Full wwpdb X-ray Structure Validation Report

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(1)Full wwPDB X-ray Structure Validation Report. O i. May 22, 2020 02:44 am BST PDB ID Title. : :. Authors Deposited on Resolution. : : :. 4ISK Crystal structure of E.coli thymidylate synthase with dUMP and the BGC 945 inhibitor Tochowicz, A.; Finer-Moore, J.; Stroud, R.M. 2013-01-16 1.75 Å(reported). This is a Full wwPDB X-ray Structure Validation Report for a publicly released PDB entry. We welcome your comments at [email protected] A user guide is available at https://www.wwpdb.org/validation/2017/XrayValidationReportHelp with specic help available everywhere you see the i symbol.. O. The following versions of software and data (see references MolProbity Mogul Xtriage (Phenix) EDS buster-report Percentile statistics Refmac CCP4 Ideal geometry (proteins) Ideal geometry (DNA, RNA) Validation Pipeline (wwPDB-VP). : : : : : : : : : : :. O) were used in the production of this report: i. 4.02b-467 1.8.5 (274361), CSD as541be (2020) 1.13 2.11 1.1.7 (2018) 20191225.v01 (using entries in the PDB archive December 25th 2019) 5.8.0158 7.0.044 (Gargrove) Engh & Huber (2001) Parkinson et al. (1996) 2.11.

(2) Page 2. Full wwPDB X-ray Structure Validation Report. 1 Overall quality at a glance. O. 4ISK. i. The following experimental techniques were used to determine the structure:. X-RAY DIFFRACTION. The reported resolution of this entry is 1.75 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 Rf ree Clashscore Ramachandran outliers Sidechain outliers RSRZ outliers. Whole archive (#Entries) 130704 141614 138981 138945 127900. Similar resolution (#Entries, resolution range(Å)) 2340 2466 2437 2437 2298. (1.76-1.76) (1.76-1.76) (1.76-1.76) (1.76-1.76) (1.76-1.76). The table below summarises the geometric issues observed across the polymeric chains and their t to the electron density. The red, orange, yellow and green segments on the lower bar indicate the fraction of residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria respectively. 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% The upper red bar (where present) indicates the fraction of residues that have poor t to the electron density. The numeric value is given above the bar.. Mol Chain Length 1. A. 264. 1. B. 264. 1. C. 264. 1. D. 264. 1. E. 264. 1. F. 264. Quality of chain. Continued on next page....

(3) Page 3. Full wwPDB X-ray Structure Validation Report. Continued from previous page.... Mol Chain Length 1. G. 264. 1. H. 264. Quality of chain. 4ISK.

(4) Page 4. Full wwPDB X-ray Structure Validation Report. 2 Entry composition. 4ISK. O i. There are 6 unique types of molecules in this entry. The entry contains 37528 atoms, of which 18746 are hydrogens and 0 are deuteriums. In the tables below, the ZeroOcc column contains the number of atoms modelled with zero occupancy, 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 protein called Thymidylate synthase.. Mol Chain Residues 1. A. 264. 1. B. 264. 1. C. 264. 1. D. 264. 1. E. 264. 1. F. 264. 1. G. 264. 1. H. 264. Total 4243 Total 4263 Total 4239 Total 4243 Total 4242 Total 4263 Total 4239 Total 4242. C 1375 C 1380 C 1375 C 1375 C 1375 C 1380 C 1375 C 1375. Atoms H 2091 H 2102 H 2086 H 2090 H 2089 H 2102 H 2086 H 2089. N 371 N 374 N 371 N 371 N 371 N 374 N 371 N 371. O 394 O 395 O 395 O 395 O 395 O 395 O 395 O 395. S 12 S 12 S 12 S 12 S 12 S 12 S 12 S 12. ZeroOcc AltConf Trace 20. 0. 0. 0. 2. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 27. 1. 0. 20. 0. 0. 200. 0. 0. There are 8 discrepancies between the modelled and reference sequences:. Chain Residue Modelled Actual A B C D E F G H. 1 1 1 1 1 1 1 1. CXM CXM CXM CXM CXM CXM CXM CXM. -. Comment. EXPRESSION EXPRESSION EXPRESSION EXPRESSION EXPRESSION EXPRESSION EXPRESSION EXPRESSION. TAG TAG TAG TAG TAG TAG TAG TAG. Reference. UNP UNP UNP UNP UNP UNP UNP UNP. P0A884 P0A884 P0A884 P0A884 P0A884 P0A884 P0A884 P0A884. Molecule 2 is 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (three-letter code: UMP) (formula: C9 H13 N2 O8 P)..

(5) Page 5. Full wwPDB X-ray Structure Validation Report. Mol Chain Residues 2. A. 1. 2. C. 1. 2. G. 1. Total 31 Total 31 Total 31. Atoms. C 9 C 9 C 9. H 11 H 11 H 11. N 2 N 2 N 2. O 8 O 8 O 8. P 1 P 1 P 1. 4ISK. ZeroOcc AltConf 0. 0. 0. 0. 0. 0. Molecule 3 is MAGNESIUM ION (three-letter code: MG) (formula: Mg).. Mol Chain Residues 3. G. 1. 3. D. 1. 3. E. 1. 3. H. 1. 3. B. 1. 3. C. 1. 3. A. 1. Atoms. Total 1 Total 1 Total 1 Total 1 Total 1 Total 1 Total 1. Mg 1 Mg 1 Mg 1 Mg 1 Mg 1 Mg 1 Mg 1. ZeroOcc AltConf 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. Molecule 4 is N-(4-{[(6S)-2-(hydroxymethyl)-4-oxo-4,6,7,8-tetrahydro-1H-cyclopenta[ g]quinazolin-6-yl](prop-2-yn-1-yl)amino}benzoyl)-L-gamma-glutamyl-D-glutamic acid (three-letter code: 1JY) (formula: C32 H33 N5 O10 )..

(6) Page 6. Full wwPDB X-ray Structure Validation Report. Mol Chain Residues 4. A. 1. 4. B. 1. 4. C. 1. 4. D. 1. 4. E. 1. 4. F. 1. 4. G. 1. 4. H. 1. Total 47 Total 47 Total 47 Total 47 Total 47 Total 47 Total 47 Total 47. Atoms C 32 C 32 C 32 C 32 C 32 C 32 C 32 C 32. N 5 N 5 N 5 N 5 N 5 N 5 N 5 N 5. O 10 O 10 O 10 O 10 O 10 O 10 O 10 O 10. 4ISK. ZeroOcc AltConf 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. Molecule 5 is 2'-deoxy-5'-uridylic acid (three-letter code: UMC) (formula: C H 9. 15 N2 O8 P)..

(7) Page 7. Full wwPDB X-ray Structure Validation Report. Mol Chain Residues 5. B. 1. 5. D. 1. 5. E. 1. 5. F. 1. 5. H. 1. Molecule 6 is water.. Mol Chain Residues 6. A. 184. 6. B. 169. 6. C. 168. 6. D. 131. 6. E. 129. 6. F. 92. 6. G. 74. Total 32 Total 32 Total 32 Total 32 Total 32. Atoms. C 9 C 9 C 9 C 9 C 9. H 12 H 12 H 12 H 12 H 12. Atoms. Total 540 Total 495 Total 492 Total 381 Total 377 Total 276 Total 210. H 356 H 326 H 324 H 250 H 248 H 184 H 136. N 2 N 2 N 2 N 2 N 2. O 184 O 169 O 168 O 131 O 129 O 92 O 74. O 8 O 8 O 8 O 8 O 8. P 1 P 1 P 1 P 1 P 1. 4ISK. ZeroOcc AltConf 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. ZeroOcc AltConf 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. Continued on next page....

(8) Page 8. Full wwPDB X-ray Structure Validation Report. Continued from previous page.... Mol Chain Residues 6. H. 53. Atoms. Total 147. H 94. O 53. ZeroOcc AltConf 0. 0. 4ISK.

(9) Page 9. Full wwPDB X-ray Structure Validation Report. 4ISK. O. 3 Residue-property plots. i. 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 and electron density. Residues are color-coded 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. A red dot above a residue indicates a poor t to the electron density (RSRZ > 2). 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: Thymidylate synthase. L174. C168. • • Y164. C146. L143. R126 R127 I128 I129. D110 Q111 I112 T113 T114 V115 L116 N117 Q118 T114. • P104 D105 D110 Q111. • V93 R107. W83 A84 D85 E86. E74. I69. D66. I264. E248 I249. Y242. P236. K233. •. W61. • L52. T47. P43. Q17. D20 R21 T22 G23 L227. W201. C192. M188. •. L5. M1. • • •. Chain A:. • Molecule 1: Thymidylate synthase. P236. R225. C192. V185. Y181. L174. C168. • L143 I231. C146. K140. V135. R225. R127. T103 P104. V93. D89. A84 D85 E86. E74. I69. R49. P43. T22. K18 N19. D13. I264. D253. Y242. •. K10. M1. •. Chain B:. • Molecule 1: Thymidylate synthase. • I264. K259. D253. I249 E250. W201 T202. Y164. • • • • F149 F150. C146. V135. R127. D122 P123 D124. T114. D110. T103 P104 D105 G106 R107. A100. K96. V93. N76. N19 D20. M1. • • •. Chain C:. • Molecule 1: Thymidylate synthase. • F152 Y153 V154 A155 D156. M141 A142 L143 A144 P145 C146. R127. • D105 G106 R107 H108 I109 D110 Q111 I112 T113 T114 V115 L116. R99. V93. • E86. W80. E74. A70. R53. Q39. R35. H32. L27. G23. D13. L7. M1 K2 Q3. • • •. Chain D:.

