Full wwpdb/emdatabank EM Map/Model Validation Report io

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1 Full wwpdb/emdatabank EM Map/Model Validation Report io Apr 12, :52 AM EDT PDB ID : 5Y81 EMDB ID: : EMD-6816 Title : NuA4 TEEAA sub-complex Authors : Wang, X.; Cai, G. Deposited on : Resolution : 4.70 Å(reported) This is a Full wwpdb/emdatabank EM Map/Model Validation Report for a publicly released PDB/EMDB entry. We welcome your comments at validation@mail.wwpdb.org A user guide is available at with specic help available everywhere you see the io symbol. MolProbity : 4.02b-467 Percentile statistics : v01 (using entries in the PDB archive December 27th 2017) Ideal geometry (proteins) : Engh & Huber (2001) Ideal geometry (DNA, RNA) : Parkinson et. al. (1996) Validation Pipeline (wwpdb-vp) : rb

2 Page 2 Full wwpdb/emdatabank EM Map/Model Validation Report 5Y81 1 Overall quality at a glance io The following experimental techniques were used to determine the structure: ELECTRON MICROSCOPY The reported resolution of this entry is 4.70 Å. Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown in the following graphic. The table shows the number of entries on which the scores are based. Metric Whole archive EM structures (#Entries) (#Entries) Clashscore Ramachandran outliers Sidechain outliers The table below summarises the geometric issues observed across the polymeric chains. The red, orange, yellow and green segments on the bar indicate the fraction of residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria. A grey segment represents the fraction of residues that are not modelled. The numeric value for each fraction is indicated below the corresponding segment, with a dot representing fractions <=5% Mol Chain Length Quality of chain 1 B C D H A F G E 41

3 Page 3 Full wwpdb/emdatabank EM Map/Model Validation Report 5Y81 2 Entry composition io There are 8 unique types of molecules in this entry. The entry contains atoms, of which 0 are hydrogens and 0 are deuteriums. In the tables below, the AltConf column contains the number of residues with at least one atom in alternate conformation and the Trace column contains the number of residues modelled with at most 2 atoms. ˆ Molecule 1 is a protein called Transcription-associated protein 1. Mol Chain Residues Atoms AltConf Trace 1 B 981 Total C N O S ˆ Molecule 2 is a protein called Chromatin modication-related protein EAF1. Mol Chain Residues Atoms AltConf Trace 2 C 140 Total C N O S ˆ Molecule 3 is a protein called Eaf1-disorder domain. Mol Chain Residues Atoms AltConf Trace 3 D 360 Total C N O ˆ Molecule 4 is a protein called Chromatin modication-related protein EAF5. Mol Chain Residues Atoms AltConf Trace 4 H 154 Total C N O ˆ Molecule 5 is a protein called Transcription-associated protein 1. Mol Chain Residues Atoms AltConf Trace 5 A 2007 Total C N O ˆ Molecule 6 is a protein called Actin-related protein 4. Mol Chain Residues Atoms AltConf Trace 6 F 421 Total C N O S

4 Page 4 Full wwpdb/emdatabank EM Map/Model Validation Report 5Y81 There is a discrepancy between the modelled and reference sequences: Chain Residue Modelled Actual Comment Reference F 0 - expression tag UNP P80428 ˆ Molecule 7 is a protein called Actin. Mol Chain Residues Atoms AltConf Trace 7 G 351 Total C N O S ˆ Molecule 8 is a protein called Chromatin modication-related protein EAF1. Mol Chain Residues Atoms AltConf Trace 8 E 41 Total C N O S

5 Page 5 Full wwpdb/emdatabank EM Map/Model Validation Report 5Y81 3 Residue-property plots io These plots are drawn for all protein, RNA and DNA chains in the entry. The rst graphic for a chain summarises the proportions of the various outlier classes displayed in the second graphic. The second graphic shows the sequence view annotated by issues in geometry. Residues are colorcoded according to the number of geometric quality criteria for which they contain at least one outlier: green = 0, yellow = 1, orange = 2 and red = 3 or more. Stretches of 2 or more consecutive residues without any outlier are shown as a green connector. Residues present in the sample, but not in the model, are shown in grey. Molecule 1: Transcription-associated protein 1 Chain B: H3497 D3498 D3499 A3503 P3504 D3505 M3506 T3507 I3508 L3509 K3510 V3511 E3512 I3513 F3514 N3515 S3516 I3517 Q3518 T3519 M3520 F3521 V3522 N3525 V3526 L3527 K3528 D3529 H3530 F3531 F3535 F3538 E3539 D3540 F3541 W3542 L3543 F3544 R3545 K3546 Q3547 S3550 Q3551 Y3552 S3553 S3554 F3555 V3556 F3557 M3558 S3559 K3432 N3433 V3434 E3435 T3436 R3437 R3438 R3439 S3440 I3441 Q3442 F3443 N3444 L3445 P3446 I3447 A3448 I3449 P3450 L3451 S3452 P3453 Q3454 V3455 R3456 I3457 M3458 S3461 V3462 S3463 F3464 T3465 T3466 L3467 H3468 N3472 E3473 F3474 G3479 F3480 D3481 P3482 D3483 D3484 I3485 Q3486 D3487 F3488 M3489 A3490 D3491 K3492 L3493 N3494 A3495 A3496 P3355 G3356 Q3357 Y3358 L3359 L3360 V3366 H3367 F3368 I3369 K3370 I3371 A3372 R3373 F3374 L3375 P3376 T3377 V3381 S3387 Y3388 R3389 R3390 L3391 M3392 I3393 R3394 G3395 G3398 S3399 V3400 H3401 S3402 F3403 A3404 V3405 Q3406 Y3407 P3408 A3409 V3410 R3411 R3415 E3416 E3417 R3418 Q3421 L3422 Y3423 R3424 L3425 F3426 N3427 K3428 L3245 F3246 R3247 L3248 I3249 N3250 V3251 L3252 L3253 P3264 P3273 Y3291 I3292 R3293 F3296 F3300 Y3307 L3314 R3315 Y3316 W3317 R3318 E3322 R3327 C3338 F3344 I3354 N3150 I3159 A3160 K3161 S3162 Y3163 P3164 Q3165 A3166 L3167 H3168 F3169 Q3170 L3171 R3172 T3173 T3174 I3181 MET MET Q3203 P3204 T3217 A3218 Y3219 P3220 L3221 L3222 A3223 L3229 R3236 T3241 D3242 E3243 D3244 L3068 S3069 E3070 E3071 P3072 S3076 F3077 A3078 A3081 I3082 Y3085 L3086 A3089 N3094 S3095 K3096 I3097 R3098 E3099 L3100 L3101 C3102 R3103 I3104 L3105 W3106 L3107 I3108 S3109 I3110 D3111 G3115 M3116 L3117 T3118 N3119 P3129 I3134 T3135 F3136 Q3139 L3140 L3141 T3142 S3143 L3144 S3145 A3149 E2980 C2991 N2997 E2998 L2999 T3000 T3001 S3007 N3008 TYR G3015 K3019 A3020 F3023 L3033 TYR E3038 A3039 N3040 Q3041 A3042 F3043 A3044 T3045 A3046 V3047 D3050 L3053 A3054 K3055 A3056 W3057 A3058 Q3059 W3060 G3061 F3062 F3063 N3064 D3065 R3066 R3067 D2900 L2901 V2902 Q2906 I2912 N2913 N2914 A2915 P2921 A2922 L2923 HIS TYR R2938 H2941 E2942 I2943 A2944 W2945 V2946 I2947 H2952 H2957 N2958 D2961 V2962 C2963 I2964 S2965 Q2966 L2967 A2968 R2969 I2970 Y2971 T2972 K2827 W2828 R2834 Y2835 T2836 P2837 A2838 H2839 K2840 W2841 L2842 L2843 H2844 G2845 F2846 Q2847 Q2848 Y2849 M2850 E2851 F2852 L2853 E2854 A2855 T2856 T2866 A2874 Q2875 E2876 Q2882 R2885 D2886 R2887 L2888 P2889 TRP D2894 V2895 N2896 M2897 W2898 N2899 Q2723 A2737 L2740 HIS TRP D2744 V2745 L2746 T2747 E2748 H2752 E2761 R2765 V2766 TRP R2773 E2777 Q2778 S2779 V2780 K2781 S2782 V2783 P2787 T2788 P2789 R2790 R2791 Q2792 F2797 R2807 G2809 C2817 D2818 E2819 G2820 I2821 Q2822 L2823 S2824 L2825 I2826 TYR W2633 Y2634 Q2635 S2636 I2637 N2638 I2639 L2640 E2641 S2642 I2643 T2647 S2648 I2649 D2650 N2651 T2652 K2653 I2654 I2655 E2656 E2659 L2662 L2663 E2664 L2665 Q2670 E2671 M2674 F2675 L2678 R2681 I2690 G2691 E2695 Q2696 I2697 W2700 R2715 TYR

