Full wwpdb/emdatabank EM Map/Model Validation Report i

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1 Full wwpdb/emdatabank EM Map/Model Validation Report i Oct 9, :26 AM EDT PDB ID : 5MLC EMDB ID: : EMD-3525 Title : Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions Authors : Graf, M.; Arenz, S.; Huter, P.; Doenhoefer, A.; Novacek, J.; Wilson, D.N. Deposited on : Resolution : 3.90 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 specific help available everywhere you see the i 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 5MLC 1 Overall quality at a glance i The following experimental techniques were used to determine the structure: ELECTRON MICROSCOPY The reported resolution of this entry is 3.90 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 RNA backbone 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 A B C D E F G H 220

3 Page 3 Full wwpdb/emdatabank EM Map/Model Validation Report 5MLC Mol Chain Length Quality of chain 9 I L M N O P Q R S T U V W X Y Z

4 Page 4 Full wwpdb/emdatabank EM Map/Model Validation Report 5MLC 2 Entry composition i There are 32 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. Molecule 1 is a RNA chain called 23S ribosomal RNA, chloroplastic. Mol Chain Residues Atoms AltConf Trace 1 A 2750 Total C N O P Molecule 2 is a RNA chain called 5S ribosomal RNA, chloroplastic. Mol Chain Residues Atoms AltConf Trace 2 B 120 Total C N O P Molecule 3 is a RNA chain called 4.8S ribosomal RNA, chloroplastic. Mol Chain Residues Atoms AltConf Trace 3 C 93 Total C N O P Molecule 4 is a protein called 50S ribosomal protein L2, chloroplastic. Mol Chain Residues Atoms AltConf Trace 4 D 246 Total C N O S Molecule 5 is a protein called 50S ribosomal protein L3, chloroplastic. Mol Chain Residues Atoms AltConf Trace 5 E 219 Total C N O S Molecule 6 is a protein called 50S ribosomal protein L4, chloroplastic. Mol Chain Residues Atoms AltConf Trace 6 F 205 Total C N O S

5 Page 5 Full wwpdb/emdatabank EM Map/Model Validation Report 5MLC Molecule 7 is a protein called 50S ribosomal protein L5, chloroplastic. Mol Chain Residues Atoms AltConf Trace 7 G 179 Total C N O S Molecule 8 is a protein called 50S ribosomal protein L6, chloroplastic. Mol Chain Residues Atoms AltConf Trace 8 H 178 Total C N O S Molecule 9 is a protein called 50S ribosomal protein L9, chloroplastic. Mol Chain Residues Atoms AltConf Trace 9 I 45 Total C N O Molecule 10 is a protein called 50S ribosomal protein L13, chloroplastic. Mol Chain Residues Atoms AltConf Trace 10 L 196 Total C N O S Molecule 11 is a protein called 50S ribosomal protein L14, chloroplastic. Mol Chain Residues Atoms AltConf Trace 11 M 120 Total C N O S Molecule 12 is a protein called 50S ribosomal protein L15, chloroplastic. Mol Chain Residues Atoms AltConf Trace 12 N 182 Total C N O S Molecule 13 is a protein called 50S ribosomal protein L16, chloroplastic. Mol Chain Residues Atoms AltConf Trace 13 O 135 Total C N O S Molecule 14 is a protein called 50S ribosomal protein L17, chloroplastic.

6 Page 6 Full wwpdb/emdatabank EM Map/Model Validation Report 5MLC Mol Chain Residues Atoms AltConf Trace 14 P 116 Total C N O S Molecule 15 is a protein called 50S ribosomal protein L18, chloroplastic. Mol Chain Residues Atoms AltConf Trace 15 Q 118 Total C N O S Molecule 16 is a protein called 50S ribosomal protein L19, chloroplastic. Mol Chain Residues Atoms AltConf Trace 16 R 114 Total C N O S Molecule 17 is a protein called 50S ribosomal protein L20, chloroplastic. Mol Chain Residues Atoms AltConf Trace 17 S 116 Total C N O S Molecule 18 is a protein called 50S ribosomal protein L21, chloroplastic. Mol Chain Residues Atoms AltConf Trace 18 T 134 Total C N O Molecule 19 is a protein called 50S ribosomal protein L22, chloroplastic. Mol Chain Residues Atoms AltConf Trace 19 U 152 Total C N O S Molecule 20 is a protein called 50S ribosomal protein L23, chloroplastic. Mol Chain Residues Atoms AltConf Trace 20 V 91 Total C N O S Molecule 21 is a protein called 50S ribosomal protein L24, chloroplastic.

7 Page 7 Full wwpdb/emdatabank EM Map/Model Validation Report 5MLC Mol Chain Residues Atoms AltConf Trace 21 W 129 Total C N O S Molecule 22 is a protein called 50S ribosomal protein L27, chloroplastic. Mol Chain Residues Atoms AltConf Trace 22 X 108 Total C N O Molecule 23 is a protein called 50S ribosomal protein L28, chloroplastic. Mol Chain Residues Atoms AltConf Trace 23 Y 75 Total C N O S Molecule 24 is a protein called 50S ribosomal protein L29, chloroplastic. Mol Chain Residues Atoms AltConf Trace 24 Z 94 Total C N O S Molecule 25 is a protein called 50S ribosomal protein L32, chloroplastic. Mol Chain Residues Atoms AltConf Trace Total C N O Molecule 26 is a protein called 50S ribosomal protein L33, chloroplastic. Mol Chain Residues Atoms AltConf Trace Total C N O S Molecule 27 is a protein called 50S ribosomal protein L34, chloroplastic. Mol Chain Residues Atoms AltConf Trace Total C N O S Molecule 28 is a protein called 50S ribosomal protein L35, chloroplastic.

8 Page 8 Full wwpdb/emdatabank EM Map/Model Validation Report 5MLC Mol Chain Residues Atoms AltConf Trace Total C N O S Molecule 29 is a protein called 50S ribosomal protein L36, chloroplastic. Mol Chain Residues Atoms AltConf Trace Total C N O S Molecule 30 is a protein called Ribosome-recycling factor, chloroplastic. Mol Chain Residues Atoms AltConf Trace Total C N O S Molecule 31 is a protein called PSRP5alpha, chloroplastic. Mol Chain Residues Atoms AltConf Trace Total C N O S Molecule 32 is a protein called PSRP6, chloroplastic. Mol Chain Residues Atoms AltConf Trace Total C N O S