(10) P236 E237 S238. I231. R225 P226 L227. L220 S221. M213 D214. •. •. • • • •. R127. N121 D122 P123. T114 V115 L116 N117 Q118. W101 P102 T103 P104 D105 G106 R107 H108 I109 D110. • • •. V200 W201 T202 G203 G204 D205. D85 E86 N87 G88. A70. D66. L60. H51 L52 R53 S54 I55 I56. Q39. R35. •. •. • • • • •. • • • • • •. •. D20 R21 T22. H32. •. L12. L7. V93. •. • • • •. • • • • • • • • •. •. M1 K2 Q3. V196. D193. H186 M187 M188. Y181 A182 L183. F176. Q162 L163 Y164. A155 D156 G157 K158. C146 H147 A148 F149 F150. L143. D139. N134. I128 I129. K233 R234 K235. P224 R225 P226. H217 L218 Q219 L220. W201. D198. M188 A189 Q190 Q191 C192 D193 L194 E195. L183. L174 P175 F176 N177 I178. C168. L163 Y164. D156 G157 K158. P145 C146 H147 A148 F149 F150. L138 D139 K140 M141. V135. K259 I264. V130. F247 E248. • •. • • • • •. • • •. • •. • •. • • • • •. •. •. S125 R126 R127. N121. T114 V115 L116. P102 T103 P104 D105 G106 R107 H108 I109 D110. Q97. D89. W80. D66. H51 L52 R53. T47. R35. H32. I29. G23 T24 G25. D20. K10 V11 L12 D13 E14 G15 T16 Q17. L5 E6 L7. M1. •. • • • • • • •. • • •. •. • • •. P261 V262 A263 I264. E250 G251 Y252 D253 P254 H255 P256. F240 D241 Y242. K235 P236 E237. I231. R225 P226. S221 R222. T216 H217 L218. W201 T202 G203. D193. Q190. Y181. L174 P175 F176. C168. Y164. F149 F150. C146. A142 L143. • • • •. •. • • •. • •. • • •. R127. D124. T114. G106 R107 H108 I109 D110. R99 A100 W101. V93. D81 E82 W83 A84 D85 E86 N87 G88. N76 V77 T78. I69 A70. D66. W61. I55. H51 L52. Q39. Q17 K18 N19 D20 R21 T22 G23 T24. M8. M1 K2 Q3. • •. • • • •. • •. •. • • • • • • •. A263 I264. •. •. Y242 R243 E248. •. • • • • I231 I232 K233 R234 K235 P236 E237. L227. L220. M188. F176. L163 Y164. • • • •. D20 R21 T22 G23 T24. E137 L138 D139 K140. S125 R126. D110 Q111 I112 T113 T114 V115 L116. A100 W101 P102 T103 P104 D105 G106 R107. Q97. V93. D89. W83 A84 D85 E86. H73 E74 N75 N76 V77 T78. I69 A70. D66. W61. H51 L52 R53 S54 I55. M8. W133. L143 A144 P145 C146. M1. R127. • •. •. • • • • •. • • •. I264. E248 I249 E250. F240 D241 Y242 R243. P236. L230 I231. M188. L184. L174. C168. •. •. Page 10 Full wwPDB X-ray Structure Validation Report 4ISK. • Molecule 1: Thymidylate synthase. Chain E:. • Molecule 1: Thymidylate synthase. Chain F:. • Molecule 1: Thymidylate synthase. Chain G:. • Molecule 1: Thymidylate synthase. Chain H:.

(11) V262 A263 I264. •. Full wwPDB X-ray Structure Validation Report. F247 E248 I249. I239 F240 D241 Y242. • •. Page 11. 4ISK.

(12) Page 12. Full wwPDB X-ray Structure Validation Report. 4 Data and renement statistics. Property. Space group Cell constants a, b, c, α, β , γ Resolution (Å) % Data completeness (in resolution range) Rmerge Rsym < I/σ(I) > 1 Renement program R, Rf ree Rf ree test set Wilson B-factor (Å2 ) Anisotropy Bulk solvent ksol (e/Å3 ), Bsol (Å2 ) L-test for twinning2 Estimated twinning fraction Fo ,Fc correlation Total number of atoms Average B, all atoms (Å2 ). O. 4ISK. i. Value. P 1 21 1 95.90Å 85.50Å 134.30Å 90.00◦ 109.40◦ 90.00◦ 29.81 1.75 29.81 1.75 97.8 (29.81-1.75) 97.9 (29.81-1.75) 0.07 (Not available) 2.14 (at 1.75Å) PHENIX (phenix.rene: 1.7.2_869) 0.184 , 0.233 0.185 , 0.233 4020 reections (2.00%) 20.4 0.692 0.44 , 51.0 < |L| > = 0.44, < L2 > = 0.26 0.012 for h,-k,-h-l 0.96 37528 38.0. Source. Depositor Depositor Depositor EDS Depositor EDS Depositor Depositor Xtriage Depositor Depositor DCC wwPDB-VP Xtriage Xtriage EDS Xtriage Xtriage EDS wwPDB-VP wwPDB-VP. The analyses of the Patterson function reveals a signicant o-origin peak that is 38.27 % of the origin peak, indicating pseudo-translational symmetry. The chance of nding a peak of this or larger height randomly in a structure without pseudo-translational symmetry is equal to 3.7798e-04. The detected translational NCS is most likely also responsible for the elevated intensity ratio. Xtriage's analysis on translational NCS is as follows:. 1 Intensities. estimated from amplitudes. values of < |L| >, < L2 > for acentric reections are 0.5, 0.333 respectively for untwinned datasets, and 0.375, 0.2 for perfectly twinned datasets. 2 Theoretical.

(13) Page 13. Full wwPDB X-ray Structure Validation Report. 5 Model quality 5.1. O i. Standard geometry. 4ISK. O i. Bond lengths and bond angles in the following residue types are not validated in this section: 1JY, MG, UMP, UMC, CXM 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 1 1 1 1 1 1 1 1 All. A B C D E F G H All. Bond lengths. RMSZ 0.69 0.67 0.64 0.63 0.61 0.52 0.57 0.51 0.61. Bond angles. #|Z| >5 1/2201 (0.0%) 1/2213 (0.0%) 0/2202 0/2202 0/2202 0/2213 0/2202 0/2202 2/17637 (0.0%). RMSZ 0.74 0.74 0.70 0.75 0.71 0.68 0.69 0.66 0.71. #|Z| >5 0/2990 0/3004 0/2990 1/2990 (0.0%) 0/2990 0/3004 0/2990 0/2990 1/23948 (0.0%). All (2) bond length outliers are listed below:. Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å) 1 1. A B. 192 192. CYS CYS. CB-SG CB-SG. -5.47 -5.06. 1.72 1.73. 1.81 1.81. All (1) bond angle outliers are listed below:. Mol Chain Res Type 1. D. 35. ARG. Atoms. NE-CZ-NH1. Z Observed( ) Ideal( ) o. 5.65. 123.12. o. 120.30. There are no chirality outliers. There are no planarity outliers.. 5.2. Too-close contacts. O 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.

(14) Page 14. Full wwPDB X-ray Structure Validation Report. 4ISK. the asymmetric unit, whereas Symm-Clashes lists symmetry related clashes.. Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes 1 1 1 1 1 1 1 1 2 2 2 3 3 3 3 3 3 3 4 4 4 4 4 4 4 4 5 5 5 5 5 6 6 6 6 6 6 6 6 All. A B C D E F G H A C G A B C D E G H A B C D E F G H B D E F H A B C D E F G H All. 2152 2161 2153 2153 2153 2161 2153 2153 20 20 20 1 1 1 1 1 1 1 47 47 47 47 47 47 47 47 20 20 20 20 20 184 169 168 131 129 92 74 53 18782. 2091 2102 2086 2090 2089 2102 2086 2089 11 11 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 12 12 12 356 326 324 250 248 184 136 94 18746. 2080 2093 2080 2080 2079 2092 2080 2079 11 11 11 0 0 0 0 0 0 0 30 30 30 30 30 30 30 30 13 13 12 12 12 0 0 0 0 0 0 0 0 16998. 28 34 24 25 46 36 36 40 1 2 1 0 0 0 0 0 0 0 5 4 5 6 15 5 5 8 3 4 2 3 2 3 11 2 3 8 5 3 2 289. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0. The all-atom clashscore is dened as the number of clashes found per 1000 atoms (including.

(15) Page 15. Full wwPDB X-ray Structure Validation Report. 4ISK. hydrogen atoms). The all-atom clashscore for this structure is 8. All (289) close contacts within the same asymmetric unit are listed below, sorted by their clash magnitude.. Atom-1. Atom-2. 1:B:146[A]:CYS:SG 1:D:146:CYS:SG 1:F:146:CYS:SG 1:E:146:CYS:SG 1:H:146:CYS:SG 1:B:146[A]:CYS:SG 1:D:146:CYS:SG 1:F:3:GLN:OE1 1:B:10:LYS:NZ 1:D:3:GLN:NE2 1:B:49:ARG:NH2 1:F:146:CYS:SG 1:C:105:ASP:OD2 1:C:127:ARG:HD3 1:B:89:ASP:OD1 1:B:103:THR:HB 1:D:146:CYS:SG 1:G:116:LEU:HD21 1:E:127:ARG:HD3 4:G:303:1JY:CBN 1:A:248:GLU:OE1 1:G:259:LYS:NZ 4:E:303:1JY:H22 1:E:51:HIS:CE1 4:D:303:1JY:H17 4:H:303:1JY:H15 1:A:110:ASP:O 1:A:114:THR:OG1 1:C:231:ILE:HD11 1:B:13:ASP:OD2 1:C:104:PRO:O 1:B:110:ASP:O 1:F:146:CYS:SG 1:A:1:CXM:HE1 4:E:303:1JY:H15 1:H:129:ILE:O 1:C:146:CYS:SG 1:E:137:GLU:OE2. 5:B:301:UMC:H6 5:D:301:UMC:H6 5:F:301:UMC:C6 5:E:301:UMC:C6 5:H:301:UMC:C6 5:B:301:UMC:C6 5:D:301:UMC:C6 6:F:454:HOH:O 6:B:520:HOH:O 6:D:471:HOH:O 6:B:506:HOH:O 5:F:301:UMC:C5 1:C:107:ARG:HD3 1:C:127:ARG:O 6:B:561:HOH:O 1:B:104:PRO:HD2 5:D:301:UMC:C5 1:G:188:MET:SD 1:E:127:ARG:O 4:G:303:1JY:H17 6:A:530:HOH:O 6:G:444:HOH:O 6:E:528:HOH:O 1:E:53:ARG:HD3 4:D:303:1JY:CBN 4:H:303:1JY:CBN 1:A:114:THR:HG23 6:A:471:HOH:O 1:C:250:GLU:HB2 6:B:447:HOH:O 1:C:105:ASP:HB2 1:B:114:THR:HG23 5:F:301:UMC:H5A 1:A:43:PRO:HA 4:E:303:1JY:CBN 6:H:402:HOH:O 2:C:301:UMP:C6 1:E:140:LYS:NZ. Interatomic distance (Å) 1.14 1.16 2.02 2.03 2.05 2.06 2.06 1.59 1.83 1.91 1.97 2.59 1.72 1.72 1.92 1.59 2.68 2.19 1.80 2.15 2.03 2.03 1.87 2.24 2.18 2.19 1.89 2.08 1.71 2.08 1.91 1.92 2.31 1.72 2.22 2.09 2.86 2.27. Clash overlap (Å) 1.72 1.63 1.48 1.47 1.43 1.42 1.40 1.20 1.10 0.98 0.94 0.90 0.89 0.89 0.87 0.84 0.82 0.82 0.81 0.77 0.75 0.74 0.74 0.73 0.73 0.72 0.72 0.72 0.72 0.71 0.71 0.70 0.70 0.70 0.70 0.69 0.68 0.68. Continued on next page....