6 Page 6 Full wwpdb/emdatabank EM Map/Model Validation Report 5Y81 Y3560 T3568 P3569 H3570 K3571 I3572 H3573 V3574 D3575 K3576 T3577 S3578 G3579 N3580 V3581 F3582 T3583 M3586 L3587 R3590 F3591 P3592 R3595 P3598 L3599 N3602 L3605 D3610 S3611 P3612 N3617 E3618 P3619 V3620 T3625 P3626 N3627 I3632 G3633 N3644 L3645 F3646 T3647 I3648 S3649 R3650 A3651 L3652 I3653 E3654 P3655 D3656 N3657 E3658 L3659 N3660 T3661 Y3662 L3663 A3664 L3665 F3666 I3667 R3668 D3669 E3670 I3671 I3672 S3673 W3674 L3678 H3679 R3680 Q3687 V3692 V3696 D3697 L3698 I3699 I3700 R3701 K3702 V3703 A3704 Q3705 L3706 G3707 H3708 L3709 T3712 P3713 T3714 V3715 T3716 T3717 Q3718 F3719 I3720 L3721 D3722 C3723 I3724 A3727 R3731 N3732 L3733 D3737 V3738 N3739 F3740 M3741 P3742 W3743 F3744 Molecule 2: Chromatin modication-related protein EAF1 Chain C: T648 I649 S652 E653 E670 S673 A674 H675 M676 T677 H678 R679 L680 T681 Y684 L685 S686 N687 I688 E689 R690 R691 T692 P693 W694 Q695 C696 F697 E698 R699 F700 V701 Q702 L703 N704 E705 R706 F707 D711 L712 K713 G714 P715 R716 A717 H718 S719 A720 Q721 Q722 W723 L724 I725 E726 Q732 R733 Q734 S739 P740 R754 A758 A763 C767 E772 CYS MET T795 P796 A797 L801 Q805 A809 HIS TYR TYR MET TYR TYR HIS HIS Molecule 3: Eaf1-disorder domain Chain D: X1 X2 X3 X4 X7 X8 X11 X12 X13 X16 X38 X39 X55 X59 X60 X61 X62 X63 X64 X65 X66 X74 X75 X79 X80 X102 X139 X140 X150 X151 X152 X153 X154 X155 X156 X159 X160 X161 X162 X165 X166 X167 X168 X169 X170 X171 X172 X173 X174 X175 X176 X180 X181 X182 X185 X215 X216 X233 X266 X277 X278 X281 X282 X285 X286 X289 X290 X306 X309 X310 X313 X328 X331 X362 X373 X384 X385 X386 X396 X414 X415 X416 X417 X418 X419 X420 X421 X422 X423 X424 X425 X426 X427 X428 X429 X430 X438 X439 X440 X441 X442 X443 X444 X460 Molecule 4: Chromatin modication-related protein EAF5 Chain H:

7 Page 7 Full wwpdb/emdatabank EM Map/Model Validation Report 5Y81 MET K3 Q12 T16 S19 E24 L25 N28 G29 G30 G31 MET K45 Q51 L54 L55 I56 N57 E58 L59 T60 N61 L62 R63 G76 N86 P89 T93 HIS E106 D109 L113 L114 D115 E116 K117 Y118 D119 K122 I129 R130 M131 E135 K142 Q147 HIS HIS MET HIS MET R181 E182 K183 L184 L185 K186 L187 Y188 R189 D190 T191 V192 L193 N194 K195 L196 T200 TYR E222 D223 E227 T228 P229 G230 S231 L235 I243 MET D256 R261 F265 D269 MET Molecule 5: Transcription-associated protein 1 Chain A: MET T4 F14 L21 Y25 L31 M35 E36 P41 L56 TYR HIS S70 R85 CYS MET T91 V106 N111 M119 L122 T123 K130 K136 L137 D138 S139 F140 F159 TYR L214 S217 M218 F219 S220 C227 T230 M231 K239 Q240 L241 T242 S243 T244 S245 L246 L256 HIS N287 T302 S303 F304 A314 P315 D320 L328 I329 I330 R331 L332 L333 Q334 D335 C336 L340 S341 K345 E346 L347 L348 H349 A350 T351 R352 H353 T357 L362 L367 D368 Y369 D372 E373 L376 G380 MET H384 P389 L390 A391 Y392 E405 E410 I411 E412 D424 E425 S426 T430 V431 Q432 I433 K451 P458 K461 M465 R474 L478 D483 M486 K487 G490 R491 L503 D509 N510 D511 E515 E516 F517 M518 R519 L522 HIS MET MET E559 Y566 A567 P568 L572 P573 T574 P575 D578 P579 I580 K581 D582 A583 Y587 R588 M591 S592 F593 L594 K595 T596 I597 L601 F604 N605 TYR TRP TYR E629 E630 V631 F634 K635 D636 L637 F638 F648 HIS HIS MET S674 E681 L682 Y685 L686 F690 M691 Q692 MET A696 P707 F708 V709 M713 L714 G718 T732 F736 L741 L744 L751 N757 F776 P777 P786 H787 L791 S799 E804 P805 L806 F809 T814 S818 P833 I834 L838 L842 M845 L851 P852 E856 E860 P866 V871 L872 A873 P874 Y875 L876 P877 F878 K881 P882 Q889 Y890 P891 D892 L893 V894 G897 T900 L901 Y912 F913 D914 P915 I916 I917 V924 A927 N930 N938 I948 G953 R957 Q958 F959 L960 K961 P962 P963 T964 D965 L966 T967 E968 K969 T970 E971 L972 D973 A976 I977 A978 D979 F980 K981 I982 N983 P986 E987 D988 V989 P990 L991 S992 V993 T994 P995 G996 I997 Q998 I1003 S1006 S1009 D1010 I1011 H1012 Y1013 R1014 A1017 L1027 K1030 S1031 S1032 A1033 E1034 F1035 P1036 T1037 N1038 Y1039 T1040 E1041 L1042 L1043 K1044 T1045 A1046 K1051 V1067 N1068 K1069 R1070 D1071 Y1072 V1086 T1090 S1091 I1092 K1093 E1094 L1095 K1096 D1097 D1098 A1099 M1100 D1101 L1102 L1103 N1104 N1105 L1106 L1107 C1111 T1117 N1121 N1126 MET S1142 A1152 L1153 S1154 I1157 P1158 E1159 K1174 CYS TYR E1182