9 Page 9 Full wwpdb/emdatabank EM Map/Model Validation Report 5MLC 3 Residue-property plots i These plots are drawn for all protein, RNA and DNA chains in the entry. The first 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: 23S ribosomal RNA, chloroplastic Chain A: C1103 C1104 C1107 A1112 A1113 A1114 G1115 A1116 G1119 C1120 U1125 C1130 A1131 C1132 U1133 G1134 C1137 G1138 A1139 G1140 C1141 G1142 C1143 U1147 U1158 G1159 A1160 A1161 C1162 G1166 C1167 U1168 A1169 A1170 G1171 C1172 U1177 A1182 G1189 G1194 U1195 A1196 A1197 A1198 A1199 A1200 A1201 C1013 C1014 C1015 G1016 G1017 A1018 C1023 A1024 G1025 C1026 U1027 U1036 A1039 U1040 G1041 A1042 C1043 U1047 C1048 A1049 G1050 U1051 G1052 A1053 U1054 A1055 A1056 A1060 G1061 G1062 G1070 A1074 C1081 A1082 G1083 G1084 A1085 G1086 G1087 U1088 U1089 U1090 C1093 U1094 A1095 G1096 A1097 A1098 G1099 C1100 A919 C923 U924 A932 U937 G938 A939 C940 C941 U942 C C A A A U A A C A952 G955 G956 U957 G966 C967 C968 A969 G974 A975 C976 G981 A985 U986 A987 A988 G989 U995 C996 G997 A1001 G1002 A1003 G1004 A1007 A1008 A1009 C1010 A1011 G1012 C813 U814 A815 G816 C817 U818 G819 C823 U824 C825 A830 G836 U837 U838 G839 A840 G841 G842 C855 U856 G857 G866 G867 G868 G869 U870 A871 U880 G884 G887 C888 G889 G890 G891 C892 C893 G896 A897 G898 C901 G902 G903 U904 A905 C906 C907 A908 G916 G680 A681 C688 U697 C698 U701 C702 G706 G722 U731 A732 A733 G734 G740 U741 G749 U757 U758 G759 A763 A764 G768 C769 G770 G771 A772 A775 A785 G786 G787 G788 A793 A794 U795 G796 A799 C800 U801 C802 G803 A804 G810 A811 G812 A582 G583 A584 A585 G589 C590 C591 G592 G593 C597 U598 G603 G609 U613 G614 A618 A619 G622 A623 A624 C627 A628 A633 G634 A639 G646 A649 G650 U651 C652 U653 U654 C655 A656 U657 A658 G659 U666 G667 U668 C669 A670 G673 C674 U675 G485 G486 U487 A491 A492 G493 A494 A495 C496 U502 C503 G504 A508 A514 U515 A516 G517 A518 A519 C520 A521 U522 G523 C536 A539 A540 G541 C542 A543 G544 G548 G553 G554 A555 C556 C557 A558 G559 A560 C567 C568 G569 C570 G571 U572 G573 C574 G580 A581 C375 U376 G377 A378 C379 C380 C381 G382 A383 G384 U385 A389 U390 G393 G394 G398 U399 A403 U404 C407 G410 U411 U415 C416 A417 G418 G423 A424 G432 C433 G436 U439 A440 A441 A442 C445 U446 C447 C448 G452 G458 A459 G467 U468 A469 G U C G U G298 C299 U300 A304 A309 A313 G314 U315 G316 G317 A318 G319 U320 G321 C322 C328 A331 G332 A333 U334 G335 G336 U337 G338 A339 A340 A341 G342 U343 C344 G347 C351 C358 A362 C U A G C U U A U G C373 U374 U219 G224 G227 U228 A229 G230 G233 C234 G235 A236 G237 C238 G239 A240 A250 G251 C252 A255 A256 A257 C258 C259 G260 U261 G262 A263 A264 A265 A266 C267 G268 G269 G270 G271 U272 U273 G274 U275 G276 G277 G278 A279 G280 A281 G282 C A A U A C A A G C G105 U110 A116 A117 U118 A119 U128 G132 A133 A134 C135 U136 U137 C138 U139 G140 G143 A144 A145 U146 C147 U150 G157 C158 A159 A160 C169 U170 A176 C177 A181 A184 U185 A189 G190 G200 A201 A202 A203 A204 G205 A206 A207 A212 A213 U1 U2 C3 A4 A5 A6 C7 G8 A9 G10 A13 A14 G26 A33 G34 G35 G42 A45 C46 G47 A48 G49 G50 A51 G55 U61 A70 U73 G74 G79 G80 G81 G82 A83 G84 U85 A90 A94 G95 C96 A97 G98 A99 G100 A101 U102 C103 C104

10 Page 10 Full wwpdb/emdatabank EM Map/Model Validation Report 5MLC A1202 C1203 U1209 G1213 G1218 U1219 U1220 C1221 U1224 G1225 U1226 U1227 A1228 G1229 G1230 G1231 A1232 G1233 A1236 C1237 G1238 C1239 G1240 U1241 G1242 C1243 C1250 G1251 C1252 G1253 U1254 G1257 A1258 C1259 G1260 A1261 A1262 G1263 C1264 G1265 A1268 G1269 C1270 G1271 A1272 G1273 A1274 G1277 U1278 C1279 G1280 G1281 C1282 U1283 A1289 G1292 C1293 A1294 A1295 A1296 C1310 G1315 C1316 C1317 A1321 A1322 U1327 G1332 U1337 C1338 C1339 A1342 A1343 G1344 G1345 U1346 C1351 G1359 G1362 A1363 G1364 U1365 C1366 A1367 G1368 C1371 C1372 U1373 A1374 A1375 G1385 A1386 G1389 G1395 A1399 U1400 G1401 G1402 A1403 C1404 A1405 G1410 U1411 G1412 A1416 U1417 U1418 C1419 C1420 U1426 C1429 U1432 U1433 G1434 U1435 U1436 G1437 G1438 U1439 C1440 C1441 C1442 G1443 A1444 G1445 A1448 C1449 A1471 A1472 G1473 A1474 U1475 G1476 G1477 U1478 U1479 A1480 C1493 G1494 C1495 A1496 A1497 G1498 G1499 U1500 G1501 A C C C U G U U U U U C A G G G U A A G A1522 A1523 G1524 G1527 U1528 A1529 G1530 A1531 G1532 A1533 A1534 A1535 A1536 U1537 C1540 U1541 C1542 G1543 A1544 G1545 C1546 C1547 A1548 A1549 U1550 G1551 U1552 U1553 C1554 U1558 A1559 C1560 C1567 U1568 A1569 C1570 G1571 G1572 C1573 G1574 G1580 G1589 C1590 C1591 A1592 U1593 A1594 C1595 A1600 G1601 G1602 A1603 A1604 A1605 A1606 G1607 C1608 U1609 C1610 G1611 A1612 A1613 C1614 G1615 A1616 C1617 C1618 U1619 U1620 C1621 A1622 A1623 C1624 A1628 G1629 G1630 C1634 G1643 A1644 A1645 A1646 C1647 C1653 A1662 G1663 A1671 U1672 C1682 G1683 C1684 G1687 A1690 U1693 C1694 U1695 C1696 U1697 C1698 A1701 G1702 G1710 A1713 C1730 G1731 G1732 G1733 A1734 G1735 A1736 U1742 G1743 C1744 C1748 U1749 C1750 A1751 C1752 A1753 A1754 A1755 G1756 G1759 G1760 G1763 G1766 U1767 G1768 G1774 G1778 A1783 G1786 A1790 C1791 C1792 A1796 A1797 C1798 A1801 U1806 C1807 C1810 A1811 A1812 A1819 A1820 G1821 A1822 A1825 U1826 G1827 U1828 A1829 U1830 C1843 G1866 A1867 U1870 G1875 A1876 G1880 A1881 U1882 G1883 A1884 C1885 A1886 G1887 G1888 G1889 G1896 C1897 G1898 A1899 G1910 G1911 U1912 G1913 A1914 A1915 C1919 G1920 G1921 G1924 U1925 A A C U A U A A1933 C1934 G1935 C1939 G1943 G1944 U1945 A1950 A1951 A1952 U1953 U1954 C1955 C1956 U1957 U1958 G1959 U1965 U1969 C1975 C1979 A1980 C1981 G1982 A1983 A1984 A1985 G1986 G1999 G2000 G2001 U2005 G2006 U2007 G2018 G2026 U2030 A2033 C2034 A2035 U2036 G2037 G2043 A2044 A2045 G2046 A2047 U2048 G2049 A2053 A2056 C2057 U2065 G2066 C2069 A2070 A2074 G2075 A2076 U2080 G2083 A2084 A2085 G2086 C2092 U2093 G2094 G2101 G2102 U2106 G2107 G2108 C2109 U2110 U2111 U2112 G2113 G2114 U2118 G2124 C2125 G2126 C2127 A2128 G2129 C2130 U2131 U2132 A2133 U2136 G2141 G2142 C2143 G2144 A2145 A2146 G2147 A2148 C2153 C2154 C2159 C2160 G2161 C2169 C2170 G2171 A2176 U2177 C2178 U2181 G2184 A2185 U2186 A2187 C2188 C2193 A2197 U2203 A2204 G2205 A2206 A2207 U2208 U2209 A2212 U2216 U2217 G2218 U2219 G2220 U2221 C2222 A2223 G2224 G2225 A2226 C2227 C2228 U2229 A2230 A2242 U2248 G2252 U2253 A2254 G2255 A2256 U2260 U2261 U2262 C2263 U2264 G2267 G2268 G2269 G2272 A2285 G2296 G2299 U2300 A2303 A2304 A2305 G2306 G2307 U2308 U2309 U2310 C2314 G2315 G2321 A2322 A2326 G2327 A2328 U2329 C2335 U2336 C2337 G2338 A2339 G2340 U2341 G2342 C2343 A2344 A2345 A2346 G2347 G2348 C2349 A2350 G2351 A2352 A2353 G2354 G2355 G2356 G2362 C2367 C2374 C2378 G2387 G2388 G2389 G2396 U2397 C2398 G2399 G2400 C2401 C2402 G2408 A2409 U2410 C2411 C2412 G2419 C2420 C2421 G2422 A2423 G2424 G2432 C2433 U2436 C2439 U2440 C2441 A2442 G2446 A2447 A2452 U2458 G2462 G2463 G2464 A2465 U2466 A2467 G2472 C2473 U2474 G2475 A2476 C2481 C2484 U2490 U2491 C2492 A2493 C2494 A2495 G2501 G2502 G2503 G2511 C2516 U2517 C2518 G2519 A2520 U2521 G2522 U2523 U2530 C2534 C2535 G2543 C2544 U2545 G2546 U2552 A2559 G2560 U2564 U2571 A2578 U2579 A2583 G2584 A2589 C2590 G2591 G2595 U2602 C2603 A2607 A2619 G2620 U2621 U2622 G2625 U2626 C2627 C2628 A2629 U2630 A2631 G2642 C2643 G2644 U2645 U2646 A2647 G2648 A2649 U2653 U2654 G2655 A2656 G2657 A2658 G2659 G2660 A2661 C2662 C2663 U2664 U2665 U2666 G2672 U2673 G2678 G2685 A2688 A2689 G2690 G2691 A2692 A2696 C2697 C2698 U2699 C2700 U2701 G2702 G2703 U2704 G2705 U2706 A2707 C2708 C2721 C2722 A2723 C2724 A2729 A2730 C2731 G2732 U2738 A2739 G2740 C2741 C2742 A2743 A2744 G2747 G2750 A2751 G2752 C2753 G2754 G2762 A2766 C2770 A2771 U2774 A2775 A2776 A2782 A2783 G2784 C2785 C2786 C2787 C2791 C2792 A2796 U2797 G2798 A2799 C2808 U2809 A2810 U2811