(16) Page 16. Full wwPDB X-ray Structure Validation Report. Continued from previous page.... Atom-1. Atom-2. 4:B:303:1JY:H17 4:B:303:1JY:CAR 1:G:66:ASP:OD2 1:E:102:PRO:O 4:F:302:1JY:CBN 4:G:303:1JY:CAR 1:E:116:LEU:HD21 1:E:248:GLU:OE1 1:C:76:ASN:OD1 4:H:303:1JY:O 4:D:303:1JY:CAR 1:G:104:PRO:O 4:H:303:1JY:CAS 1:F:83:TRP:CZ3 4:E:303:1JY:CAS 4:A:303:1JY:CAR 1:A:127:ARG:O 1:D:112:ILE:O 1:C:231:ILE:CD1 1:C:103:THR:OG1 1:E:110:ASP:O 4:G:303:1JY:CAR 1:E:51:HIS:CE1 1:G:110:ASP:O 4:A:303:1JY:H17 1:H:86:GLU:CD 1:E:51:HIS:CE1 1:H:103:THR:HB 1:E:51:HIS:CE1 1:E:51:HIS:CE1 1:H:146:CYS:SG 1:B:225:ARG:HG3 1:G:168:CYS:SG 1:E:51:HIS:CE1 1:F:110:ASP:O 1:C:225:ARG:HD2 4:F:302:1JY:CAS 4:C:303:1JY:CBN 1:C:110:ASP:O 4:D:303:1JY:CAR 1:H:7:LEU:HD13. 4:B:303:1JY:CBN 4:B:303:1JY:CBN 6:G:428:HOH:O 6:E:505:HOH:O 4:F:302:1JY:H15 4:G:303:1JY:CBN 1:E:188:MET:SD 6:E:434:HOH:O 6:C:473:HOH:O 4:H:303:1JY:H31 4:D:303:1JY:CBN 1:G:105:ASP:CB 4:H:303:1JY:CBN 4:F:302:1JY:H8 4:E:303:1JY:CBN 4:A:303:1JY:CBN 1:A:127:ARG:HD3 1:D:116:LEU:HD23 1:C:250:GLU:HB2 1:C:107:ARG:HG2 1:E:114:THR:HG23 4:G:303:1JY:CAO 1:E:53:ARG:HG2 1:G:114:THR:HG23 4:A:303:1JY:CBN 1:H:86:GLU:N 4:E:303:1JY:C 1:H:104:PRO:HD2 1:E:53:ARG:CG 1:E:53:ARG:CD 5:H:301:UMC:C5 1:B:253:ASP:O 1:G:174:LEU:HB2 4:E:303:1JY:O 1:F:114:THR:HG23 1:C:253:ASP:O 4:F:302:1JY:CBN 4:C:303:1JY:H15 1:C:114:THR:HG23 4:D:303:1JY:CAO 1:H:32:HIS:CD2. Interatomic distance (Å) 2.22 2.71 2.13 2.13 2.26 2.72 2.37 2.15 2.15 1.97 2.74 2.45 2.75 2.34 2.75 2.78 1.99 2.00 2.28 2.00 1.99 2.78 2.36 1.99 2.31 2.55 2.84 1.82 2.85 2.83 2.88 2.02 2.41 2.55 2.02 2.02 2.79 2.32 2.03 2.80 2.38. Clash overlap (Å) 0.68 0.67 0.67 0.67 0.66 0.65 0.65 0.65 0.64 0.64 0.64 0.64 0.64 0.63 0.62 0.62 0.62 0.62 0.62 0.61 0.61 0.61 0.61 0.61 0.61 0.60 0.60 0.60 0.60 0.60 0.60 0.60 0.60 0.59 0.59 0.59 0.59 0.59 0.59 0.59 0.59. Continued on next page.... 4ISK.

(17) Page 17. Full wwPDB X-ray Structure Validation Report. Continued from previous page.... Atom-1. Atom-2. 1:C:259:LYS:NZ 1:G:104:PRO:O 1:C:105:ASP:HB3 1:B:146[A]:CYS:SG 1:D:146:CYS:SG 1:D:7:LEU:HD13 4:H:303:1JY:CAS 1:E:146:CYS:SG 1:A:86:GLU:H 4:C:303:1JY:CBN 1:G:5:LEU:HD11 1:G:89:ASP:OD2 1:C:135:VAL:HG12 1:G:183:LEU:HD11 1:A:233:LYS:HE3 4:B:303:1JY:CAR 1:D:110:ASP:O 1:G:135:VAL:HG12 1:G:146:CYS:SG 1:A:74:GLU:HG2 1:G:233:LYS:NZ 1:B:107:ARG:CZ 1:B:86:GLU:CD 1:G:103:THR:OG1 1:H:86:GLU:H 1:E:103:THR:OG1 1:A:146:CYS:SG 1:G:51:HIS:CE1 1:F:52:LEU:HA 4:D:303:1JY:OXT 1:E:116:LEU:CD2 1:E:83:TRP:CZ3 1:C:146:CYS:SG 1:E:233:LYS:NZ 1:H:183:LEU:HD11 1:A:249:ILE:HG23 1:H:186:HIS:CE1 1:A:5:LEU:HD11 1:A:116:LEU:HD21 1:A:20:ASP:OD2 1:E:231:ILE:N. 6:C:519:HOH:O 1:G:105:ASP:HB2 1:C:107:ARG:HB3 5:B:301:UMC:C5 5:D:301:UMC:H5A 1:D:32:HIS:CD2 4:H:303:1JY:CAO 5:E:301:UMC:C5 1:A:86:GLU:CD 4:C:303:1JY:CAS 1:G:47:THR:HG21 6:G:417:HOH:O 1:F:109:ILE:HD12 1:G:247:PHE:CE1 1:A:248:GLU:HB2 4:B:303:1JY:CAO 1:D:114:THR:HG23 1:H:109:ILE:HD12 2:G:301:UMP:C6 1:B:74:GLU:CD 1:G:248:GLU:OE1 6:B:485:HOH:O 1:B:86:GLU:H 1:G:107:ARG:HB3 1:H:86:GLU:CD 1:E:107:ARG:HB3 2:A:301:UMP:C6 1:G:53:ARG:HG3 1:F:55:ILE:HD12 6:D:492:HOH:O 1:E:188:MET:SD 4:E:303:1JY:H8 2:C:301:UMP:C5 6:E:434:HOH:O 1:H:247:PHE:CE1 1:A:249:ILE:O 1:H:196:VAL:HG11 1:A:47:THR:HG21 1:A:188:MET:SD 1:A:22:THR:OG1 1:E:231:ILE:HD12. Interatomic distance (Å) 2.36 2.02 1.85 2.88 2.42 2.39 2.82 2.90 2.08 2.82 1.86 2.17 1.88 2.40 1.88 2.84 2.06 1.88 2.99 2.26 2.32 2.55 2.10 2.06 2.11 2.08 3.01 2.43 1.90 2.19 2.96 2.44 3.01 2.40 2.44 2.09 2.44 1.92 2.50 2.20 2.25. Clash overlap (Å) 0.58 0.58 0.58 0.58 0.58 0.58 0.58 0.58 0.57 0.57 0.57 0.56 0.56 0.56 0.56 0.56 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.54 0.54 0.54 0.54 0.54 0.54 0.53 0.53 0.53 0.53 0.53 0.53 0.52 0.52 0.52 0.52 0.52. Continued on next page.... 4ISK.