8 Page 8 Full wwpdb/emdatabank EM Map/Model Validation Report 5Y81 L1200 C1201 Y1202 D1203 E1204 Y1207 N1208 K1209 R1210 N1222 V1223 K1224 S1225 S1226 S1227 V1228 F1229 L1230 K1231 D1247 T1248 Q1249 S1250 E1251 A1255 I1256 T1257 D1258 K1262 I1265 T1271 L1280 E1286 T1290 D1291 I1292 V1293 C1294 E1295 L1296 N1300 P1301 K1302 S1315 T1318 P1321 S1335 P1336 L1345 P1346 M1349 A1356 L1361 S1362 L1363 P1364 E1372 E1373 L1374 F1375 R1376 L1377 A1385 T1400 K1417 A1420 I1421 A1422 L1423 A1431 L1441 F1445 K1446 T1447 MET S1452 P1453 I1456 N1470 P1474 N1488 HIS T1496 L1506 L1507 E1508 Y1513 G1519 C1530 V1534 L1543 Q1546 M1547 P1548 H1560 P1563 D1567 L1580 E1581 R1582 K1583 L1584 R1585 L1586 Q1587 L1588 D1589 S1590 P1591 L1596 A1597 R1598 N1605 P1606 V1607 T1608 M1615 Q1629 R1630 N1646 F1647 Y1648 D1649 F1650 Y1651 I1652 S1653 N1654 V1662 F1673 N1674 T1675 M1676 N1680 TRP M1691 K1707 TYR HIS L1716 L1735 Q1740 N1741 P1742 L1745 D1749 F1750 S1751 S1759 K1763 F1767 H1768 N1769 K1776 L1788 CYS A1798 A1816 TYR K1829 N1844 TYR HIS H1857 D1858 L1859 F1860 R1861 F1862 L1867 S1868 F1871 I1872 I1879 I1894 K1895 L1896 E1897 D1898 F1912 D1917 F1918 P1919 R1932 HIS E1937 A1938 V1942 V1948 P1951 V1952 L1953 HIS MET A1960 G1961 T1962 P1963 D1964 T1965 W1966 I1967 N1968 V1973 MET S1979 Y1986 Q1987 F1988 L1989 I1990 S1991 H1992 P1993 D1994 N1998 S2005 H2009 N2012 F2016 M2017 D2023 L2036 Y2037 W2038 E2039 L2043 MET L2090 H2091 L2092 A2095 S2107 HIS E2115 D2130 HIS TRP L2140 L2147 E2155 L2168 Y2169 F2172 K2173 W2179 I2180 M2181 E2182 N2183 L2184 P2185 I2195 HIS HIS V2202 A2219 I2225 I2226 E2229 I2243 T2244 S2251 S2252 V2253 G2256 V2257 A2260 W2261 F2267 N2270 H2289 MET L2301 L2318 L2325 P2331 S2334 L2338 I2352 S2356 I2360 P2367 T2368 V2369 K2370 A2381 I2384 S2389 L2390 S2391 K2392 L2401 F2402 D2403 HIS N2408 N2409 T2410 V2414 R2415 P2419 F2420 L2421 G2430 S2442 R2450 F2462 TYR P2467 F2480 N2481 R2482 N2490 I2491 P2496 P2497 P2505 E2506 V2511 V2514 L2517 E2518 L2519 K2524 G2525 H2526 I2527 A2528 S2529 M2530 L2533 CYS S2538 S2539 D2540 F2541 I2542 D2543 S2544 F2549 I2556 H2557 R2558 F2564 V2567 Y2568 K2569 S2570 I2571 P2572 L2587 TYR HIS S2597 N2601 N2604 L2607 K2612 K2624 Y2625 L2626 Molecule 6: Actin-related protein 4 Chain F: P0 M1 S2 L6 Q7 V8 Y9 G10 G11 D12 A16 V17 V18 I19 D20 P21 G22 S23 Y24 T25 T26 N27 I28 G29 Y30 S31 G32 F35 P36 L40 P41 S42 V43 Y44 G45 K46 Y47 T48 A49 D50 N53 I56 F57 S58 S61 I62 R66 K67 D68 Y69 E70 L71 K72 P73 I74 V80 I81 D82 W83 D84 T85 A86 Q87 E88 Q89 W90 Q91 W92 A93 L94 Q95 N96 E97 L98 Y99 L100 G105 I106 P107 L110 T111 E112 P113 V114 W115 N116 S117 T118 E119 N120 R121 K122 K123 S124 L125 E126 V127 L128 L129 M132 Q133 F134 C137 C145 F148

9 Page 9 Full wwpdb/emdatabank EM Map/Model Validation Report 5Y81 G151 R152 P153 L156 D163 T164 S168 P169 I170 V171 M174 T175 L176 S177 K178 S179 T180 R181 R182 N183 F184 I185 A186 G187 K188 F189 I190 N191 H192 L193 I194 I204 P205 K210 Q211 R212 K213 P214 E215 F216 I217 K218 K219 D226 L229 Y230 A233 N234 G237 F238 E241 C242 K243 E244 T245 L246 C247 H248 I249 K253 T254 L255 E256 E257 T258 E261 S264 T265 A266 K267 S272 P273 W274 N275 E276 E277 I278 N282 R285 Y286 G287 F288 A289 E290 E291 L292 K296 E297 D298 D299 I300 P301 A302 N303 W304 P305 R306 S307 N308 S309 G310 V311 TRP TYR E381 L382 L388 V389 Y390 D397 L400 R401 L404 A405 H406 N407 G412 G413 T414 S415 S416 L420 L428 L432 P433 S434 L435 K436 F437 R438 I439 L440 T441 T442 G443 H444 T445 I446 E447 R448 Q449 Y450 Q451 S452 W453 L454 G455 I458 L459 T460 S461 L462 G463 T464 F465 H466 Q467 L468 W469 Y475 L483 L484 R487 F488 R489 Molecule 7: Actin Chain G: MET V5 A6 A7 L8 V9 I10 S14 G15 M16 C17 K18 A19 G20 F21 A22 G23 D24 D25 A26 P27 R28 A29 V30 S33 I34 V35 G36 R37 HIS MET MET S52 Y53 V54 G55 A58 L65 T66 L67 R68 Y69 P70 I71 E72 H73 T77 N78 W79 D80 D81 M82 E83 K84 I85 W86 H87 H88 Y91 R95 E99 E100 H101 P102 V103 L104 L105 T106 E107 A108 P109 M110 N111 P112 K113 S114 N115 R116 E117 Q121 F124 E125 V129 P130 A131 F132 Y133 V134 S135 I136 Q137 A138 V139 L140 Y143 S144 R147 T148 T149 G150 I151 V152 L153 D154 S155 G156 D157 G158 V159 T160 H161 V162 V163 P164 I165 Y166 F169 P172 H173 A174 I175 L176 R177 I178 D179 L180 D184 L185 T186 D187 Y188 L189 M190 K191 I192 R196 TYR T203 R206 E207 I208 V209 R210 D211 I212 K213 L216 A220 F223 E226 A230 I236 E237 K238 S239 L242 P243 Q246 T249 I250 G251 N252 E253 R254 F255 R256 A257 P258 E259 A260 L261 L269 E270 S271 A272 G273 I274 D275 Q276 T277 T278 Y279 N280 S281 I282 M283 D286 V287 D288 V289 R290 K291 E292 L293 N296 I297 V298 M299 S300 T304 I309 A310 E311 R312 M313 Q314 K315 E316 I317 K326 V327 K328 I329 I330 A331 P332 R335 K336 Y337 S338 V339 W340 G343 S344 I345 L346 A347 S348 L349 T350 T351 F352 Q353 Q354 M355 W356 I357 S358 K359 Q360 E361 Y362 D363 E364 P367 V370 H371 H372 K373 C374 F375 Molecule 8: Chromatin modication-related protein EAF1 Chain E: T357 H358 Q359 N360 I361 L362 L363 E364 E365 A366 K367 W368 M369 Q370 F373 K374 E375 G376 H377 K378 Y379 K380 V381 A382 I383 C384 T385 A386 M387 A388 Q389 A390 I391 K392 D393 Y394 W395 T396 Y397

10 Page 10 Full wwpdb/emdatabank EM Map/Model Validation Report 5Y81 4 Experimental information io Property Value Source Reconstruction method SINGLE PARTICLE Depositor Imposed symmetry POINT, Not provided Depositor Number of particles used Depositor Resolution determination method FSC CUT-OFF Depositor CTF correction method PHASE FLIPPING AND AMPLITUDE Depositor CORRECTION Microscope FEI TITAN KRIOS Depositor Voltage (kv) 300 Depositor Electron dose (e /Å 2 ) 30 Depositor Minimum defocus (nm) Not provided Depositor Maximum defocus (nm) Not provided Depositor Magnication Not provided Depositor Image detector GATAN K2 SUMMIT (4k x 4k) Depositor