11 Page 11 Full wwpdb/emdatabank EM Map/Model Validation Report 5MLC Molecule 2: 5S ribosomal RNA, chloroplastic Chain B: U A2 U3 U4 C5 U6 G7 U11 C12 C13 U14 A15 G16 C28 C31 A32 A36 C44 G45 A46 G54 G55 U56 U57 U64 A65 C66 U67 G68 G87 G88 A89 G90 G91 U92 U109 C110 G111 A120 U121 Molecule 3: 4.8S ribosomal RNA, chloroplastic Chain C: G100 A101 A102 C103 G1 A2 C7 G13 A14 G15 A16 U25 U A U C A U U A C G A36 U37 G50 G53 A61 U62 G63 U64 G67 C68 A69 G70 C71 A74 A78 U79 C80 C81 C85 A86 G87 A88 C91 A92 C93 A94 G95 A96 C97 U98 U99 Molecule 4: 50S ribosomal protein L2, chloroplastic Chain D: K182 V188 G189 V196 R200 L201 G202 R203 W209 R213 V220 G229 R234 I237 S241 P242 T243 P249 R253 R256 K257 R258 N259 S262 R268 R269 R270 S271 HIS TYR N26 N27 L28 I29 G52 R56 V75 N84 H91 K97 E117 V118 K121 T129 D130 M131 I137 H138 I142 G147 L150 Molecule 5: 50S ribosomal protein L3, chloroplastic Chain E: Q209 A237 P241 T257 I266 I278 V282 L289 L292 K300 P303 S85 I90 L97 G98 M99 T113 E119 I122 D132 G133 Y134 M151 P152 M165 R166 H167 L173 F179 E193 G194 D195 M196 V197 D198 I199 CYS TYR CYS Molecule 6: 50S ribosomal protein L4, chloroplastic Chain F: K64 V65 G66 E67 N71 L72 R81 L92 Q93 N94 R97 T102 Y116 P117 Q118 V139 I140 T149 V169 E180 D200 L206 F207 F208 D211 L212 L226 K227 L228 L229 T230 L234 V246 G260 HIS P56 I57 L58 E63

12 Page 12 Full wwpdb/emdatabank EM Map/Model Validation Report 5MLC Molecule 7: 50S ribosomal protein L5, chloroplastic Chain G: HIS HIS TYR I16 N22 N52 Q78 I89 F92 K93 V94 R95 T105 L106 R107 I119 T126 R127 N133 S136 E159 T174 T177 D178 G189 E194 Molecule 8: 50S ribosomal protein L6, chloroplastic Chain H: L143 I144 L145 S150 H151 V163 K164 V165 V173 R176 Q183 T187 I188 P194 V209 G217 HIS TRP CYS E40 I43 V50 V54 A55 I56 L69 G70 E71 K84 L107 L111 V138 Molecule 9: 50S ribosomal protein L9, chloroplastic Chain I: TYR HIS V87 TRP HIS CYS K43 K44 L53 K54 E55 D56 I57 G64 Q65 D68 F73 P80 Molecule 10: 50S ribosomal protein L13, chloroplastic Chain L: R82 W83 M84 L87 E88 I95 S104 A119 T120 D121 L122 S142 S146 K160 V161 A162 R175 G182 R205 D238 R242 D243 I246 K250 CYS T55 P75 P78 Molecule 11: 50S ribosomal protein L14, chloroplastic Chain M: M1 Q5 R23 I24 Y32 A33 R34 I35 G36 D37 I58 V63 E68 L69 I76 D81 N82 A83 I86 I98 I102 E105 L106 R107 Q108 K109 F110 I113 V114 A117 P118 E119 V120 Molecule 12: 50S ribosomal protein L15, chloroplastic