(18) Page 18. Full wwPDB X-ray Structure Validation Report. Continued from previous page.... Atom-1. Atom-2. 1:H:262:VAL:HG13 1:H:3:GLN:NE2 4:E:303:1JY:CAS 4:B:303:1JY:CBQ 1:D:231:ILE:HD13 4:C:303:1JY:CAO 1:D:86:GLU:CD 1:E:78:THR:O 1:B:107:ARG:NH2 1:F:127[B]:ARG:HD2 1:C:249:ILE:HG23 1:G:11:VAL:O 1:B:135:VAL:HG12 1:F:252:TYR:CE2 1:G:7:LEU:HD13 1:E:125:SER:O 1:A:168:CYS:SG 1:H:52:LEU:HA 1:B:181:TYR:O 1:F:263:ALA:O 1:G:104:PRO:HG3 1:E:8:MET:HB3 1:E:53:ARG:NH2 1:B:74:GLU:OE1 4:H:303:1JY:H20 1:A:1:CXM:HE2 1:E:83:TRP:CH2 1:F:218:LEU:O 1:G:116:LEU:CD2 1:G:104:PRO:HB3 1:D:70:ALA:O 1:F:252:TYR:HA 1:A:112:ILE:O 1:G:105:ASP:OD1 1:A:264:ILE:HB 1:B:111:GLN:O 1:D:105:ASP:OD2 1:F:78:THR:HA 4:E:303:1JY:OAG 1:D:184:LEU:O 4:A:303:1JY:CAR. 1:H:262:VAL:O 1:H:35:ARG:O 4:E:303:1JY:CAO 4:B:303:1JY:CAO 1:D:250:GLU:HG3 4:C:303:1JY:CAS 1:D:86:GLU:H 6:E:529:HOH:O 6:B:485:HOH:O 6:F:467:HOH:O 1:C:249:ILE:O 1:G:15:GLY:HA3 1:D:109:ILE:HD12 1:F:254:PRO:HG3 1:G:32:HIS:CD2 6:E:491:HOH:O 1:A:174:LEU:HB2 1:H:55:ILE:HD12 1:B:185:VAL:HG23 4:F:302:1JY:H1 1:H:103:THR:C 1:E:220:LEU:HD21 1:E:75:ASN:O 6:B:554:HOH:O 6:H:420:HOH:O 1:A:227:LEU:HD21 4:E:303:1JY:CAN 1:F:221:SER:OG 1:G:188:MET:SD 1:H:104:PRO:HA 1:D:74:GLU:HG3 6:F:461:HOH:O 1:A:116:LEU:HD23 1:G:105:ASP:C 6:A:553:HOH:O 1:B:114:THR:OG1 6:D:478:HOH:O 1:F:81:ASP:OD1 6:E:527:HOH:O 1:D:188:MET:HG3 4:A:303:1JY:CAO. Interatomic distance (Å) 2.07 2.32 2.88 2.88 1.92 2.88 2.14 2.18 2.43 2.11 2.11 2.12 1.93 2.47 2.47 2.20 2.52 1.95 2.12 2.12 2.33 1.95 2.36 2.20 2.12 1.94 2.97 2.25 2.96 1.94 2.13 2.14 2.13 2.52 2.14 2.28 2.20 2.14 2.20 2.15 2.91. Clash overlap (Å) 0.52 0.52 0.52 0.51 0.51 0.51 0.51 0.51 0.51 0.51 0.50 0.50 0.50 0.50 0.49 0.49 0.49 0.49 0.49 0.49 0.49 0.49 0.49 0.49 0.48 0.48 0.48 0.48 0.48 0.48 0.48 0.48 0.48 0.48 0.48 0.48 0.48 0.48 0.47 0.47 0.47. Continued on next page.... 4ISK.

(19) Page 19. Full wwPDB X-ray Structure Validation Report. Continued from previous page.... Atom-1. Atom-2. 1:B:140:LYS:CE 1:E:51:HIS:NE2 1:G:190:GLN:NE2 1:B:18:LYS:HE3 1:D:141:MET:SD 1:G:104:PRO:CG 1:A:1:CXM:CE 1:B:1:CXM:HE1 1:F:231:ILE:HD13 1:G:126:ARG:HG2 1:C:19:ASN:HB2 1:F:8:MET:HG2 1:H:176:PHE:CD2 1:A:83:TRP:CD1 1:G:158:LYS:HA 1:E:248:GLU:HB2 1:A:126:ARG:NH1 1:D:152:PHE:CZ 1:E:86:GLU:H 1:H:110:ASP:O 1:H:1:CXM:HG3 1:H:225:ARG:HB3 1:F:61:TRP:CD1 1:G:125:SER:OG 1:H:102:PRO:HD2 1:C:122:ASP:N 4:C:303:1JY:CBQ 4:H:303:1JY:H13 1:C:124:ASP:OD1 1:C:202:THR:HG21 1:H:225:ARG:HB3 1:H:56:ILE:O 1:E:263:ALA:O 1:F:85:ASP:C 1:H:183:LEU:HD11 1:A:249:ILE:CG2 1:E:263:ALA:HB3 1:C:104:PRO:O 1:C:105:ASP:OD2 1:B:168:CYS:SG 1:B:19:ASN:ND2. 6:B:548:HOH:O 1:E:53:ARG:HG2 1:G:235:LYS:HB2 1:D:154:VAL:O 1:D:145:PRO:HD3 1:H:103:THR:O 1:A:227:LEU:HD21 1:B:43:PRO:HA 1:F:250:GLU:HG3 1:H:205:ASP:OD2 1:F:124:ASP:OD2 1:F:216:THR:HG23 4:H:303:1JY:H17 1:A:143:LEU:HD13 1:G:195:GLU:O 6:E:434:HOH:O 1:E:20:ASP:HB2 1:D:188:MET:SD 1:E:86:GLU:CD 1:H:114:THR:HG23 1:H:227:LEU:HD21 1:H:226:PRO:HD2 1:F:66:ASP:HB3 1:G:127:ARG:HG3 1:H:134:ASN:ND2 1:C:123:PRO:CD 4:C:303:1JY:CAO 4:H:303:1JY:H17 1:F:18:LYS:HE2 1:F:202:THR:HG21 1:H:226:PRO:CD 1:H:60:LEU:HG 4:E:303:1JY:H1 1:F:85:ASP:OD1 1:H:247:PHE:CD1 1:A:249:ILE:O 4:E:303:1JY:CAT 1:C:105:ASP:CB 1:C:107:ARG:CD 1:B:174:LEU:HB2 6:B:551:HOH:O. Interatomic distance (Å) 2.61 2.29 2.29 2.15 2.54 2.62 2.45 1.96 1.95 2.15 2.15 1.97 2.50 2.50 2.14 2.15 2.30 3.09 2.19 2.16 1.97 1.97 2.51 2.15 2.31 2.79 2.93 1.67 2.17 1.99 2.46 2.17 2.17 2.55 2.52 2.64 2.47 2.61 2.57 2.56 2.50. Clash overlap (Å) 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.44 0.44 0.44 0.44. Continued on next page.... 4ISK.

(20) Page 20. Full wwPDB X-ray Structure Validation Report. Continued from previous page.... Atom-1. Atom-2. 1:E:51:HIS:NE2 1:A:236:PRO:HG2 1:B:1:CXM:CN 1:E:236:PRO:HG2 1:F:127[A]:ARG:HD2 1:D:230:LEU:C 4:D:303:1JY:H17 1:E:83:TRP:CH2 1:E:139:ASP:N 1:D:248:GLU:HG3 1:F:193:ASP:OD1 1:G:138:LEU:HD13 1:C:96:LYS:HE2 1:F:231:ILE:N 4:G:303:1JY:CAO 4:A:303:1JY:CBQ 1:F:190:GLN:O 1:E:231:ILE:HB 1:H:101:TRP:O 1:F:225:ARG:HB3 4:F:302:1JY:CAS 1:C:135:VAL:HB 1:B:236:PRO:HG2 1:E:112:ILE:O 1:F:142:ALA:O 1:G:104:PRO:HG3 1:H:236:PRO:HG2 1:B:140:LYS:HE2 1:E:100:ALA:O 4:E:303:1JY:CBQ 1:H:105:ASP:HB2 1:B:103:THR:HB 1:F:8:MET:SD 1:A:69:ILE:HD13 1:C:249:ILE:O 1:A:129:ILE:HD12 1:D:231:ILE:N 1:E:176:PHE:CD2 1:E:61:TRP:CD1 1:G:141:MET:SD 1:G:97:GLN:HA. 1:E:53:ARG:CD 1:A:242:TYR:CD2 1:B:1:CXM:HG2 1:E:242:TYR:CD2 6:F:456:HOH:O 1:D:231:ILE:HD12 4:D:303:1JY:CAO 4:E:303:1JY:H6 1:E:139:ASP:OD1 1:D:249:ILE:N 1:F:235:LYS:NZ 1:H:127:ARG:HH22 1:C:100:ALA:O 1:F:231:ILE:HD12 4:G:303:1JY:CBQ 4:A:303:1JY:CAO 1:F:235:LYS:NZ 1:E:248:GLU:HB3 1:H:108:HIS:HA 1:F:226:PRO:HD2 4:F:302:1JY:CAO 1:F:101:TRP:CE2 1:B:242:TYR:CD2 1:E:116:LEU:HD23 1:F:143:LEU:HD13 1:H:103:THR:O 1:H:242:TYR:CE1 6:B:548:HOH:O 1:E:102:PRO:HD3 4:E:303:1JY:CAO 1:H:107:ARG:HB2 1:B:104:PRO:CD 1:F:216:THR:HG23 1:A:84:ALA:HB2 1:C:249:ILE:CG2 1:E:133:TRP:CH2 1:D:231:ILE:HD12 4:E:303:1JY:H17 1:E:66:ASP:HB3 1:G:145:PRO:HD3 1:G:97:GLN:OE1. Interatomic distance (Å) 2.80 2.53 2.47 2.53 2.15 2.38 2.47 2.53 2.51 2.32 2.51 1.83 2.17 2.33 2.95 2.96 2.35 1.99 2.18 2.00 2.96 2.54 2.53 2.19 2.18 2.19 2.53 2.17 2.19 2.97 2.01 2.41 2.59 2.02 2.67 2.54 2.33 2.55 2.54 2.58 2.19. Clash overlap (Å) 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42. Continued on next page.... 4ISK.