11 Page 11 Full wwpdb/emdatabank EM Map/Model Validation Report 5Y81 5 Model quality io 5.1 Standard geometry io The Z score for a bond length (or angle) is the number of standard deviations the observed value is removed from the expected value. A bond length (or angle) with Z > 5 is considered an outlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (or angles). Mol Chain Bond lengths Bond angles RMSZ # Z >2 RMSZ # Z >2 1 B / /8237 (0.0%) 2 C / /1110 (0.2%) 4 H / /1039 (0.2%) 5 A /9944 (0.0%) /13772 (0.2%) 6 F / / G / / E / /473 All All /24040 (0.0%) /33025 (0.1%) All (1) bond length outliers are listed below: Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å) 5 A 410 C-N All (38) bond angle outliers are listed below: Mol Chain Res Type Atoms Z Observed( o ) Ideal( o ) 5 A 777 N-CA-CB B 3129 N-CA-CB A 891 N-CA-CB A 1919 N-CA-CB H 89 N-CA-CB A 707 N-CA-CB A 2497 N-CA-CB A 786 N-CA-CB A 573 N-CA-CB A 1474 N-CA-CB A 575 N-CA-CB A 579 N-CA-CB A 2331 N-CA-CB C 796 N-CA-CB A 1336 N-CA-CB A 1963 N-CA-CB

12 Page 12 Full wwpdb/emdatabank EM Map/Model Validation Report 5Y81 Mol Chain Res Type Atoms Z Observed( o ) Ideal( o ) 5 A 882 N-CA-CB A 833 N-CA-CB A 2496 N-CA-CB C 740 N-CA-CB A 1993 N-CA-CB A 1951 N-CA-CB A 1548 N-CA-CB B 2921 N-CA-CB A 877 N-CA-CB A 2185 N-CA-CB A 458 N-CA-CB A 874 N-CA-CB A 1563 N-CA-CB A 1321 N-CA-CB A 1453 N-CA-CB A 852 N-CA-CB A 805 N-CA-CB A 1742 N-CA-CB H 229 N-CA-CB A 866 N-CA-CB A 568 N-CA-CB A 2505 N-CA-CB There are no chirality outliers. There are no planarity outliers. 5.2 Too-close contacts io In the following table, the Non-H and H(model) columns list the number of non-hydrogen atoms and hydrogen atoms in the chain respectively. The H(added) column lists the number of hydrogen atoms added and optimized by MolProbity. The Clashes column lists the number of clashes within the asymmetric unit, whereas Symm-Clashes lists symmetry related clashes. Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes 1 B C D H A F G

13 Page 13 Full wwpdb/emdatabank EM Map/Model Validation Report 5Y81 Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes 8 E All All The all-atom clashscore is dened as the number of clashes found per 1000 atoms (including hydrogen atoms). The all-atom clashscore for this structure is 40. All (1656) close contacts within the same asymmetric unit are listed below, sorted by their clash magnitude. 1:B:3106:TRP:CZ3 1:B:3668::HD :G:163::CG2 7:G:175::HG :G:163::HG22 7:G:175::CG :G:163::CG2 7:G:175::CG :B:3139::CB 1:B:3418::HH :G:163::CG2 7:G:175::CD :B:3236::HG3 1:B:3338:CYS:CB :B:3474::CE2 1:B:3526::HG :B:3427::CB 1:B:3443::HE :B:3106:TRP:CH2 1:B:3668::HD :B:3171::HD23 1:B:3172::N :B:3474::CE2 1:B:3526::CG :A:2243::HA 5:A:2252::CB :B:3427::HB2 1:B:3443::CE :B:3625::CB 1:B:3727::HB :B:3403::CB 1:B:3457::HB :B:3043::CB 1:B:3060:TRP:NE :B:3106:TRP:CH2 1:B:3668::CD :B:3106:TRP:HH2 1:B:3668::CG :B:3731::NH2 2:C:694:TRP:CD :B:2828:TRP:CB 1:B:2842::HD :B:2828:TRP:CB 1:B:2842::CD :B:3427::CB 1:B:3443::CE :B:3139::CB 1:B:3418::NH :B:3043::CB 1:B:3060:TRP:HE :B:2633:TRP:CB 5:A:2624::CB :B:3731::NH2 2:C:694:TRP:HD :B:3253::CD2 1:B:3314::CB :B:3731::HD2 2:C:694:TRP:NE :C:721::O 2:C:724::CB :B:3244::HA 1:B:3247::CD :B:3367:HIS:HE1 5:A:912:TYR:O

14 Page 14 Full wwpdb/emdatabank EM Map/Model Validation Report 5Y81 1:B:3568::HB 1:B:3569::CD :B:3705::CB 1:B:3709::HA :B:3106:TRP:CH2 1:B:3668::CG :B:3450::C 1:B:3451::HD :B:3427::CA 1:B:3443::CE :B:3667::CD1 1:B:3692::CB :F:442::CG2 6:F:448::HE :B:3424::NH1 1:B:3447::HA :B:3719::HA 1:B:3722::OD :A:333::CB 5:A:376::CB :D:418::CB 6:F:441::H :A:1093::O 5:A:1095::N :A:430::O 5:A:432::N :B:3427::CA 1:B:3443::HE :B:3374::CB 1:B:3392:MET:CB :B:3100::HD13 1:B:3101::N :F:444:HIS:O 6:F:446::N :G:163::HG21 7:G:175::CD :B:3474::CD2 1:B:3526::HG :B:3163:TYR:CB 1:B:3167::CD :A:1372::O 5:A:1375::N :A:1043::O 5:A:1046::HB :B:3450::O 1:B:3451::CD :F:213::HB3 6:F:214::CD :A:2243::CB 5:A:2252::C :B:3568::HB 1:B:3569::HD :A:1363::O 5:A:1364::CB :B:3474::CE2 1:B:3526::HG :F:62::O 6:F:71::HD :B:3528::CB 1:B:3632::O :B:3427::HA 1:B:3443::CE :B:3236::CG 1:B:3338:CYS:CB :A:1091::CB 5:A:1099::HA :B:3360::CB 1:B:3424::HH :B:3099::HB2 1:B:3425::HD :B:3106:TRP:CH2 1:B:3668::CB :B:3496::HB1 2:C:684:TYR:CE :B:3106:TRP:HH2 1:B:3668::CD :B:3367:HIS:CE1 5:A:912:TYR:O :A:1091::CA 5:A:1099::HB :B:3450::O 1:B:3451::HD

15 Page 15 Full wwpdb/emdatabank EM Map/Model Validation Report 5Y81 1:B:3068::HD23 1:B:3081::CB :A:2243::CA 5:A:2252::CB :B:3625::CB 1:B:3727::CB :A:631::CB 5:A:1587::CB :A:137::O 5:A:139::N :B:2690::HA 1:B:3715::CB :F:213::HB3 6:F:214::HD :B:3360::CB 1:B:3424::NH :B:2647::CB 1:B:2651::OD :B:2659::HG3 1:B:2681::CB :B:3740::C 1:B:3742::HD :B:3171::CD2 1:B:3172::N :B:3244::HA 1:B:3247::HD :B:3106:TRP:HB2 1:B:3665::HD :A:239::O 5:A:241::N :B:3253::HD21 1:B:3314::CB :B:3053::CB 1:B:3056::HB :B:3496::HB1 2:C:684:TYR:HE :B:3106:TRP:CZ3 1:B:3668::CD :F:87::O 6:F:132:MET:HE :B:3427::HA 1:B:3443::CZ :F:442::HG21 6:F:448::HE :B:3116:MET:O 1:B:3119::N :B:3568::CB 1:B:3569::CD :A:1292::O 5:A:1294:CYS:N :G:138::CB 7:G:165::HD :G:163::HG22 7:G:175::CD :B:3407:TYR:H 1:B:3408::CD :A:1091::CB 5:A:1099::CB :B:3068::HB2 1:B:3078::CB :B:3106:TRP:HH2 1:B:3668::HG :B:3163:TYR:CB 1:B:3167::HD :C:673::HA 2:C:681::HG :G:163::HG21 7:G:175::HD :B:2828:TRP:CB 1:B:2842::HD :B:3068::HD23 1:B:3081::HB :B:2638::O 1:B:2642::N :B:3474::CD2 1:B:3526::HG :B:3068::HB2 1:B:3078::HB :B:3705::CB 1:B:3709::CA :B:2670::CA 1:B:2837::HG