13 Page 13 Full wwpdb/emdatabank EM Map/Model Validation Report 5MLC Chain N: R192 L198 L201 A216 F217 S218 L225 V232 P236 G237 R238 K239 I242 K243 E244 R252 K259 T78 R79 L82 K96 G99 G107 G108 S109 Q117 I125 M134 P135 L136 Y137 R138 R139 I140 R144 M150 I160 F170 G173 E174 E175 K184 G185 I186 I187 N188 P189 TYR HIS Molecule 13: 50S ribosomal protein L16, chloroplastic Chain O: M1 L2 R6 Q12 H13 R14 G15 R16 S21 G30 T43 S44 R52 A53 R59 G62 I68 F69 P70 D71 K72 P73 R77 K87 Y92 K98 L103 S107 G108 V109 A110 E111 V118 A119 I120 K124 M125 F131 G135 Molecule 14: 50S ribosomal protein L17, chloroplastic Chain P: R114 E124 L125 V126 M11 K12 H13 I17 D25 R32 G33 L34 L38 L39 G42 S52 A53 M54 V58 M61 L64 A65 G68 K72 Q75 A76 L77 I80 Y81 E82 K83 V86 F90 R100 R109 T110 L111 Molecule 15: 50S ribosomal protein L18, chloroplastic Chain Q: P115 I123 F166 HIS HIS R49 R50 E51 H81 T90 T100 M101 Q102 K103 Molecule 16: 50S ribosomal protein L19, chloroplastic Chain R: I122 L126 A130 R144 R152 I168 V169 I170 Q173 I177 R182 I183 I187 A188 E193 I194 V195 R218 L222 K225 L226 S230 V117 K118 L119 HIS CYS CYS Molecule 17: 50S ribosomal protein L20, chloroplastic

14 Page 14 Full wwpdb/emdatabank EM Map/Model Validation Report 5MLC Chain S: T2 R3 R6 G7 Y8 R11 R12 R13 R14 R18 S23 T32 R41 H47 R52 D56 R59 R72 H83 L90 L97 A98 Q99 C107 N113 K117 CYS TYR Molecule 18: 50S ribosomal protein L21, chloroplastic Chain T: CYS CYS P101 P112 P116 P117 P118 P119 R120 I123 F124 S131 R132 Q133 V136 I137 W141 A150 T151 K155 I156 V157 K160 T166 Y171 I172 G173 T174 P175 I176 V177 T178 V185 Q189 V197 R207 R213 I221 S233 T234 Molecule 19: 50S ribosomal protein L22, chloroplastic Chain U: TYR HIS HIS E25 E31 I32 T33 T34 R35 G36 Y37 S38 R54 Y58 M68 Y74 P75 A83 A87 F93 N94 N97 I109 T110 S122 R127 C130 H131 I132 T133 I134 V135 L136 T153 P154 K155 K156 L157 I158 A159 G162 L163 R176 HIS TYR TYR Molecule 20: 50S ribosomal protein L23, chloroplastic Chain V: HIS CYS HIS HIS Y104 P105 V111 Y112 Q113 I114 L115 I119 E131 L135 D139 D143 I151 N163 R167 Y175 L178 A184 K190 I191 G192 I193 F194 Molecule 21: 50S ribosomal protein L24, chloroplastic Chain W: HIS CYS R47 I48 K49 C56 R67 H68 V75 I89 I92 H93 V99 I100 I101 L104 K107 T108 Q119 E126 S132 L136 D145 R146 R156 R159 K163 D169 T170 P171 W174 K175 Molecule 22: 50S ribosomal protein L27, chloroplastic

15 Page 15 Full wwpdb/emdatabank EM Map/Model Validation Report 5MLC Chain X: R76 Q85 V107 D112 I119 D120 G129 P130 D131 V137 E141 I142 N146 P147 N148 K154 R159 R162 K166 TYR CYS H59 Molecule 23: 50S ribosomal protein L28, chloroplastic Chain Y: R72 R73 I74 V88 S89 N92 H93 Q104 W109 G113 R120 L121 L134 G142 R146 CYS CYS Molecule 24: 50S ribosomal protein L29, chloroplastic Chain Z: L68 T72 I80 K84 R91 L92 Q93 R94 S95 V112 L116 T117 R122 V128 G129 K130 R131 L132 S133 D137 K138 V145 V146 L152 HIS CYS HIS V59 Molecule 25: 50S ribosomal protein L32, chloroplastic Chain 2: A2 V3 P4 K5 K6 R7 T8 S9 I10 Y11 I15 R16 L29 L34 T40 S43 Molecule 26: 50S ribosomal protein L33, chloroplastic Chain 3: D6 C15 T16 G17 C18 N24 K25 G26 G29 V30 L48 C52 C55 H61 I64 K65 Molecule 27: 50S ribosomal protein L34, chloroplastic Chain 4: CYS G92 L96 C97 L98 S104 T120 G123 C139 T140 K141 T142 N143 S146 G147 K148 R149 A150 S151 P152 HIS CYS

16 Page 16 Full wwpdb/emdatabank EM Map/Model Validation Report 5MLC Molecule 28: 50S ribosomal protein L35, chloroplastic Chain 5: CYS HIS Y90 K100 D142 L150 P151 R157 K158 V159 Molecule 29: 50S ribosomal protein L36, chloroplastic Chain 6: M1 V7 Q36 G37 Molecule 30: Ribosome-recycling factor, chloroplastic Chain 9: TYR HIS CYS CYS TRP TYR CYS CYS S89 T95 N109 R114 TYR TYR TYR L191 L206 I217 R218 Y225 L242 V271 Molecule 31: PSRP5alpha, chloroplastic Chain 7: HIS Q97 Q102 M106 K110 L114 W131 P132 P133 K137 K140 N141 V142 Molecule 32: PSRP6, chloroplastic Chain 8: CYS CYS S48 S49 R50 K54 P64 K73 R74 P81 L82 P83 P86 A87 E88 V92 S93 S94

17 Page 17 Full wwpdb/emdatabank EM Map/Model Validation Report 5MLC 4 Experimental information i Property Value Source Reconstruction method SINGLE PARTICLE Depositor Imposed symmetry POINT, C1 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 ) 2.6 Depositor Minimum defocus (nm) Not provided Depositor Maximum defocus (nm) Not provided Depositor Magnification Not provided Depositor Image detector FEI FALCON II (4k x 4k) Depositor

18 Page 18 Full wwpdb/emdatabank EM Map/Model Validation Report 5MLC 5 Model quality i 5.1 Standard geometry i 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 A /66169 (0.0%) / (0.0%) 10 L /1521 (0.1%) /2062 (0.1%) 11 M / / N / / O / / P / / Q / / R /928 (0.1%) / S / / T /1034 (0.1%) /1405 (0.4%) 19 U /1184 (0.1%) / B / / V /744 (0.1%) / W /1030 (0.1%) /1374 (0.1%) 22 X / /1172 (0.1%) 23 Y / / Z / / / / / / / / / / / /403 3 C / / / / / / / /528 4 D / / E / / F /1648 (0.1%) / G / / H /1407 (0.1%) / I / /480 All All /98702 (0.0%) / (0.0%)