(21) Page 21. Full wwPDB X-ray Structure Validation Report. Continued from previous page.... Atom-1. Atom-2. 1:H:122:ASP:N 1:D:127:ARG:O 1:H:118:GLN:O 1:E:52:LEU:HA 1:G:225:ARG:HB3 1:G:105:ASP:OD1 1:G:80:TRP:CE2 1:F:222:ARG:NH2 1:G:104:PRO:HG3 1:A:116:LEU:CD2 1:G:104:PRO:HG3 1:H:231:ILE:N 1:F:236:PRO:HG2 1:F:251:GLY:O 1:H:162:GLN:HA 1:D:80:TRP:CE2 1:E:97:GLN:OE1 1:H:116:LEU:HD21 4:H:303:1JY:CBQ 1:E:69:ILE:HD13 1:A:118:GLN:HE22 1:E:101:TRP:C 1:F:99:ARG:CZ 1:F:101:TRP:C 1:B:85:ASP:OD1 1:D:168:CYS:SG 1:A:5:LEU:HA 1:B:103:THR:OG1 4:C:303:1JY:H13 1:H:236:PRO:HG2 1:F:69:ILE:HD13 1:G:35:ARG:HD3 1:A:61:TRP:CD1 1:B:69:ILE:HD13 1:H:116:LEU:CD2 4:A:303:1JY:H15 1:E:83:TRP:CZ2 1:D:99:ARG:CZ 1:H:51:HIS:CE1 1:D:236:PRO:HG2 1:F:168:CYS:SG. 1:H:123:PRO:CD 1:D:127:ARG:HD3 1:H:122:ASP:N 1:E:55:ILE:HD12 1:G:226:PRO:HD2 1:G:105:ASP:O 4:G:303:1JY:H9 1:F:256:PRO:HD2 1:H:104:PRO:HA 1:A:188:MET:SD 1:H:104:PRO:CA 1:H:231:ILE:HD12 1:F:242:TYR:CD2 6:F:444:HOH:O 1:H:200:VAL:O 4:D:303:1JY:H9 1:E:97:GLN:HA 1:H:188:MET:SD 4:H:303:1JY:CAO 1:E:84:ALA:CB 1:A:127:ARG:HD3 1:E:101:TRP:CD1 1:F:240:PHE:CE1 1:F:101:TRP:CD1 1:B:85:ASP:C 1:D:174:LEU:HB2 1:A:5:LEU:HD23 1:B:107:ARG:HG2 4:C:303:1JY:H17 1:H:242:TYR:CD1 1:F:84:ALA:CB 1:G:198:ASP:OD2 1:A:66:ASP:HB3 1:B:84:ALA:CB 1:H:188:MET:SD 4:A:303:1JY:H13 4:E:303:1JY:H6 1:D:240:PHE:CE1 1:H:53:ARG:HD3 1:D:242:TYR:CG 1:F:174:LEU:HB2. Interatomic distance (Å) 2.82 2.19 2.40 2.00 2.01 2.37 2.54 2.35 2.02 3.08 2.49 2.35 2.55 2.21 2.20 2.54 2.20 2.60 2.96 2.50 1.85 2.94 3.04 2.94 2.59 2.60 1.90 2.20 1.81 2.55 2.51 2.21 2.56 2.51 3.09 1.81 2.55 3.04 2.56 2.56 2.62. Clash overlap (Å) 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.40 0.40 0.40 0.40 0.40 0.40. Continued on next page.... 4ISK.

(22) Page 22. Full wwPDB X-ray Structure Validation Report. Continued from previous page.... Atom-1. Atom-2. 1:B:107:ARG:NH1 1:B:143:LEU:HA 1:E:1:CXM:HG3. 6:B:485:HOH:O 1:B:143:LEU:HD12 1:E:227:LEU:HD21. Interatomic distance (Å) 2.55 1.91 2.03. 4ISK. Clash overlap (Å) 0.40 0.40 0.40. There are no symmetry-related clashes.. 5.3. Torsion angles. O i. 5.3.1 Protein backbone Oi. In the following table, the Percentiles column shows the percent Ramachandran outliers of the chain as a percentile score with respect to all X-ray entries followed by that with respect to entries of similar resolution. The Analysed column shows the number of residues for which the backbone conformation was analysed, and the total number of residues.. Mol Chain. Analysed. 1. A. 262/264 (99%). 1. B. 1. Favoured Allowed Outliers Percentiles 256 (98%). 5 (2%). 1 (0%). 34. 17. 263/264 (100%). 256 (97%). 5 (2%). 2 (1%). 19. 6. C. 262/264 (99%). 253 (97%). 7 (3%). 2 (1%). 19. 6. 1. D. 262/264 (99%). 254 (97%). 7 (3%). 1 (0%). 34. 17. 1. E. 262/264 (99%). 254 (97%). 7 (3%). 1 (0%). 34. 17. 1. F. 263/264 (100%). 253 (96%). 9 (3%). 1 (0%). 34. 17. 1. G. 262/264 (99%). 249 (95%). 10 (4%). 3 (1%). 14. 3. 1. H. 262/264 (99%). 250 (95%). 11 (4%). 1 (0%). 34. 17. All. All. 2098/2112 (99%). 2025 (96%). 61 (3%). 12 (1%). 25. 10. All (12) Ramachandran outliers are listed below:. Mol Chain Res Type 1 1 1 1 1 1 1. B C G D G G H. 104 105 105 93 13 107 93. PRO ASP ASP VAL ASP ARG VAL. Continued on next page....

(23) Page 23. Full wwPDB X-ray Structure Validation Report. 4ISK. Continued from previous page.... Mol Chain Res Type 1 1 1 1 1. B C A E F. 93 93 93 93 93. VAL VAL VAL VAL VAL. 5.3.2 Protein sidechains Oi In the following table, the Percentiles column shows the percent sidechain outliers of the chain as a percentile score with respect to all X-ray entries followed by that with respect to entries of similar resolution. The Analysed column shows the number of residues for which the sidechain conformation was analysed, and the total number of residues.. Mol Chain. Analysed. 1. A. 232/232 (100%). 1. B. 1. Rotameric Outliers Percentiles 228 (98%). 4 (2%). 60. 42. 233/232 (100%). 231 (99%). 2 (1%). 78. 67. C. 232/232 (100%). 228 (98%). 4 (2%). 60. 42. 1. D. 232/232 (100%). 226 (97%). 6 (3%). 46. 23. 1. E. 232/232 (100%). 229 (99%). 3 (1%). 69. 54. 1. F. 233/232 (100%). 229 (98%). 4 (2%). 60. 42. 1. G. 232/232 (100%). 227 (98%). 5 (2%). 52. 29. 1. H. 232/232 (100%). 227 (98%). 5 (2%). 52. 29. All. All. 1858/1856 (100%). 1825 (98%). 33 (2%). 60. 40. All (33) residues with a non-rotameric sidechain are listed below:. Mol Chain Res Type 1 1 1 1 1 1 1 1 1 1. A A A A B B C C C C. 17 20 105 127 127[A] 127[B] 20 105 107 127. GLN ASP ASP ARG ARG ARG ASP ASP ARG ARG. Continued on next page....

(24) Page 24. Full wwPDB X-ray Structure Validation Report. 4ISK. Continued from previous page.... Mol Chain Res Type 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1. D D D D D D E E E F F F F G G G G G H H H H H. 39 53 107 114 127 143 20 127 143 39 86 143 176 17 20 53 105 127 20 39 122 127 143. GLN ARG ARG THR ARG LEU ASP ARG LEU GLN GLU LEU PHE GLN ASP ARG ASP ARG ASP GLN ASP ARG LEU. Some sidechains can be ipped to improve hydrogen bonding and reduce clashes. All (2) such sidechains are listed below:. Mol Chain Res Type 1 1. H H. 162 186. GLN HIS. 5.3.3 RNA Oi There are no RNA molecules in this entry.. 5.4. Non-standard residues in protein, DNA, RNA chains. O i. 8 non-standard protein/DNA/RNA residues are modelled in this entry. In the following table, the Counts columns list the number of bonds (or angles) for which Mogul statistics could be retrieved, the number of bonds (or angles) that are observed in the model and the number of bonds (or angles) that are dened in the Chemical Component Dictionary. The.

(25) Page 25. Full wwPDB X-ray Structure Validation Report. 4ISK. Link column lists molecule types, if any, to which the group is linked. 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| > 2 is considered an outlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (or angles).. Mol Type Chain Res Link. Bond lengths. Bond angles. 1. CXM. D. 1. 1. Counts 6,10,11. RMSZ 0.96. #|Z| > 2 0. Counts 5,11,13. RMSZ 1.31. #|Z| > 2 1 (20%). 1 1 1 1. CXM CXM CXM CXM. B H F C. 1 1 1 1. 1 1 1 1. 6,10,11 6,10,11 6,10,11 6,10,11. 2.44 0.67 0.66 0.81. 1 (16%) 0 0 0. 5,11,13 5,11,13 5,11,13 5,11,13. 1.39 0.96 1.07 1.36. 1 (20%) 0 0 1 (20%). 1. CXM. A. 1. 1. 6,10,11. 0.81. 0. 5,11,13. 1.83. 1 (20%). 1 1. CXM CXM. G E. 1 1. 1 1. 6,10,11 6,10,11. 1.02 0.54. 0 0. 5,11,13 5,11,13. 1.87 1.06. 1 (20%) 0. In the following table, the Chirals column lists the number of chiral outliers, the number of chiral centers analysed, the number of these observed in the model and the number dened in the Chemical Component Dictionary. Similar counts are reported in the Torsion and Rings columns. '-' means no outliers of that kind were identied.. Mol Type Chain Res Link Chirals Torsions Rings 1 1 1 1 1 1 1 1. CXM CXM CXM CXM CXM CXM CXM CXM. D B H F C A G E. 1 1 1 1 1 1 1 1. 1 1 1 1 1 1 1 1. -. 0/7/10/12 1/7/10/12 1/7/10/12 0/7/10/12 1/7/10/12 0/7/10/12 5/7/10/12 0/7/10/12. -. All (1) bond length outliers are listed below:. Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å) 1. B. 1. CXM. CE-SD. -5.82. 1.43. 1.78. All (5) bond angle outliers are listed below:. Mol Chain Res Type Atoms 1 1 1 1. G A C B. 1 1 1 1. CXM CXM CXM CXM. C-CA-N C-CA-N C-CA-N C-CA-N. Z Observed( ) Ideal( ) o. -3.83 -3.31 -2.44 -2.25. 102.81 103.76 105.33 105.67. o. 109.73 109.73 109.73 109.73. Continued on next page....