16 Page 16 Full wwpdb/emdatabank EM Map/Model Validation Report 5Y81 1:B:3450::C 1:B:3451::CD :B:3163:TYR:CB 1:B:3167::HD :A:1859::O 5:A:1861::N :B:3068::CD2 1:B:3081::HB :G:163::HG23 7:G:175::HG :B:3377::CB 1:B:3390::O :A:1091::HA 5:A:1099::HB :B:3407:TYR:H 1:B:3408::HD :B:3043::CB 1:B:3060:TRP:CD :A:1097::O 5:A:1099::N :B:3618::O 1:B:3620::N :A:1152::O 5:A:1154::N :B:3244::HA 1:B:3247::HD :A:2243::CB 5:A:2253::N :B:3403::CB 1:B:3457::CB :A:424::O 5:A:426::N :B:3719::O 1:B:3722::HB :B:3404::H 1:B:3457::HG :A:1441::O 5:A:1445::N :B:3171::O 1:B:3174::N :G:163::HG23 7:G:175::CG :D:79::O 3:D:80::O :G:163::CG2 7:G:175::HD :B:3427::HB2 1:B:3443::CD :A:1091::CB 5:A:1099::CA :B:2670::N 1:B:2837::HG :B:2638::O 1:B:2642::HB :A:1043::O 5:A:1046::CB :B:3618::O 1:B:3619::C :C:715::O 2:C:717::N :B:3099::CB 1:B:3425::HD :C:713::O 2:C:714::O :B:3703::O 1:B:3704::O :B:3427::CA 1:B:3443::CZ :F:87::O 6:F:132:MET:CE :B:3474::CD2 1:B:3526::CG :B:3649::OG 1:B:3705::HA :F:442::HG21 6:F:448::NE :A:1292::C 5:A:1294:CYS:H :B:3244::CA 1:B:3247::HD :B:3424::HH12 1:B:3447::HA

17 Page 17 Full wwpdb/emdatabank EM Map/Model Validation Report 5Y81 1:B:3741:MET:N 1:B:3742::CD :B:3106:TRP:HB2 1:B:3665::CD :F:71::HD11 6:F:229::HD :F:66::NH1 6:F:66::HB :A:1372::O 5:A:1374::N :A:1157::O 5:A:1159::N :B:2659::CG 1:B:2681::CB :A:1227::O 5:A:1231::CB :B:3411::O 1:B:3415::N :F:91::HB2 6:F:132:MET:CE :A:1300::O 5:A:1302::N :F:211::OE1 6:F:217::HD :B:3085:TYR:C 1:B:3104::CD :B:3391::O 1:B:3402::CB :D:418::CB 6:F:441::N :B:3424::NE 1:B:3445::CB :B:3649::CB 1:B:3705::HA :B:3492::HE3 1:B:3492::HA :A:516::O 5:A:518:MET:N :B:3422::H 1:B:3422::HD :F:442::CG2 6:F:448::NE :B:2822::O 1:B:2825::N :B:3253::HD23 1:B:3314::CB :B:3106:TRP:CH2 1:B:3668::HB :B:3668::HE 1:B:3672::HD :B:3171::HD23 1:B:3172::CA :B:3247::HG3 1:B:3247::HH :B:3171::CD2 1:B:3172::H :B:3649::HB2 1:B:3704::O :B:3053::CB 1:B:3056::CB :E:391::HA 8:E:394:TYR:HB :C:722::C 2:C:724::H :G:138::HB1 7:G:165::HD :B:3740::CB 1:B:3742::HD :F:129::HD22 6:F:129::H :B:2817:CYS:CB 1:B:2852::CZ :B:3474::CG 1:B:3526::HG :B:3667::HD12 1:B:3692::CB :B:3644::HA 1:B:3647::OG :F:213::CB 6:F:214::CD :A:244::O 5:A:245::O

18 Page 18 Full wwpdb/emdatabank EM Map/Model Validation Report 5Y81 1:B:3244::O 1:B:3247::HG :B:3424::HE 1:B:3445::CB :G:139::HG13 7:G:165::HG :B:2690::CA 1:B:3715::CB :B:3244::CA 1:B:3247::CD :B:3667::HD13 1:B:3692::CB :G:286::HB3 7:G:288::OD :B:3731::CD 2:C:694:TRP:HE :H:51::O 4:H:55::N :G:163::HG22 7:G:175::HD :A:1091::CA 5:A:1099::CB :B:3055::O 1:B:3059::N :B:3740::C 1:B:3742::CD :B:2640::HD21 1:B:2662::CB :B:3085:TYR:C 1:B:3104::HD :B:3219:TYR:N 1:B:3220::HD :B:3731::CD 2:C:694:TRP:NE :A:1506::O 5:A:1508::N :B:2638::O 1:B:2642::CB :B:3253::HD22 1:B:3314::CB :B:3618::CB 1:B:3620::O :F:87::HG3 6:F:132:MET:HE :B:3106:TRP:HZ3 1:B:3668::HD :A:1069::O 5:A:1072:TYR:N :B:3568::HG22 1:B:3569::HD :A:511::O 5:A:515::CB :F:442::OG1 6:F:443::N :B:3106:TRP:CH2 1:B:3668::NH :B:3107::HA 1:B:3110::HD :B:3731::CZ 2:C:694:TRP:HD :B:3407:TYR:N 1:B:3408::CD :G:151::HG23 7:G:297::HA :B:3568::CB 1:B:3569::HD :G:151::HG21 7:G:297::HG :A:239::C 5:A:241::H :B:2748::HB3 1:B:2752:HIS:CD :F:428::HB3 6:F:437::HE :B:2821::CB 1:B:2849:TYR:CE :A:511::O 5:A:515::N :B:3474::CZ 1:B:3526::HG :B:3354::HA 1:B:3371::H

19 Page 19 Full wwpdb/emdatabank EM Map/Model Validation Report 5Y81 1:B:3219:TYR:H 1:B:3220::HD :B:3418::O 1:B:3422::CD :B:3388:TYR:CB 1:B:3404::HB :B:3106:TRP:CZ2 1:B:3668::CB :B:2961::C 1:B:2963:CYS:H :B:3418::CB 1:B:3418::HH :B:3551::O 1:B:3554::N :F:428::HB3 6:F:437::CE :B:3474::HE2 1:B:3526::CG :G:16:MET:N 7:G:16:MET:SD :A:1650::O 5:A:1652::N :B:3055::CB 1:B:3059::HG :B:3652::O 1:B:3652::HD :B:3169::CE1 1:B:3451::HD :G:138::HA 7:G:152::HG :B:3526::O 1:B:3530:HIS:N :F:87::CG 6:F:132:MET:CE :B:3424::CD 1:B:3445::CB :F:87::HG2 6:F:132:MET:HE :F:62::O 6:F:71::CD :B:2651::O 1:B:2653::N :F:45::HA3 6:F:56::HG :A:1993::O 5:A:1998::N :G:16:MET:H 7:G:16:MET:CE :B:3062::HZ 1:B:3657::C :G:138::HB3 7:G:165::HD :B:2821::HA 1:B:2849:TYR:OH :B:3731::HD2 2:C:694:TRP:CD :B:3068::CB 1:B:3078::CB :B:3703::O 1:B:3704::C :B:3427::N 1:B:3443::CZ :F:91::OE1 6:F:132:MET:SD :B:3576::H 1:B:3576::HD :B:3618::O 1:B:3620::O :A:302::O 5:A:304::N :D:155::O 3:D:159::N :B:3481::CB 1:B:3482::CD :A:1859::O 5:A:1862::N :A:914::O 5:A:915::C :B:3568::CG2 1:B:3569::HD :B:3418::HB2 1:B:3418::HH