19 Page 19 Full wwpdb/emdatabank EM Map/Model Validation Report 5MLC Chiral center outliers are detected by calculating the chiral volume of a chiral center and verifying if the center is modelled as a planar moiety or with the opposite hand.a planarity outlier is detected by checking planarity of atoms in a peptide group, atoms in a mainchain group or atoms of a sidechain that are expected to be planar. Mol Chain #Chirality outliers #Planarity outliers 18 T 0 1 All (29) bond length outliers are listed below: Atoms Z Observed(Å) Ideal(Å) 1 A 1554 C O3 -P U 158 C-N T 118 C-N A 1435 U O3 -P H 71 CD-OE F 180 CD-OE W 169 C-N A 1618 C O3 -P A 1264 C N1-C A 1264 C C4-C A 1239 C C3 -O A 1264 C N1-C A 2530 U N1-C A 1239 C O3 -P H 71 CD-OE A 2530 U C4-C R 230 C-O A 2530 U N1-C A 1608 C O3 -P A 1264 C N3-C F 211 CB-CG A 1698 C N1-C A 2530 U N3-C A 1698 C C4-C V 131 CD-OE L 84 C-N A 1015 C N1-C A 261 U O3 -P A 399 U N1-C All (41) bond angle outliers are listed below:

20 Page 20 Full wwpdb/emdatabank EM Map/Model Validation Report 5MLC Atoms Z Observed( o ) Ideal( o ) 1 A 261 U N1-C1 -C A 1618 C P-O3 -C A 763 A C2 -C3 -O A 50 G C2 -C3 -O A 261 U C2 -C3 -O A 1411 U C2 -C3 -O A 1618 C OP2-P-O A 1239 C OP1-P-O A 313 A C2 -C3 -O A 1264 C C6-N1-C A 1435 U OP2-P-O A 1435 U O3 -P-O T 118 N-CA-CB A 266 A O4 -C1 -N A 2628 C C2 -C3 -O A 2254 A C4 -C3 -O A 1264 C N3-C4-C A 1239 C C4 -C3 -O A 1493 C C2 -C3 -O A 2216 U C2 -C3 -O A 1536 A C2 -C3 -O W 171 N-CA-CB A 1608 C O3 -P-O T 116 N-CA-CB A 1439 U C2 -C3 -O T 101 N-CA-CB L 78 N-CA-CB T 117 N-CA-CB A 1260 G C4 -C3 -O A 261 U C4 -C3 -C A 2408 G C4 -C3 -O A 1399 A C4 -C3 -O A 261 U C4 -C3 -O T 118 O-C-N A 654 U C2 -C3 -O A 856 U C2 -C3 -O L 75 N-CA-CB A 1050 G C2 -C3 -O X 76 NE-CZ-NH A 1002 G N9-C1 -C A 1610 C C2 -C3 -O There are no chirality outliers.

21 Page 21 Full wwpdb/emdatabank EM Map/Model Validation Report 5MLC All (1) planarity outliers are listed below: Group 18 T 116 Peptide 5.2 Too-close contacts i 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 A B C D E F G H I L M N O P Q R S T U V W X Y Z

22 Page 22 Full wwpdb/emdatabank EM Map/Model Validation Report 5MLC Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes All All The all-atom clashscore is defined as the number of clashes found per 1000 atoms (including hydrogen atoms). The all-atom clashscore for this structure is 4. All (575) close contacts within the same asymmetric unit are listed below, sorted by their clash magnitude. Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 1:A:133:A:C6 24:Z:131::NH :A:133:A:C2 24:Z:131::NH :T:118::C 18:T:119::N :A:133:A:C5 24:Z:131::NH :U:158::C 19:U:159::N :A:137:U:N3 1:A:160:A:N :A:81:G:N2 1:A:102:U:O :A:1049:A:N1 1:A:1168:U:O :A:133:A:C6 24:Z:131::CZ :A:137:U:O2 1:A:160:A:H :A:133:A:N1 24:Z:131::CZ :A:219:U:H3 1:A:442:A:N :A:1524:G:N3 31:7:102::NE :A:1239:C:H2 1:A:1240:G:H :A:262:G:C8 1:A:262:G:H :A:2666:U:N3 1:A:2688:A:C :A:2227:C:O2 1:A:2230:A:N :A:1242:G:H8 1:A:1242:G:H :A:1529:A:N1 1:A:1537:U:N :A:133:A:C2 24:Z:131::CZ :A:1524:G:C2 31:7:102::NE :A:2666:U:O4 1:A:2688:A:N :A:137:U:O2 1:A:160:A:C :A:2517:U:O2 1:A:2521:U:O :A:940:C:O2 1:A:956:G:N :A:219:U:O2 1:A:219:U:H :A:1239:C:C5 1:A:1240:G:N :A:2666:U:H3 1:A:2688:A:H :A:2666:U:N3 1:A:2688:A:H :A:110:U:OP2 24:Z:130::NZ :A:1239:C:C2 1:A:1240:G:H :A:133:A:N1 24:Z:131::NH

23 Page 23 Full wwpdb/emdatabank EM Map/Model Validation Report 5MLC Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 1:A:1242:G:C8 1:A:1242:G:H :A:1535:A:O2 4:D:97::NZ :A:137:U:C2 1:A:160:A:C :A:2321:G:H22 1:A:2329:U:H :U:33::HG22 19:U:135::HG :A:1047:U:N3 1:A:1169:A:N :A:227:G:O2 1:A:228:U:OP :A:137:U:N3 1:A:160:A:C :A:98:G:N2 1:A:100:G:H :A:2663:C:C4 1:A:2750:G:C :A:2663:C:C5 1:A:2750:G:C :P:61::HE1 14:P:80::HD :D:142::HD11 4:D:150::HD :A:1434:G:O6 1:A:1623:A:N :A:137:U:C2 1:A:160:A:H :A:219:U:H3 1:A:442:A:H :A:2666:U:C4 1:A:2688:A:N :M:102::HD11 11:M:117::HB :E:199::HD11 5:E:278::HD :A:1438:G:C2 1:A:1623:A:HO :A:941:C:O2 1:A:955:G:N :A:98:G:C2 1:A:100:G:N :A:541:G:O6 1:A:2037:G:OP :A:1749:U:O4 1:A:1755:A:N :A:98:G:N2 1:A:100:G:N :A:1242:G:H8 1:A:1242:G:C :A:158:C:N4 24:Z:129::O :A:1950:A:N1 1:A:1957:U:O :R:130::HB1 16:R:177::HD :A:1530:G:H22 1:A:1536:A:H :T:118::C 18:T:119::CA :A:2663:C:C5 1:A:2750:G:N :A:1049:A:N1 1:A:1168:U:C :A:2521:U:H2 1:A:2521:U:O :A:2128:A:C6 1:A:2131:U:C :A:1004:G:O6 1:A:1016:G:N :V:178::HD12 20:V:184::HB :A:1438:G:O2 1:A:1623:A:O :A:2329:U:H2 1:A:2329:U:O :A:2665:U:H2 1:A:2666:U:C :A:1663:G:N7 31:7:142::HB