(26) Page 26. Full wwPDB X-ray Structure Validation Report. Continued from previous page.... Mol Chain Res Type Atoms 1. D. 1. CXM. C-CA-N. 4ISK. Z Observed( ) Ideal( ) o. -2.18. 105.79. o. 109.73. There are no chirality outliers. All (8) torsion outliers are listed below:. Mol Chain Res Type 1 1 1 1 1 1 1 1. H C G G G G B G. 1 1 1 1 1 1 1 1. Atoms. CXM CXM CXM CXM CXM CXM CXM CXM. O-C-CA-CB O-C-CA-CB N-CA-CB-CG CB-CG-SD-CE C-CA-N-CN C-CA-CB-CG C-CA-CB-CG CA-CB-CG-SD. There are no ring outliers. 4 monomers are involved in 7 short contacts:. Mol Chain Res Type Clashes Symm-Clashes 1 1 1 1. 5.5. B H A E. 1 1 1 1. CXM CXM CXM CXM. Carbohydrates. 2 1 3 1. 0 0 0 0. O i. There are no carbohydrates in this entry.. 5.6. Ligand geometry. O i. Of 23 ligands modelled in this entry, 7 are monoatomic - leaving 16 for Mogul analysis. In the following table, the Counts columns list the number of bonds (or angles) for which Mogul statistics could be retrieved, the number of bonds (or angles) that are observed in the model and the number of bonds (or angles) that are dened in the Chemical Component Dictionary. The Link column lists molecule types, if any, to which the group is linked. 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| > 2 is considered an outlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (or angles)..

(27) Page 27. Full wwPDB X-ray Structure Validation Report. Mol Type Chain Res Link. Bond lengths. 4ISK. Bond angles. 4. 1JY. E. 303. -. Counts 40,50,50. RMSZ 1.13. #|Z| > 2 5 (12%). Counts 42,70,70. RMSZ 2.61. #|Z| > 2 11 (26%). 4. 1JY. F. 302. -. 40,50,50. 1.30. 6 (15%). 42,70,70. 2.84. 12 (28%). 4. 1JY. B. 303. -. 40,50,50. 1.22. 3 (7%). 42,70,70. 2.93. 12 (28%). 4. 1JY. A. 303. -. 40,50,50. 1.24. 4 (10%). 42,70,70. 2.72. 13 (30%). 2. UMP. C. 301. -. 18,21,21. 1.17. 1 (5%). 21,31,31. 0.99. 1 (4%). 5. UMC. B. 301. -. 21,21,21. 1.04. 3 (14%). 28,31,31. 1.88. 7 (25%). 4. 1JY. H. 303. -. 40,50,50. 1.16. 4 (10%). 42,70,70. 2.48. 10 (23%). 5. UMC. D. 301. -. 21,21,21. 1.01. 2 (9%). 28,31,31. 1.70. 5 (17%). 5. UMC. F. 301. -. 21,21,21. 1.01. 2 (9%). 28,31,31. 1.80. 4 (14%). 2. UMP. A. 301. -. 18,21,21. 0.93. 1 (5%). 21,31,31. 0.94. 1 (4%). 5. UMC. H. 301. -. 21,21,21. 0.92. 1 (4%). 28,31,31. 1.82. 7 (25%). 4. 1JY. G. 303. -. 40,50,50. 1.33. 5 (12%). 42,70,70. 2.67. 13 (30%). 5. UMC. E. 301. -. 21,21,21. 1.12. 1 (4%). 28,31,31. 1.59. 4 (14%). 4. 1JY. C. 303. -. 40,50,50. 1.16. 5 (12%). 42,70,70. 2.50. 13 (30%). 4. 1JY. D. 303. -. 40,50,50. 1.07. 2 (5%). 42,70,70. 2.52. 11 (26%). 2. UMP. G. 301. -. 18,21,21. 0.91. 1 (5%). 21,31,31. 0.83. 0. In the following table, the Chirals column lists the number of chiral outliers, the number of chiral centers analysed, the number of these observed in the model and the number dened in the Chemical Component Dictionary. Similar counts are reported in the Torsion and Rings columns. '-' means no outliers of that kind were identied.. Mol Type Chain Res Link Chirals. Torsions. Rings. 4. 1JY. E. 303. -. -. 6/32/52/52. 0/4/4/4. 4. 1JY. F. 302. -. -. 5/32/52/52. 0/4/4/4. 4. 1JY. B. 303. -. -. 4/32/52/52. 0/4/4/4. 4 2 5 4 5 5 2 5. 1JY UMP UMC 1JY UMC UMC UMP UMC. A C B H D F A H. 303 301 301 303 301 301 301 301. -. -. 7/32/52/52 1/7/22/22 1/10/35/35 10/32/52/52 1/10/35/35 2/10/35/35 1/7/22/22 2/10/35/35. 0/4/4/4 0/2/2/2 0/2/2/2 0/4/4/4 0/2/2/2 0/2/2/2 0/2/2/2 0/2/2/2. 4 5 4. 1JY UMC 1JY. G E C. 303 301 303. -. -. 8/32/52/52 1/10/35/35 7/32/52/52. 0/4/4/4 0/2/2/2 0/4/4/4. Continued on next page....

(28) Page 28. Full wwPDB X-ray Structure Validation Report. Continued from previous page.... Mol Type Chain Res Link Chirals 4 2. 1JY UMP. D G. 303 301. -. -. Torsions. 7/32/52/52 1/7/22/22. 4ISK. Rings. 0/4/4/4 0/2/2/2. All (46) bond length outliers are listed below:. Mol Chain Res Type Atoms 4 4 4 4 4 4 4 4 4 5 4 4 4 4 4 4 2 4 4 4 4 4 4 4 2 4 5 4 4 5 4 5 5 4 5 5. A G F G H D B H B E G A E F C B C E F E F G C H A A D C C B E D F G F B. 303 303 302 303 303 303 303 303 303 301 303 303 303 302 303 303 301 303 302 303 302 303 303 303 301 303 301 303 303 301 303 301 301 303 301 301. 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY UMC 1JY 1JY 1JY 1JY 1JY 1JY UMP 1JY 1JY 1JY 1JY 1JY 1JY 1JY UMP 1JY UMC 1JY 1JY UMC 1JY UMC UMC 1JY UMC UMC. CBK-CBN CAU-NBU CBN-CBO CBK-CBN CAL-CAA CBK-CBN CAL-CAA CBK-CBN CBK-CBN C2-N3 CAL-CAA CAO-CBN CBK-CBN CBK-CBN CBK-CBN CAO-CBN C4-N3 CAL-CAA CAU-NBU CAO-CBN CAL-CAA CAO-CBN CAL-CAA CAU-NBU C4-N3 CAU-NBU C2-N1 CAN-CBM CBN-CBO C2-N3 CBM-NBB C2-N3 C2-N1 CBN-CBO C2-N3 C4-N3. Z Observed(Å) Ideal(Å). 4.13 3.85 -3.70 3.67 3.59 3.55 3.31 3.30 3.30 -3.29 3.22 3.20 3.19 3.04 3.01 2.92 2.90 2.80 -2.77 2.73 2.71 2.63 2.55 -2.49 2.40 -2.40 -2.33 -2.32 -2.31 -2.27 -2.26 -2.25 -2.25 -2.24 -2.22 -2.20. 1.46 1.50 1.47 1.46 1.28 1.45 1.28 1.45 1.45 1.32 1.27 1.42 1.45 1.44 1.44 1.41 1.38 1.26 1.44 1.41 1.26 1.41 1.25 1.44 1.37 1.44 1.32 1.38 1.48 1.33 1.33 1.34 1.32 1.48 1.34 1.33. 1.39 1.46 1.51 1.39 1.18 1.39 1.18 1.39 1.39 1.38 1.18 1.36 1.39 1.39 1.39 1.36 1.33 1.18 1.46 1.36 1.18 1.36 1.18 1.46 1.33 1.46 1.35 1.41 1.51 1.38 1.37 1.38 1.35 1.51 1.38 1.37. Continued on next page....

(29) Page 29. Full wwPDB X-ray Structure Validation Report. Continued from previous page.... Mol Chain Res Type Atoms 4 4 4 2 4 4 4 5 4 5. F C H G A E F B D H. 302 303 303 301 303 303 302 301 303 301. 1JY 1JY 1JY UMP 1JY 1JY 1JY UMC 1JY UMC. CBM-NBB CAU-NBU CBN-CBO C4-N3 CAL-CAA CAN-CBM CAO-CBN C2-N1 CAO-CBN C4-N3. 4ISK. Z Observed(Å) Ideal(Å). -2.19 -2.18 -2.18 2.18 2.18 -2.12 2.11 -2.08 2.05 -2.04. 1.34 1.44 1.48 1.36 1.24 1.38 1.40 1.32 1.40 1.34. 1.37 1.46 1.51 1.33 1.18 1.41 1.36 1.35 1.36 1.37. All (124) bond angle outliers are listed below:. Mol Chain Res Type 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 5 4 4 4 4 4 4 4 4 4 4 4 4. D F B A G F A H B E B E G H C F C D F E G C H A D F C E. 303 302 303 303 303 302 303 303 303 303 303 303 303 303 303 301 303 303 302 303 303 303 303 303 303 302 303 303. 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY UMC 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY. Atoms. CBR-CBM-NBB CBR-CBM-NBB CBL-NBB-CBM CBR-CBM-NBB CBR-CBM-NBB CBL-NBB-CBM CBL-NBB-CBM CBR-CBM-NBB CBR-CBM-NBB CBR-CBM-NBB CBN-CBO-NBU CBL-NBB-CBM CBL-NBB-CBM CBL-NBB-CBM CBR-CBM-NBB C2'-C1'-N1 CBN-CBO-NBU CBL-NBB-CBM CBR-CBI-NBA CBR-CBI-NBA CB-CA-N CBL-NBB-CBM CBR-CBI-NBA CBR-CBI-NBA CBR-CBI-NBA CB-CA-N CAZ-CBT-NBD CBN-CBO-NBU. Z Observed( ) Ideal( ) o. -9.77 -9.16 9.07 -9.00 -8.95 8.54 8.20 -8.18 -8.12 -7.49 -7.34 7.09 6.74 6.65 -6.62 -6.56 -6.49 6.31 -6.27 -6.16 -6.10 5.97 -5.92 -5.92 -5.86 -5.70 -5.66 -5.29. 118.29 118.62 122.69 118.71 118.74 122.33 122.10 119.16 119.19 119.53 101.46 121.35 121.11 121.05 120.00 107.59 102.77 120.82 120.03 120.11 101.32 120.59 120.27 120.28 120.32 101.90 101.95 104.61. o. 123.60 123.60 116.54 123.60 123.60 116.54 116.54 123.60 123.60 123.60 112.69 116.54 116.54 116.54 123.60 115.61 112.69 116.54 124.40 124.40 110.19 116.54 124.40 124.40 124.40 110.19 110.19 112.69. Continued on next page....