20 Page 20 Full wwpdb/emdatabank EM Map/Model Validation Report 5Y81 1:B:3168:HIS:O 1:B:3172::HB :F:213::C 6:F:213::HE :B:3168:HIS:HA 1:B:3171::HD :B:3411::HD2 1:B:3587::CB :F:91::HB2 6:F:132:MET:SD :B:3106:TRP:CB 1:B:3665::HD :A:1097::O 5:A:1100:MET:N :B:3731::HD2 2:C:694:TRP:HE :A:996::O 5:A:998::N :C:722::O 2:C:726::CB :G:140::CD1 7:G:343::N :B:2744::O 1:B:2747::HG :F:87::CG 6:F:132:MET:HE :A:1006::CB 5:A:1009::CB :A:2567::C 5:A:2569::H :F:442::HG21 6:F:448::CG :B:3404::N 1:B:3457::HG :A:1506::C 5:A:1508::H :B:3173::CB 1:B:3451::HA :B:3667::HD11 1:B:3692::CB :A:1629::O 5:A:1630::O :G:140::HD12 7:G:343::N :A:976::O 5:A:977::CB :B:3171::O 1:B:3174::OG :G:242::HD12 7:G:246::HB :A:1361::O 5:A:1363::N :B:2633:TRP:CB 5:A:2624::C :B:3719::CA 1:B:3722::OD :G:18::HG2 7:G:30::HG :G:14::HA 7:G:71::HB :A:976::HA 5:A:992::CB :B:3253::HD12 1:B:3318::HG :B:3106:TRP:CE3 1:B:3665::HD :B:3493::O 1:B:3510::NZ :B:3466::HG22 1:B:3573:HIS:HB :G:298::HG22 7:G:330::HB :B:3169::HE1 1:B:3451::CD :B:3656::O 1:B:3658::N :A:430::O 5:A:431::C :B:3060:TRP:CE3 1:B:3064::ND :B:3486::O 1:B:3486::NE

21 Page 21 Full wwpdb/emdatabank EM Map/Model Validation Report 5Y81 5:A:1200::O 5:A:1203::CB :G:178::HD11 7:G:277::HG :B:3062::CZ 1:B:3657::C :B:3705::CB 1:B:3709::CB :F:87::C 6:F:132:MET:CE :A:217::O 5:A:220::N :B:3100::CD1 1:B:3101::N :A:1590::O 5:A:1591::CB :B:2655::HG22 1:B:2656::N :B:3116:MET:O 1:B:3118::N :B:3247::HG2 1:B:3248::H :A:1650::O 5:A:1653::N :B:3555::O 1:B:3559::N :G:286::CB 7:G:288::OD :B:3068::CD2 1:B:3081::CB :B:3731::CZ 2:C:694:TRP:CD :A:890:TYR:O 5:A:893::N :F:72::HB3 6:F:72::NZ :B:2853::O 1:B:2856::OG :B:3102:CYS:SG 1:B:3134::CB :E:390::O 8:E:394:TYR:N :A:1091::CB 5:A:1099::HB :B:2944::HA 1:B:2970::HD :B:3068::HB3 1:B:3078::HA :B:3461::CB 1:B:3464::CZ :G:140::HD12 7:G:343::H :A:2567::O 5:A:2569::N :D:140::O 6:F:178::NZ :F:71::HD12 6:F:229::HD :A:1032::O 5:A:1033::CB :B:2818::O 1:B:2821::CB :B:3496::CB 2:C:684:TYR:CE :A:1097::O 5:A:1098::C :B:2967::O 1:B:2967::HD :B:3047::O 1:B:3050::O :C:805::O 2:C:809::N :A:239::C 5:A:241::N :B:3106:TRP:CH2 1:B:3668::HG :A:1091::HA 5:A:1099::CB :A:736::N 5:A:1543::C :A:328::O 5:A:332::CB

22 Page 22 Full wwpdb/emdatabank EM Map/Model Validation Report 5Y81 6:F:91::HB2 6:F:132:MET:HE :F:213::HB3 6:F:214::HD :F:66::HH11 6:F:66::HB :G:108::HB1 7:G:109::CD :A:1296::HA 5:A:1356::HB :A:1605::O 5:A:1608::N :B:3219:TYR:N 1:B:3220::CD :A:976::CA 5:A:992::CB :D:439::O 3:D:443::N :G:150::O 7:G:293::CD :G:19::HB3 7:G:29::HB :G:9::O 7:G:340:TRP:NE :F:87::HG3 6:F:132:MET:CE :G:102::HB3 7:G:131::HB :G:237::HG2 7:G:251::HA :F:213::HE3 6:F:213::CA :G:163::HG23 7:G:175::CG :G:220::HB1 7:G:226::HG :A:1300::C 5:A:1302::H :B:3457::O 1:B:3457::HD :B:3247::NH2 1:B:3247::HG :B:3435::OE1 1:B:3435::N :A:1255::O 5:A:1258::N :B:3100::HD13 1:B:3101::CA :B:3625::N 1:B:3626::HD :D:55::O 3:D:59::N :F:211::OE1 6:F:217::CD :A:900::CB 5:A:948::CD :C:717::O 2:C:718:HIS:CB :B:2777::O 1:B:2781::N :B:3099::HB2 1:B:3425::CD :B:3489:MET:CE 1:B:3511::HG :B:3474::CD2 1:B:3526::CG :B:2941:HIS:CD2 1:B:2941:HIS:H :B:3169::HE1 1:B:3451::CG :B:3404::H 1:B:3457::CG :B:3740::CA 1:B:3742::HD :A:1068::O 5:A:1070::N :B:3097::HD13 1:B:3097::N :D:419::CB 6:F:439::HD :B:3171::HD23 1:B:3172::H

23 Page 23 Full wwpdb/emdatabank EM Map/Model Validation Report 5Y81 1:B:3427::ND2 1:B:3428::N :B:3494::HA 1:B:3497:HIS:HB :B:3062::HZ 1:B:3658::N :B:3244::CA 1:B:3247::HD :B:3659::O 1:B:3662:TYR:CB :C:721::O 2:C:724::CA :A:2005::O 5:A:2009:HIS:N :B:3057:TRP:O 1:B:3061::N :B:3462::O 1:B:3464::CD :G:163::CG2 7:G:175::HD :G:185::O 7:G:189::N :B:3492::CA 1:B:3492::HE :F:129::N 6:F:129::HD :A:1091::C 5:A:1099::HB :A:516::O 5:A:519::N :A:578::O 5:A:582::N :F:455::HA2 6:F:458::HD :G:164::HG2 7:G:174::HB :A:1650::O 5:A:1651:TYR:C :G:138::HB1 7:G:165::CD :G:287::HG12 7:G:290::NH :B:3741:MET:N 1:B:3742::HD :G:236::O 7:G:254::NH :A:239::O 5:A:242::N :B:2882::HA 1:B:2885::HG :B:3625::H 1:B:3626::HD :B:3649::HB2 1:B:3705::HA :A:1069::CB 5:A:1072:TYR:CB :F:129::CD2 6:F:129::H :F:210::HB2 6:F:219::HA :F:415::HA 6:F:420::HD :A:972::O 5:A:973::O :B:3656::C 1:B:3658::H :A:1090::C 5:A:1092::H :B:3062::HZ 1:B:3658::CA :C:722::C 2:C:724::N :A:856::O 5:A:860::N :F:8::HG22 8:E:368:TRP:HB :H:57::O 4:H:61::N :A:1032::O 5:A:1033::HB :B:3247::HG2 1:B:3248::N