24 Page 24 Full wwpdb/emdatabank EM Map/Model Validation Report 5MLC Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 1:A:219:U:O2 1:A:219:U:C :A:2328:A:O2 1:A:2329:U:H :A:1524:G:N2 31:7:102::NE :A:133:A:C4 24:Z:131::NH :O:68::HD13 13:O:103::HD :A:2328:A:HO2 1:A:2329:U:H :T:123::HG22 18:T:166::HB :A:1227:U:N3 1:A:1261:A:N :A:234:C:O2 28:5:100::NZ :A:2128:A:C6 1:A:2131:U:O :Q:100::HG23 15:Q:123::HD :A:102:U:C5 1:A:103:C:C :A:446:U:O2 1:A:448:C:C :9:225:TYR:CE1 30:9:242::HD :A:2224:G:O6 1:A:2228:C:N :A:2663:C:C4 1:A:2750:G:N :A:2128:A:N6 1:A:2131:U:C :E:90::HD11 5:E:179::CE :A:1439:U:H2 1:A:1440:C:O :A:609:G:C2 1:A:670:A:C :A:1047:U:C4 1:A:1169:A:N :A:1530:G:N2 1:A:1536:A:H :V:119::HD12 20:V:135::HG :A:1049:A:C2 1:A:1168:U:O :A:1476:G:O6 1:A:2721:C:N :L:119::HA 10:L:122::HD :P:38::HD23 14:P:58::HG :T:160::HD2 18:T:176::HD :A:133:A:N6 24:Z:131::NH :R:119::HD23 16:R:122::HD :B:66:C:C5 2:B:110:C:C :A:446:U:C2 1:A:448:C:N :A:26:G:C2 1:A:523:G:N :A:932:A:O2 22:X:85::NE :O:118::HG21 13:O:131::CD :E:237::HB3 5:E:241::HG :A:261:U:H3 1:A:266:A:H :A:1880:G:N7 12:N:252::NH :A:2784:G:H2 1:A:2784:G:N :T:118::CA 18:T:119::N :A:1475:U:O2 1:A:1476:G:N

25 Page 25 Full wwpdb/emdatabank EM Map/Model Validation Report 5MLC Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 1:A:1228:A:O2 1:A:1229:G:O :A:2339:A:H2 1:A:2340:G:O :A:651:U:H2 1:A:652:C:C :A:966:G:OP1 28:5:157::NH :A:2472:G:H2 1:A:2473:C:H :A:1870:U:H3 1:A:1896:G:H :A:1227:U:N3 1:A:1261:A:C :A:2218:G:C2 1:A:2220:G:C :A:6:A:C2 3:C:98:U:C :4:120::HG23 27:4:123::HA :A:227:G:HO2 1:A:228:U:P :Z:68::O 24:Z:122::NH :A:2344:A:H2 1:A:2345:A:C :A:956:G:C6 1:A:957:U:O :F:212::HD11 6:F:228::HD :A:1047:U:C2 1:A:1171:G:N :E:167:HIS:CG 5:E:289::HD :A:1239:C:C6 1:A:1240:G:N :A:26:G:N2 1:A:523:G:H :N:160::HD11 12:N:198::HD :A:255:A:O2 1:A:256:A:O :A:2472:G:H2 1:A:2473:C:C :D:129::HG22 4:D:182::HD :A:379:C:H2 1:A:380:C:H :A:446:U:O2 1:A:448:C:N :P:77::HD13 14:P:86::HG :E:97::HD11 16:R:119::HD :A:1:U:H2 1:A:2:U:C :A:389:A:C6 1:A:390:U:C :A:378:A:C8 1:A:379:C:C :A:839:G:H4 1:A:842:G:N :A:298:G:C2 1:A:299:C:C :A:981:G:OP2 13:O:16::NH :8:82::HD23 32:8:83::HD :A:2328:A:C2 1:A:2329:U:H :A:2703:G:H2 1:A:2704:U:O :A:2688:A:H2 1:A:2689:A:C :T:136::HG23 18:T:221::HG :3:15:CYS:HB3 26:3:17::O :N:225::HD13 12:N:232::HG :A:2655:G:HO2 1:A:2656:A:H

26 Page 26 Full wwpdb/emdatabank EM Map/Model Validation Report 5MLC Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 1:A:2108:G:H1 1:A:2209:U:H :A:1238:G:N2 1:A:1253:G:H :A:262:G:C5 1:A:262:G:C :A:856:U:O2 1:A:857:G:OP :A:1238:G:N2 1:A:1253:G:N :A:446:U:O2 1:A:448:C:C :C:85:C:O4 3:C:85:C:O :L:122::O 10:L:162::HB :A:494:A:O2 1:A:508:A:N :A:769:C:H2 1:A:769:C:O :M:24::HD12 11:M:33::HB :A:102:U:C4 1:A:103:C:C :Q:100::CG2 15:Q:123::HD :A:1056:A:N3 1:A:2503:G:O :A:1547:C:OP1 31:7:106::HE :7:110::HG2 31:7:114::HD :3:18:CYS:HG 26:3:55:CYS:HG :A:1047:U:N3 1:A:1169:A:C :N:99::HA2 12:N:107::HA :A:1500:U:O2 1:A:1500:U:H :9:109::HB3 30:9:206::HD :A:2362:G:N3 1:A:2398:C:H :2:34::O 25:2:34::HD :A:1559:A:H2 1:A:1559:A:N :A:2345:A:H2 1:A:2346:A:C :A:2472:G:C4 1:A:2473:C:C :W:75::HG21 21:W:89::HD :A:13:A:H2 1:A:14:A:C :W:101::HG21 21:W:104::HD :A:2644:G:O2 1:A:2799:A:N :A:2328:A:O2 1:A:2329:U:C :A:975:A:O2 1:A:1012:G:N :A:1612:A:H2 1:A:1613:A:O :A:1004:G:C6 1:A:1016:G:N :A:1693:U:H2 1:A:1694:C:H :A:2701:U:OP2 16:R:173::NE :P:65::HA 14:P:90::CE :A:1438:G:C2 1:A:1623:A:O :A:2227:C:C2 1:A:2230:A:N :A:2517:U:O2 1:A:2521:U:C :Z:93::N 24:Z:93::OE

27 Page 27 Full wwpdb/emdatabank EM Map/Model Validation Report 5MLC Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 1:A:2303:A:H4 1:A:2304:A:O :A:403:A:C4 1:A:404:U:C :B:13:C:O2 2:B:13:C:O :A:2329:U:O2 7:G:52::ND :A:415:U:O2 1:A:416:C:O :Z:130::NZ 24:Z:130::CB :A:138:C:H2 1:A:138:C:O :A:204:A:H2 1:A:219:U:O :A:956:G:C4 1:A:957:U:C :A:1410:G:N2 1:A:1420:C:C :A:133:A:C4 24:Z:131::NH :A:1024:A:OP1 18:T:132::HD :A:1227:U:H2 1:A:1228:A:O :A:2033:A:N7 25:2:6::NZ :A:333:A:N6 1:A:347:G:O :A:138:C:C2 1:A:138:C:O :A:2329:U:O2 1:A:2329:U:C :R:187::HG23 16:R:188::N :A:2535:C:H2 1:A:2535:C:O :A:1213:G:OP2 12:N:96::NZ :O:21::HB2 13:O:98::HB :S:14::HD2 17:S:32::HG :A:1242:G:C8 1:A:1242:G:C :A:771:G:H2 1:A:772:A:O :A:1819:A:H2 1:A:1820:A:C :A:133:A:N3 24:Z:131::NH :A:384:G:O2 1:A:385:U:OP :A:1693:U:H2 1:A:1694:C:C :N:185::C 12:N:186::HD :A:2307:G:H2 1:A:2308:U:C :A:740:G:OP2 4:D:203::NH :U:130:CYS:SG 19:U:131:HIS:N :A:416:C:O4 1:A:416:C:O :T:175::HG2 32:8:82::HD :A:2784:G:C2 1:A:2785:C:C :A:2521:U:O2 1:A:2521:U:C :A:956:G:C6 1:A:957:U:C :A:570:C:O2 17:S:52::NH :A:1114:A:H2 1:A:1114:A:N :A:1495:C:C2 1:A:1548:A:N :A:1950:A:N1 1:A:1957:U:C