(30) Page 30. Full wwPDB X-ray Structure Validation Report. Continued from previous page.... Mol Chain Res Type 4 4 5 4 5 4 4 4 5 4 4 4 4 4 4 5 5 4 5 5 4 4 4 4 4 5 4 4 4 4 5 4 4 4 2 4 4 5 4 4 4 4. G G E E D C B A H F E A F B B B F H H B C H B E A D G F D H B B B H A F H D D C B C. 303 303 301 303 301 303 303 303 301 302 303 303 302 303 303 301 301 303 301 301 303 303 303 303 303 301 303 302 303 303 301 303 303 303 301 302 303 301 303 303 303 303. 1JY 1JY UMC 1JY UMC 1JY 1JY 1JY UMC 1JY 1JY 1JY 1JY 1JY 1JY UMC UMC 1JY UMC UMC 1JY 1JY 1JY 1JY 1JY UMC 1JY 1JY 1JY 1JY UMC 1JY 1JY 1JY UMP 1JY 1JY UMC 1JY 1JY 1JY 1JY. Atoms. CBN-CBO-NBU CBR-CBI-NBA C2'-C1'-N1 CB-CA-N C2'-C1'-N1 CBR-CBI-NBA CB-CA-N CBN-CBO-NBU C4-N3-C2 CBN-CBO-NBU NBB-CBL-NBA NBB-CBL-NBA NBB-CBL-NBA CA-N-CBH CBR-CBI-NBA C4-N3-C2 O4'-C1'-N1 CBN-CBO-NBU C2'-C1'-N1 O2-C2-N1 NBB-CBL-NBA CBN-CAO-CBR NBB-CBL-NBA CBN-CAO-CBR CAZ-CBT-NBD C5-C4-N3 CAZ-CBT-NBD CBN-CAO-CBR CAZ-CBT-NBD NBB-CBL-NBA O4'-C1'-N1 CAZ-CAX-CBH CAZ-CBT-NBD CAM-CAV-CBK O5'-P-OP1 CAZ-CAX-CBH CAU-CAL-CAA C4-N3-C2 CBN-CBO-NBU CB-CG-CD CAM-CAV-CBK CAT-CBL-NBB. 4ISK. Z Observed( ) Ideal( ) o. -5.26 -5.13 -5.08 -4.90 -4.79 -4.78 -4.76 -4.69 -4.41 -4.36 -4.33 -4.24 -4.19 -4.15 -4.13 -4.13 4.11 -4.10 -4.10 -4.08 -3.93 -3.90 -3.89 -3.88 -3.85 3.72 -3.71 -3.67 -3.60 -3.57 3.52 -3.50 -3.48 -3.48 3.46 -3.33 -3.32 -3.28 -3.28 -3.27 -3.25 3.23. 104.64 120.82 109.40 103.06 109.76 121.07 103.27 105.51 122.13 106.02 120.35 120.46 120.52 116.72 121.52 122.37 113.65 106.42 110.60 117.99 120.87 116.84 120.92 116.86 104.59 120.83 104.79 117.09 104.95 121.35 112.89 105.21 105.13 99.93 116.17 105.61 172.10 123.07 107.67 106.56 100.15 123.45. o. 112.69 124.40 115.61 110.19 115.61 124.40 110.19 112.69 125.79 112.69 126.06 126.06 126.06 123.33 124.40 125.79 108.41 112.69 115.61 123.11 126.06 120.98 126.06 120.98 110.19 116.65 110.19 120.98 110.19 126.06 108.41 113.04 110.19 103.31 106.47 113.04 177.67 125.79 112.69 113.59 103.31 116.84. Continued on next page....

(31) Page 31. Full wwPDB X-ray Structure Validation Report. Continued from previous page.... Mol Chain Res Type 5 4 4 5 4 4 5 4 4 4 4 5 5 4 5 4 5 5 4 4 4 4 4 4 4 4 4 5 5 4 4 5 4 2 4 4 4 4 5 4 4 4. B G D E G E B F B G E H E A H D H E G F C A F D A B D H D A D F C C D C A H D G G C. 301 303 303 301 303 303 301 302 303 303 303 301 301 303 301 303 301 301 303 302 303 303 302 303 303 303 303 301 301 303 303 301 303 301 303 303 303 303 301 303 303 303. UMC 1JY 1JY UMC 1JY 1JY UMC 1JY 1JY 1JY 1JY UMC UMC 1JY UMC 1JY UMC UMC 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY UMC UMC 1JY 1JY UMC 1JY UMP 1JY 1JY 1JY 1JY UMC 1JY 1JY 1JY. Atoms. N3-C2-N1 NBB-CBL-NBA CAO-CBN-CBK C4-N3-C2 CAR-CAP-CBP CAZ-CBT-NBD C2'-C1'-N1 CAT-CBL-NBA CAX-CAZ-CBT CB-CG-CD CAZ-CAX-CBH N3-C2-N1 C5-C4-N3 CAO-CBN-CBK C1'-N1-C2 NBB-CBL-NBA O5'-P-O2P O3P-P-O1P CBN-CAO-CBR CAM-CAV-CBK CAO-CBN-CBK CB-CG-CD CB-CG-CD CAV-CBK-CBN CAV-CBK-CBN CAO-CBN-CBK CAU-CAL-CAA C5-C4-N3 C1'-N1-C2 CAT-CBL-NBB CAT-CBL-NBB C4-N3-C2 CBI-CBR-CBM OP3-P-OP2 CBT-NBD-CBJ CAM-CAV-CBK CAP-CBP-CAQ CB-CA-N O4-C4-C5 CAT-CBL-NBB CAU-CAL-CAA CAV-CBK-CBN. 4ISK. Z Observed( ) Ideal( ) o. 3.21 -3.15 -3.14 -3.12 -3.08 -3.04 -3.00 2.97 -2.94 -2.91 -2.90 2.89 2.89 -2.87 2.81 -2.80 -2.80 2.75 -2.71 -2.69 -2.67 -2.66 -2.65 -2.59 -2.56 -2.55 -2.54 2.50 2.48 2.46 2.44 -2.38 -2.38 2.38 -2.37 -2.33 2.33 -2.32 -2.31 2.24 -2.20 -2.20. 120.04 121.90 118.48 123.21 117.20 105.77 111.94 122.93 106.12 107.33 106.56 119.71 119.89 118.71 122.23 122.36 98.63 118.13 118.11 100.70 118.89 107.87 107.89 107.95 107.98 119.00 173.42 119.46 121.79 121.88 121.85 123.82 116.52 116.72 119.28 101.04 121.91 106.82 117.24 121.44 173.98 108.36. o. 116.65 126.06 121.23 125.79 120.78 110.19 115.61 116.84 113.41 113.59 113.04 116.65 116.65 121.23 118.50 126.06 106.47 107.64 120.98 103.31 121.23 113.59 113.59 110.63 110.63 121.23 177.67 116.65 118.50 116.84 116.84 125.79 118.59 107.64 122.34 103.31 118.59 110.19 122.17 116.84 177.67 110.63. Continued on next page....

(32) Page 32. Full wwPDB X-ray Structure Validation Report. Continued from previous page.... Mol Chain Res Type 4 4 5 4 4 4 4 5 4 4 5 5. E A B A G H F F E C B H. 303 303 301 303 303 303 302 301 303 303 301 301. 1JY 1JY UMC 1JY 1JY 1JY 1JY UMC 1JY 1JY UMC UMC. Atoms. CAT-CBL-NBB CAM-CAV-CBK O1P-P-O5' CAU-CAL-CAA CAP-CAR-CBQ CA-N-CBH CA-N-CBH C5-C4-N3 CAS-CAQ-CBP CAZ-CAX-CBH C5-C4-N3 O3P-P-O2P. Z Observed( ) Ideal( ) o. 2.19 -2.18 -2.17 -2.17 2.16 -2.16 -2.15 2.15 -2.13 -2.13 2.11 2.01. There are no chirality outliers. All (64) torsion outliers are listed below:. Mol Chain Res Type 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 5 5 4 4 4 4 4. E B F F H H H A A G G G G C C C D D H H C D A B G. 303 303 302 302 303 303 303 303 303 303 303 303 303 303 303 303 303 303 301 301 303 303 303 303 303. 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY UMC UMC 1JY 1JY 1JY 1JY 1JY. 4ISK. Atoms. CBN-CBO-NBU-CBQ C-CA-N-CBH C-CA-N-CBH CA-CB-CG-CD C-CA-N-CBH CB-CA-N-CBH C-CA-CB-CG CBG-CBT-NBD-CBJ C-CA-N-CBH CBN-CBO-NBU-CBQ C-CA-N-CBH N-CA-CB-CG C-CA-CB-CG CBN-CBO-NBU-CBQ C-CA-N-CBH CB-CA-N-CBH CBN-CBO-NBU-CBQ C-CA-N-CBH O4'-C4'-C5'-O5' C3'-C4'-C5'-O5' CBG-CBT-NBD-CBJ CBG-CBT-NBD-CBJ CA-CB-CG-CD OAH-CAT-CBL-NBB OAH-CAT-CBL-NBB. Continued on next page.... 121.33 101.19 100.95 174.03 123.17 119.88 119.90 119.06 118.30 108.29 119.02 118.55. o. 116.84 103.31 106.73 177.67 120.32 123.33 123.33 116.65 120.78 113.04 116.65 110.68.