24 Page 24 Full wwpdb/emdatabank EM Map/Model Validation Report 5Y81 1:B:3388:TYR:HA 1:B:3405::CB :B:3247::NH1 1:B:3407:TYR:CB :B:3424::HH12 1:B:3447::CA :F:92:TRP:O 6:F:96::ND :A:410::C 5:A:412::H :A:1372::O 5:A:1373::C :A:897::O 5:A:901::N :B:3105::HD12 1:B:3105::O :B:3444::O 1:B:3446::HD :B:3618::C 1:B:3620::N :D:426::O 3:D:430::N :D:440::O 3:D:444::N :B:3509::HD11 2:C:687::HD :D:150::O 3:D:153::N :B:2899::N 1:B:2899::OD :B:3424::HD3 1:B:3445::CB :B:3169::CZ 1:B:3451::HD :B:3167::O 1:B:3167::HD :D:151::O 3:D:155::N :B:2944::HA 1:B:2970::CD :B:3644::CA 1:B:3647::OG :B:3106:TRP:CZ2 1:B:3668::HB :B:3719::HA 1:B:3722::CG :F:444:HIS:O 6:F:445::C :A:583::O 5:A:587:TYR:N :B:3375::CB 1:B:3376::CD :F:212::O 6:F:275::ND :B:3169::HE1 1:B:3451::HG :B:3427::N 1:B:3443::CE :F:442::HG22 6:F:448::HE :G:151::CG2 7:G:297::HA :A:1093::C 5:A:1095::H :B:3086::N 1:B:3104::HD :A:2415::O 5:A:2419::N :A:814::O 5:A:818::N :B:3418::O 1:B:3422::HD :F:87::HG2 6:F:132:MET:CE :A:410::C 5:A:412::N :A:1090::O 5:A:1092::N :A:1605::O 5:A:1607::N :A:2243::CB 5:A:2253::CA

25 Page 25 Full wwpdb/emdatabank EM Map/Model Validation Report 5Y81 1:B:3618::O 1:B:3620::C :G:132::N 7:G:357::O :A:2389::O 5:A:2392::N :F:204::HB 6:F:274:TRP:CE :A:1605::O 5:A:1606::C :B:3168:HIS:O 1:B:3172::N :C:754::O 2:C:758::N :B:3646::O 1:B:3649::OG :B:3667::HD13 1:B:3692::CA :D:172::N 8:E:357::OG :F:87::CG 6:F:132:MET:HE :G:124::CZ 7:G:132::HB :B:3101::HD22 1:B:3101::O :B:3391::H 1:B:3402::CB :A:1964::O 5:A:1968::N :A:1859::O 5:A:1860::C :B:3094::CB 1:B:3097::HG :B:3253::CD1 1:B:3318::HG :C:699::HD2 2:C:699::N :G:163::HG22 7:G:175::HG :G:9::HG21 7:G:344::HA :B:3173::O 1:B:3452::HB :A:2181:MET:O 5:A:2185::N :B:2914::OD1 1:B:2915::N :A:900::CB 5:A:948::HD :B:3737::OD2 1:B:3739::ND :F:428::CB 6:F:437::HE :B:3422::H 1:B:3422::CD :B:2638::C 1:B:2642::HB :B:2962::HA 1:B:2965::HB :G:297::HB 7:G:329::HG :B:2670::N 1:B:2837::CG :G:212::HG23 7:G:216::HD :B:2817:CYS:CB 1:B:2852::HZ :B:3068::HD23 1:B:3081::HB :B:3670::O 1:B:3673::OG :H:12::O 4:H:16::N :A:369:TYR:O 5:A:373::N :F:1:MET:H 7:G:371:HIS:CG :A:1292::C 5:A:1294:CYS:N :G:121::O 7:G:362:TYR:OH

26 Page 26 Full wwpdb/emdatabank EM Map/Model Validation Report 5Y81 5:A:516::O 5:A:517::C :B:3489:MET:HE1 1:B:3511::HG :B:3568::CB 1:B:3569::HD :B:3644::O 1:B:3647::OG :B:3055::C 1:B:3059::HB :B:3625::N 1:B:3626::CD :A:967::O 5:A:968::O :A:976::C 5:A:992::CB :B:3514::O 1:B:3518::N :G:151::CG2 7:G:297::HG :A:2243::CB 5:A:2253::HA :B:3468:HIS:HB2 1:B:3570:HIS:HA :H:261::O 4:H:265::N :E:382::O 8:E:385::OG :G:24::HB2 7:G:340:TRP:HH :A:1249::O 5:A:1251::N :C:713::O 2:C:714::C :A:2243::CB 5:A:2252::CB :B:3481::CB 1:B:3482::HD :B:3649::CB 1:B:3704::O :B:3105::HD12 1:B:3105::C :C:684:TYR:HA 2:C:687::HB :B:2670::HA 1:B:2837::HG :B:3407:TYR:N 1:B:3408::HD :F:233::O 6:F:237::N :F:11::N 6:F:461::O :G:137::N 7:G:137::OE :A:1345::HA 5:A:1349:MET:CB :G:347::O 7:G:353::NE :G:163::HG21 7:G:175::HD :B:3448::HA 1:B:3458:MET:HA :B:3667::HD13 1:B:3692::C :B:3060:TRP:CZ3 1:B:3064::ND :A:486:MET:O 5:A:490::N :B:3169::CE1 1:B:3451::CD :G:312::NE 7:G:316::OE :D:156::O 3:D:160::N :G:242::N 7:G:246::O :B:3019::CG 1:B:3020::N :B:3461::CB 1:B:3464::HZ :G:275::OD1 7:G:276::N

27 Page 27 Full wwpdb/emdatabank EM Map/Model Validation Report 5Y81 1:B:2633:TRP:CB 5:A:2624::CA :H:113::O 4:H:117::N :A:1093::C 5:A:1095::N :A:353:HIS:O 5:A:357::N :F:174:MET:HA 6:F:489[B]::HB :F:47:TYR:O 6:F:53::OD :G:239::HA 7:G:249::HA :A:588::O 5:A:592::N :B:3060:TRP:O 1:B:3063::N :B:3527::O 1:B:3531::N :B:3719::C 1:B:3722::HB :G:99::HA 7:G:129::HA :B:3062::CZ 1:B:3657::O :B:3253::HD11 1:B:3318::HB :C:695::O 2:C:699::HD :D:64::O 6:F:434::OG :D:396::HA 6:F:436::HE :F:72::HD2 6:F:73::HD :B:3101::HD13 1:B:3101::C :A:1296::HA 5:A:1356::CB :B:3086::N 1:B:3104::CD :B:3423:TYR:CB 1:B:3558:MET:CE :F:169::HB2 6:F:176::HB :G:163::HG23 7:G:175::HG :A:1646::O 5:A:1649::N :A:1763::O 5:A:1767::N :B:3494::HD22 1:B:3497:HIS:HB :B:3101::HD13 1:B:3101::O :A:1036::O 5:A:1038::N :A:1201:CYS:HA 5:A:1209::HA :A:1452::O 5:A:1456::N :A:424::C 5:A:426::N :B:3437::O 1:B:3440::N :B:2748::HB3 1:B:2752:HIS:HD :B:3241::O 1:B:3242::CB :B:3541::O 1:B:3544::N :H:115::O 4:H:119::N :H:183::O 4:H:187::N :B:2998::O 1:B:3001::N :B:2635::OE1 1:B:2635::N :F:191::HA 6:F:194::HD

28 Page 28 Full wwpdb/emdatabank EM Map/Model Validation Report 5Y81 6:F:254::O 6:F:258::N :B:2821::CB 1:B:2849:TYR:HE :B:3100::HD13 1:B:3100::C :B:3509::HA 1:B:3512::HB :B:3253::HD21 1:B:3314::CA :B:2967::HD12 1:B:2967::C :B:3062::CZ 1:B:3658::CA :G:138::CB 7:G:165::CD :A:1247::O 5:A:1248::CB :A:2243::CB 5:A:2252::O :B:3159::O 1:B:3163:TYR:N :B:3427::HD22 1:B:3428::N :A:1152::C 5:A:1154::H :A:217::O 5:A:219::N :A:389::O 5:A:392:TYR:N :A:483::O 5:A:487::N :B:2691::O 1:B:2695::N :B:3509::O 1:B:3513::N :B:3652::C 1:B:3652::HD :A:122::CB 5:A:219::CB :A:579::O 5:A:583::N :G:138::HA 7:G:152::CG :H:189::O 4:H:193::N :A:1091::O 5:A:1099::HB :A:976::O 5:A:992::CB :B:3100::HD22 1:B:3100::C :B:3171::C 1:B:3174::HG :B:3474::HE2 1:B:3526::HG :A:1117::O 5:A:1121::N :B:2651::O 1:B:2654::N :B:3646::CB 1:B:3720::HD :D:278::O 3:D:282::N :F:16::HB2 6:F:107::HG :F:71::CD1 6:F:229::HD :A:686::O 5:A:690::N :F:107::HB2 6:F:469:TRP:CZ :A:1580::O 5:A:1583::CB :F:213::HE3 6:F:213::HA :F:266::C 6:F:282::HD :B:2779::O 1:B:2783::N :B:2651::O 1:B:2652::C