28 Page 28 Full wwpdb/emdatabank EM Map/Model Validation Report 5MLC Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 1:A:580:G:H2 1:A:2044:A:N :A:8:G:O2 3:C:96:A:N :H:50::HG13 8:H:54::HG :R:170::HD11 16:R:182::HD :A:1228:A:O2 1:A:1229:G:H :A:2707:A:O2 1:A:2708:C:O :A:1806:U:H2 1:A:1807:C:H :A:818:U:C2 1:A:819:G:C :A:2707:A:O2 1:A:2708:C:P :H:138::HG21 8:H:165::HG :F:102::HB 6:F:139::HG :F:116:TYR:HB2 6:F:117::HD :X:119::HG23 22:X:120::O :A:542:C:O2 17:S:41::NH :D:131::SD 4:D:137::HG :P:38::CD2 14:P:58::HG :D:200::O 4:D:202::N :A:1499:G:H2 1:A:1500:U:C :F:94::ND2 6:F:149::HG :A:1194:G:O2 1:A:1195:U:O :Y:88::HG13 23:Y:92::HA :A:1007:A:H4 32:8:64::HG :A:2642:G:H2 1:A:2643:C:O :A:403:A:C5 1:A:404:U:C :Z:130::HZ3 24:Z:130::HB :A:1551:G:C2 1:A:1552:U:C :A:85:U:H3 1:A:95:G:H :E:122::HD12 5:E:165::CE :A:2738:U:C2 1:A:2739:A:C :I:53::HD13 9:I:65::HB :A:2809:U:O2 1:A:2809:U:O :A:394:G:H22 1:A:404:U:H :A:382:G:C6 1:A:436:G:N :F:208::CE1 6:F:234::HD :A:1224:U:O4 1:A:1225:G:C :W:145::CG 21:W:146::N :4:146::O 27:4:150::HB :A:2328:A:C2 1:A:2329:U:C :A:373:C:H2 1:A:374:U:C :D:84::ND2 4:D:196::HG :A:1220:U:H2 1:A:1221:C:C

29 Page 29 Full wwpdb/emdatabank EM Map/Model Validation Report 5MLC Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 1:A:2663:C:C5 1:A:2750:G:N :A:816:G:O4 12:N:117::HG :A:378:A:H2 1:A:378:A:N :A:589:G:H2 1:A:590:C:C :U:32::HG21 19:U:87::HB :A:445:C:H2 1:A:446:U:C :A:955:G:C6 1:A:956:G:C :A:2263:C:H2 1:A:2264:U:C :P:64::HD23 14:P:76::HB :A:2310:U:H3 1:A:2356:G:H :A:2707:A:C8 1:A:2708:C:C :A:1:U:H2 1:A:2:U:C :C:100:G:H2 3:C:101:A:C :D:29::O 4:D:29::HG :A:138:C:N3 1:A:139:U:C :A:1419:C:O2 1:A:1419:C:H :A:261:U:O4 1:A:266:A:N :A:880:U:OP1 13:O:6::NH :H:183::O 8:H:187::HG :T:124::CB 18:T:137::HG :A:328:C:N3 1:A:332:G:O :A:553:G:O2 1:A:554:G:O :A:932:A:C2 22:X:85::HE :A:176:A:H2 1:A:177:C:C :A:2658:A:OP2 10:L:175::NH :M:58::HD13 11:M:86::HG :N:201::HD23 12:N:218::HB :A:1950:A:C2 1:A:1957:U:N :A:2707:A:HO2 1:A:2708:C:H :A:824:U:H2 1:A:825:C:C :N:160::HD11 12:N:198::CD :X:141::HB3 22:X:142::HD :V:112:TYR:CE1 24:Z:146::HG :A:133:A:C4 24:Z:131::CZ :A:1321:A:C2 1:A:1662:A:N :P:77::HD11 14:P:83::HG :A:137:U:C4 1:A:160:A:N :E:197::CG2 5:E:266::HD :M:98::HD13 11:M:113::HG :T:176::HD13 32:8:86::HD :A:384:G:O2 1:A:385:U:P

30 Page 30 Full wwpdb/emdatabank EM Map/Model Validation Report 5MLC Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 20:V:192::HA3 24:Z:93::HE :Y:104::O 23:Y:120::HA :A:379:C:H2 1:A:380:C:C :V:135::HD13 20:V:175:TYR:CD :Y:88::HG12 23:Y:89::O :H:194::HB2 8:H:209::HG :H:194::CG 8:H:209::HG :O:53::HB1 13:O:120::CG :A:138:C:C2 1:A:139:U:C :A:1558:U:H2 1:A:1559:A:O :A:2043:G:N1 1:A:2047:A:OP :A:299:C:H2 1:A:300:U:C :C:25:U:O2 3:C:80:C:C :A:227:G:C2 1:A:228:U:OP :A:2354:G:H2 1:A:2354:G:N :A:1239:C:C4 1:A:1240:G:N :A:119:A:C8 1:A:132:G:C :F:93::HE21 6:F:93::HB :A:2663:C:C6 1:A:2750:G:N :A:79:G:N2 1:A:105:G:C :A:2653:U:O2 5:E:134:TYR:OH :A:869:G:O2 1:A:870:U:P :A:2722:C:O2 3:C:53:G:OP :D:137::HG22 4:D:188::HA :A:1957:U:N3 1:A:1959:G:O :A:2092:C:H2 1:A:2093:U:O :B:44:C:O2 7:G:107::NH :M:35::HD12 11:M:69::HD :A:144:A:C2 1:A:2224:G:N :A:2304:A:O2 1:A:2305:A:H :A:2663:C:N4 1:A:2750:G:C :V:163::OD1 20:V:163::N :G:119::HD13 7:G:189::O :Y:72::CD 23:Y:74::HD :A:2128:A:N1 1:A:2131:U:O :O:53::HB1 13:O:120::HG :A:603:G:H1 1:A:675:U:H :C:36:A:C2 3:C:80:C:C :A:1201:A:H2 1:A:1202:A:C :A:1500:U:H3 1:A:1545:G:H :A:869:G:HO2 1:A:870:U:P

