFRACTION | 10 | ( CHAIN H AND RESID 40:52 )H40 - 52 | 11 | X-RAY DIFFRACTION | 11 | ( CHAIN H AND RESID 53:66 )H53 - 66 | 12 | X-RAY DIFFRACTION | 12 | ( CHAIN H AND RESID 67:106 )H67 - 106 | 13 | X-RAY DIFFRACTION | 13 | ( CHAIN H AND RESID 107:119 )H107 - 119 | 14 | X-RAY DIFFRACTION | 14 | ( CHAIN H AND RESID 120:134 )H120 - 134 | 15 | X-RAY DIFFRACTION | 15 | ( CHAIN H AND | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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