29 Page 29 Full wwpdb/emdatabank EM Map/Model Validation Report 5Y81 1:B:3040::OD1 1:B:3060:TRP:CZ :B:3229::HD12 1:B:3229::C :B:3462::O 1:B:3464::N :B:3740::HB3 1:B:3742::HD :D:277::O 3:D:281::N :C:673::O 2:C:675:HIS:N :G:73:HIS:HA 7:G:159::HG :H:24::O 4:H:28::N :A:430::C 5:A:432::N :B:2961::C 1:B:2963:CYS:N :B:3493::C 1:B:3493::HD :B:3703::C 1:B:3704::O :B:3244::O 1:B:3247::CG :B:3474::CG 1:B:3526::CG :G:163::HG23 7:G:175::CB :G:273::O 7:G:277::N :A:1069::O 5:A:1070::C :A:487::O 5:A:491::N :G:151::HG23 7:G:151::O :A:137::O 5:A:138::C :F:413::HA3 6:F:449::HE :A:217::O 5:A:218:MET:C :A:2256::O 5:A:2260::N :A:424::C 5:A:426::H :B:2912::HD13 1:B:2912::N :B:3492::HD2 1:B:3492::N :F:112::OE1 6:F:116::ND :F:301::HG2 6:F:304:TRP:HB :A:1506::C 5:A:1508::N :B:3055::CB 1:B:3059::CG :B:3404::O 1:B:3457::CG :H:191::O 4:H:195::N :H:51::O 4:H:54::N :A:1036::C 5:A:1038::H :B:2822::O 1:B:2824::N :A:1090::C 5:A:1092::N :A:346::O 5:A:350::N :D:161::O 3:D:166::N :A:897::HA2 5:A:948::HD :B:3116:MET:O 1:B:3117::C :G:131::HA 7:G:358::HA

30 Page 30 Full wwpdb/emdatabank EM Map/Model Validation Report 5Y81 1:B:3489:MET:HE1 1:B:3511::CG :D:74::O 3:D:75::CB :E:360::O 8:E:364::HG :F:32::HA2 8:E:373::HZ :B:3418::O 1:B:3422::HD :B:3422::HD22 1:B:3422::N :C:739::HA 3:D:328::O :A:1859::C 5:A:1861::N :B:2885::HD3 1:B:2885::C :B:3068::HD22 1:B:3081::HB :B:3492::HA 1:B:3492::CE :C:721::O 2:C:724::N :D:168::O 3:D:171::N :F:80::HB 6:F:83:TRP:CZ :G:150::HA3 7:G:296::HB :H:119::O 4:H:122::N :B:3418::HH11 1:B:3418::CG :F:153::HB3 8:E:363::HD :B:2651::H 1:B:2651::ND :F:71::HD11 6:F:229::CD :G:139::N 7:G:165::HD :H:25::O 4:H:29::N :B:3062::HZ 1:B:3657::O :F:72::HZ3 6:F:72::HB :B:3062::CZ 1:B:3658::N :B:3354::CB 1:B:3355::CD :B:3427::HA 1:B:3443::HZ :G:149::HG23 7:G:166:TYR:HA :G:19::N 7:G:29::O :H:231::O 4:H:235::N :F:8::HG21 8:E:368:TRP:O :F:87::CA 6:F:132:MET:HE :F:272::OG 6:F:276::N :F:446::H 6:F:446::HD :B:3101::HD22 1:B:3104::HB :B:3106:TRP:CZ2 1:B:3668::HB :G:9::N 7:G:20::O :B:2895::HG12 1:B:2895::O :B:3489:MET:HE2 1:B:3511::HG :B:3556::O 1:B:3559::OG :G:107::HB2 7:G:111::HD

31 Page 31 Full wwpdb/emdatabank EM Map/Model Validation Report 5Y81 7:G:7::O 7:G:22::N :B:2636::HA 1:B:2639::HG :B:3394::HA 1:B:3398::HA :E:366::C 8:E:368:TRP:H :A:1938::O 5:A:1942::N :B:3019::HG3 1:B:3020::N :B:3139::CB 1:B:3418::CZ :F:308::OD1 6:F:309::N :G:33::O 7:G:33::OG :A:976::O 5:A:992::CA :A:634::O 5:A:638::N :A:872::O 5:A:876::N :B:3068::HD12 1:B:3069::N :B:3423:TYR:CB 1:B:3558:MET:HE :B:3071::O 1:B:3072::O :C:739::CB 3:D:328::O :G:147::NE 7:G:296::OD :A:878::O 5:A:881::N :A:995::CB 5:A:2558::CB :B:3169::CE1 1:B:3451::CG :B:3577::O 5:A:965::N :G:150::O 7:G:293::HD :A:2389::O 5:A:2390::C :B:2638::O 1:B:2642::CA :B:2690::CB 1:B:3715::CB :B:3423:TYR:CB 1:B:3558:MET:HE :A:682::O 5:A:686::N :B:3441::O 1:B:3441::HG :E:370::O 8:E:374::N :F:66::HB3 6:F:66::CZ :G:34::HD12 7:G:55::O :B:3169::CE1 1:B:3451::HG :B:3544::HE1 1:B:3579::HA :F:171::O 6:F:174:MET:N :A:976::O 5:A:992::HA :B:2970::O 1:B:2970::HG :G:353::HA 7:G:356:TRP:CD :A:1646::O 5:A:1647::C :A:914::O 5:A:917::N :B:2643::HG23 1:B:2643::O :F:91::H 6:F:132:MET:HE

32 Page 32 Full wwpdb/emdatabank EM Map/Model Validation Report 5Y81 6:F:99:TYR:OH 7:G:177::NH :A:430::O 5:A:433::N :B:2835:TYR:O 1:B:2839:HIS:N :B:2670::C 1:B:2837::HG :B:3085:TYR:CB 1:B:3104::CD :F:442::HG21 6:F:448::CD :G:192::HD12 7:G:253::HG :G:287::HG23 7:G:287::O :A:1091::O 5:A:1099::CB :A:982::CB 5:A:2481::CA :B:3366::HG13 1:B:3366::O :F:171::HG11 6:F:400::HD :B:3664::O 1:B:3667::HG :A:894::O 5:A:897::N :A:1107::O 5:A:1111:CYS:N :A:474::O 5:A:478::N :A:594::O 5:A:597::N :F:211::HB2 6:F:217::HD :G:172::HA 7:G:175::HD :B:3097::O 1:B:3097::HG :F:213::CE 6:F:213::HA :F:230:TYR:O 6:F:234::ND :G:5::HB 7:G:101:HIS:CE :G:159::HB 7:G:179::HA :B:3547::O 1:B:3551::N :G:357::HA 7:G:361::OE :A:927::O 5:A:930::OD :B:2851::HA 1:B:2854::HB :B:2817:CYS:CB 1:B:2852::CE :B:3106:TRP:HZ3 1:B:3668::CD :B:3483::N 1:B:3483::OD :G:144::OG 7:G:338::HB :A:341::O 5:A:345::N :B:3354::CB 1:B:3369::O :F:116::OD1 6:F:117::N :H:109::O 4:H:113::N :A:1372::C 5:A:1374::N :B:3644::C 1:B:3647::OG :F:94::O 6:F:100::N :B:2844:HIS:HA 1:B:2847::HB :B:3404::C 1:B:3457::HG