31 Page 31 Full wwpdb/emdatabank EM Map/Model Validation Report 5MLC Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 4:D:75::HG21 4:D:91:HIS:ND :M:81::OD2 11:M:83::HB :A:1694:C:C2 1:A:1695:U:C :A:2218:G:C2 1:A:2220:G:N :A:2102:G:H1 1:A:2248:U:H :3:15:CYS:SG 26:3:61:HIS:CE :A:1701:A:H2 1:A:1702:G:O :A:1749:U:C4 1:A:1755:A:N :A:2770:C:OP2 8:H:43::HD :A:701:U:H2 1:A:702:C:O :U:74:TYR:HB3 19:U:75::HD :A:404:U:H2 1:A:404:U:O :A:650:G:H2 1:A:651:U:C :W:92::HG23 21:W:92::O :A:1629:G:H2 1:A:1630:G:O :A:2421:C:H2 1:A:2422:G:O :L:243::HB3 10:L:246::HB :P:61::CE 14:P:80::HD :A:1605:A:H2 1:A:1606:A:C :C:96:A:N3 3:C:96:A:H :G:78::NE2 7:G:105::O :A:1001:A:O4 1:A:1209:U:C :A:1296:A:N6 1:A:1317:C:H :A:1763:G:C2 1:A:1766:G:C :A:966:G:C6 1:A:967:C:C :A:2707:A:O2 1:A:2708:C:H :A:2791:C:N3 1:A:2792:C:C :G:119::HG21 7:G:189::O :L:242::O 10:L:243::HB :A:1250:C:H2 1:A:1251:G:C :A:1261:A:C5 1:A:1262:A:C :A:1559:A:C2 1:A:1560:C:C :A:2387:G:C6 1:A:2388:G:C :A:680:G:H2 1:A:680:G:N :S:47:HIS:CE1 18:T:197::HG :X:146::HD22 22:X:148::HB :A:2474:U:H2 1:A:2475:G:O :A:316:G:H1 1:A:317:G:OP :A:856:U:C2 1:A:857:G:OP :B:91:G:C2 2:B:92:U:OP :G:94::HG23 7:G:95::HG

32 Page 32 Full wwpdb/emdatabank EM Map/Model Validation Report 5MLC Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 1:A:1731:G:N2 1:A:1732:G:C :A:2085:A:H2 1:A:2086:G:H :A:410:G:C6 1:A:411:U:C :A:824:U:H2 1:A:825:C:H :H:163::HG22 8:H:173::HG :H:56::HG21 8:H:84::HD :P:42::O 14:P:124::HB :A:519:A:N6 19:U:38::OG :A:1261:A:H3 1:A:1261:A:C :B:66:C:C6 2:B:110:C:N :A:1798:C:C5 4:D:220::HG :P:64::HD12 14:P:72::HD :A:2303:A:C2 26:3:48::HD :A:1042:A:C6 1:A:1043:C:N :A:1344:G:O6 1:A:1345:G:C :A:389:A:C5 1:A:390:U:C :A:572:U:C2 1:A:582:A:C :A:869:G:O2 1:A:870:U:OP :O:12::HE21 13:O:73::HD :A:2085:A:H2 1:A:2086:G:C :A:2663:C:N4 1:A:2750:G:N :D:256::O 4:D:257::C :R:168::O 16:R:183::HA :A:1230:G:O2 1:A:1258:A:N :A:591:C:H2 1:A:592:G:C :B:66:C:C6 2:B:110:C:C :C:63:G:H2 3:C:64:U:O :U:87::HB1 19:U:93::HE :D:138:HIS:ND1 4:D:189::O :A:1610:C:H6 1:A:1610:C:H :A:2111:U:O2 1:A:2112:U:C :A:2411:C:H2 1:A:2412:C:O :A:503:C:H2 1:A:504:G:O :8:81::O 32:8:82::HB :A:1084:G:N2 1:A:1130:C:C :A:1440:C:H2 1:A:1441:C:O :A:298:G:H2 1:A:298:G:N :A:618:A:H2 1:A:619:A:O :A:799:A:OP1 1:A:802:C:N :F:207::CD1 6:F:226::HD :A:2030:U:O2 25:2:4::O

33 Page 33 Full wwpdb/emdatabank EM Map/Model Validation Report 5MLC Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 1:A:976:C:O2 1:A:1012:G:O :A:1261:A:C3 1:A:1261:A:C :A:1363:A:O2 1:A:1365:U:OP :F:206::HD11 6:F:229::HD :N:160::HD11 12:N:198::HD :N:187::HG22 12:N:189::HD :W:89::HD12 21:W:99::HG :A:1026:C:H2 1:A:1027:U:O :A:1142:G:C6 1:A:1143:C:C :A:1171:G:H2 1:A:1172:C:H :A:2396:G:H2 1:A:2397:U:C :A:591:C:H2 1:A:592:G:H :T:150::HB3 18:T:189::HE :A:1374:A:H2 1:A:1375:A:C :A:1806:U:H2 1:A:1807:C:C :A:373:C:H2 1:A:374:U:H :G:133::HD22 7:G:136::HB :W:68:HIS:O 21:W:159::NH :3:52:CYS:SG 26:3:55:CYS:SG :A:668:U:H2 1:A:669:C:C :A:1743:G:C5 1:A:1744:C:C :A:227:G:HO2 1:A:239:G:H :A:2791:C:C4 1:A:2792:C:C :M:76::HG12 16:R:195::HG :P:34::HB3 14:P:54::SD :T:172::HD12 18:T:175::HA :T:155::HA 18:T:185::HA :W:93:HIS:CE1 21:W:100::HD :A:1671:A:H2 1:A:1672:U:O :A:176:A:H2 1:A:177:C:H :A:2743:A:O2 1:A:2744:A:C :A:559:G:O6 18:T:141:TRP:CD :A:654:U:O2 1:A:654:U:O :A:836:G:H2 1:A:837:U:O :M:63::HG12 11:M:106::HD :X:107::CG2 22:X:137::HG :A:2543:G:C5 1:A:2544:C:C :E:167:HIS:CD2 5:E:289::HD :U:83::HB1 19:U:136::HD :A:1202:A:H2 1:A:1203:C:C :A:539:A:C2 1:A:2056:A:H

34 Page 34 Full wwpdb/emdatabank EM Map/Model Validation Report 5MLC Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 1:A:410:G:C5 1:A:411:U:C :A:815:A:H2 1:A:817:C:C :A:2607:A:H5 4:D:234::HE :N:136::HD22 12:N:140::CD :O:43::HG22 13:O:92:TYR:CD :L:95::O 17:S:99::NE :V:115::HD21 20:V:151::CG :A:1530:G:H1 1:A:1536:A:H :A:1634:C:H2 1:A:1634:C:O :A:2472:G:C5 1:A:2473:C:C :A:2484:C:O2 13:O:124::NZ :D:91:HIS:CD2 4:D:97::HD :F:207::CE1 6:F:246::HG :A:102:U:C4 1:A:103:C:C :A:1261:A:H8 1:A:1261:A:C :A:1530:G:C2 1:A:1536:A:H :A:2307:G:H2 1:A:2308:U:O :A:309:A:N1 1:A:331:A:O :E:151::N 5:E:152::HD :O:2::N 13:O:44::OG :A:1956:C:O2 30:9:218::NH :A:1137:C:N3 1:A:1138:G:C :A:136:U:C4 1:A:137:U:O :A:1500:U:O2 1:A:1500:U:C :A:1982:G:O2 1:A:1983:A:O :A:548:G:N2 1:A:567:C:N :U:153::HB 19:U:154::HD :Z:80::HG22 24:Z:84::HD :A:2207:A:H2 1:A:2208:U:O :A:233:G:H5 1:A:235:G:N :A:393:G:H2 1:A:394:G:O :D:117::O 4:D:118::O :H:194::HG3 8:H:209::HG :Z:112::HG12 24:Z:116::HD :A:2205:G:H2 1:A:2206:A:O :A:26:G:C4 1:A:523:G:C :H:138::HG22 8:H:143::HD :A:1362:G:N3 20:V:163::ND :A:14:A:N3 25:2:15::HD :A:169:C:H2 1:A:170:U:C :A:567:C:O2 10:L:146::O