(33) Page 33. Full wwPDB X-ray Structure Validation Report. Continued from previous page.... Mol Chain Res Type 4 4 4 4 4 4 4 4 4 4 4 4 4 5 4 4 4 4 4 4 4 4 5 2 4 4 4 4 4 5 5 2 2 5 4 4 4 4 4. C D C B F A D H E E H B E F G E F H A H A H E C G H H A D D B A G F E F G C D. 303 303 303 303 302 303 303 303 303 303 303 303 303 301 303 303 302 303 303 303 303 303 301 301 303 303 303 303 303 301 301 301 301 301 303 302 303 303 303. 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY UMC 1JY 1JY 1JY 1JY 1JY 1JY 1JY 1JY UMC UMP 1JY 1JY 1JY 1JY 1JY UMC UMC UMP UMP UMC 1JY 1JY 1JY 1JY 1JY. Atoms. OAH-CAT-CBL-NBB OAH-CAT-CBL-NBB CA-CB-CG-CD CB-CA-N-CBH CB-CA-N-CBH CB-CA-N-CBH CB-CA-N-CBH N-CA-CB-CG CAZ-CAX-CBH-OAE CAZ-CAX-CBH-N CA-CB-CG-CD CBG-CBT-NBD-CBJ CA-CB-CG-CD O4'-C4'-C5'-O5' CB-CA-N-CBH OAH-CAT-CBL-NBB OAH-CAT-CBL-NBB OAH-CAT-CBL-NBB OAH-CAT-CBL-NBB CBN-CBO-NBU-CBQ CBN-CBO-NBU-CBQ CAX-CAZ-CBT-NBD O4'-C4'-C5'-O5' O4'-C4'-C5'-O5' CBG-CBT-NBD-CBJ CAZ-CAX-CBH-OAE CAZ-CAX-CBH-N CAZ-CBT-NBD-CBJ CAZ-CBT-NBD-CBJ O4'-C4'-C5'-O5' O4'-C4'-C5'-O5' O4'-C4'-C5'-O5' O4'-C4'-C5'-O5' C3'-C4'-C5'-O5' CBG-CBT-NBD-CBJ CBG-CBT-NBD-CBJ CAM-CBO-NBU-CAU CAM-CBO-NBU-CAU CAM-CBO-NBU-CAU. There are no ring outliers. 16 monomers are involved in 71 short contacts:. 4ISK.

(34) Page 34. Full wwPDB X-ray Structure Validation Report. 4ISK. Mol Chain Res Type Clashes Symm-Clashes 4 4 4 4 2 5 4 5 5 2 5 4 5 4 4 2. E F B A C B H D F A H G E C D G. 303 302 303 303 301 301 303 301 301 301 301 303 301 303 303 301. 1JY 1JY 1JY 1JY UMP UMC 1JY UMC UMC UMP UMC 1JY UMC 1JY 1JY UMP. 15 5 4 5 2 3 8 4 3 1 2 5 2 5 6 1. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0. The following is a two-dimensional graphical depiction of Mogul quality analysis of bond lengths, bond angles, torsion angles, and ring geometry for all instances of the Ligand of Interest. In addition, ligands with molecular weight > 250 and outliers as shown on the validation Tables will also be included. For torsion angles, if less then 5% of the Mogul distribution of torsion angles is within 10 degrees of the torsion angle in question, then that torsion angle is considered an outlier. Any bond that is central to one or more torsion angles identied as an outlier by Mogul will be highlighted in the graph. For rings, the root-mean-square deviation (RMSD) between the ring in question and similar rings identied by Mogul is calculated over all ring torsion angles. If the average RMSD is greater than 60 degrees and the minimal RMSD between the ring in question and any Mogul-identied rings is also greater than 60 degrees, then that ring is considered an outlier. The outliers are highlighted in purple. The color gray indicates Mogul did not nd sucient equivalents in the CSD to analyse the geometry..

(35) Page 35. Full wwPDB X-ray Structure Validation Report. Ligand 1JY E 303. Bond lengths. Bond angles. Torsions. Rings. Ligand 1JY F 302. Bond lengths. Bond angles. Torsions. Rings. 4ISK.

(36) Page 36. Full wwPDB X-ray Structure Validation Report. Ligand 1JY B 303. Bond lengths. Bond angles. Torsions. Rings. Ligand 1JY A 303. Bond lengths. Bond angles. Torsions. Rings. 4ISK.

(37) Page 37. Full wwPDB X-ray Structure Validation Report. Ligand UMP C 301. Bond lengths. Bond angles. Torsions. Rings. Ligand UMC B 301. Bond lengths. Bond angles. Torsions. Rings. 4ISK.

(38) Page 38. Full wwPDB X-ray Structure Validation Report. Ligand 1JY H 303. Bond lengths. Bond angles. Torsions. Rings. Ligand UMC D 301. Bond lengths. Bond angles. Torsions. Rings. 4ISK.

(39) Page 39. Full wwPDB X-ray Structure Validation Report. Ligand UMC F 301. Bond lengths. Bond angles. Torsions. Rings. Ligand UMP A 301. Bond lengths. Bond angles. Torsions. Rings. 4ISK.

(40) Page 40. Full wwPDB X-ray Structure Validation Report. Ligand UMC H 301. Bond lengths. Bond angles. Torsions. Rings. Ligand 1JY G 303. Bond lengths. Bond angles. Torsions. Rings. 4ISK.

(41) Page 41. Full wwPDB X-ray Structure Validation Report. Ligand UMC E 301. Bond lengths. Bond angles. Torsions. Rings. Ligand 1JY C 303. Bond lengths. Bond angles. Torsions. Rings. 4ISK.

(42) Page 42. Full wwPDB X-ray Structure Validation Report. Ligand 1JY D 303. 5.7. Bond lengths. Bond angles. Torsions. Rings. Ligand UMP G 301. Bond lengths. Bond angles. Torsions. Rings. Other polymers. O i. There are no such residues in this entry.. 5.8. Polymer linkage issues. O. There are no chain breaks in this entry.. i. 4ISK.

(43) Page 43. Full wwPDB X-ray Structure Validation Report. 6 Fit of model and data 6.1. O i. Protein, DNA and RNA chains. 4ISK. O i. In the following table, the column labelled `#RSRZ> 2' contains the number (and percentage) of RSRZ outliers, followed by percent RSRZ outliers for the chain as percentile scores relative to all X-ray entries and entries of similar resolution. The OWAB column contains the minimum, median, 95th percentile and maximum values of the occupancy-weighted average B-factor per residue. The column labelled `Q< 0.9' lists the number of (and percentage) of residues with an average occupancy less than 0.9.. Mol Chain. Analysed. 1. A. 261/264 (98%). 1. B. 1. RSRZ>. <. RSRZ>2. OWAB(Å ) Q<0.9 2. #. 0.20. 10 (3%) 40. 47. 14, 26, 46, 82. 0. 263/264 (99%). 0.10. 3 (1%) 80. 86. 14, 26, 48, 77. 0. C. 263/264 (99%). 0.14. 8 (3%) 50. 56. 15, 27, 47, 87. 2 (0%). 1. D. 263/264 (99%). 0.20. 8 (3%) 50. 56. 14, 29, 51, 71. 0. 1. E. 263/264 (99%). 0.50. 22 (8%) 11. 14. 15, 33, 60, 82. 0. 1. F. 261/264 (98%). 0.65. 29 (11%) 5. 7. 18, 35, 66, 96. 0. 1. G. 262/264 (99%). 0.90. 36 (13%) 3. 4. 20, 39, 62, 100. 1 (0%). 1. H. 254/264 (96%). 1.07. 42 (16%) 1. 2. 23, 44, 64, 100. 0. All. All. 2090/2112 (98%). 0.47. 158 (7%) 13. 18. 14, 32, 59, 100. 3 (0%). All (158) RSRZ outliers are listed below:. Mol Chain Res Type RSRZ 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1. F H E A A B G F C G C B F D H C. 264 106 264 264 22 264 105 263 264 104 104 22 23 264 103 105. ILE GLY ILE ILE THR ILE ASP ALA ILE PRO PRO THR GLY ILE THR ASP. 10.2 9.6 9.0 7.4 6.3 6.2 5.9 5.9 5.8 5.8 5.1 4.9 4.8 4.8 4.6 4.5. Continued on next page....

(44) Page 44. Full wwPDB X-ray Structure Validation Report. Continued from previous page.... Mol Chain Res Type RSRZ 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1. H E F G H H H H G H H F E G H F F G F A E F F E C H E H E F G H H G H H F B G H F H. 146 106 22 106 105 104 176 164 149 193 107 262 232 107 156 86 21 164 176 21 164 24 87 104 107 239 146 249 22 106 17 155 148 193 12 86 20 146[A] 148 241 51 150. CYS GLY THR GLY ASP PRO PHE TYR PHE ASP ARG VAL ILE ARG ASP GLU ARG TYR PHE ARG TYR THR ASN PRO ARG ILE CYS ILE THR GLY GLN ALA ALA ASP LEU GLU ASP CYS ALA ASP HIS PHE. 4.4 4.3 4.3 4.3 4.1 4.0 4.0 4.0 3.9 3.8 3.7 3.7 3.7 3.6 3.6 3.5 3.5 3.4 3.4 3.3 3.3 3.3 3.3 3.2 3.2 3.2 3.2 3.2 3.2 3.2 3.2 3.1 3.1 3.1 3.1 3.1 3.1 3.1 3.1 3.0 3.0 3.0. Continued on next page.... 4ISK.

(45) Page 45. Full wwPDB X-ray Structure Validation Report. Continued from previous page.... Mol Chain Res Type RSRZ 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1. E C F G G E G G G G E H F H G H H G H F F E E G F E G F E E F E C H H H H E F G H A. 23 164 164 25 12 76 150 10 220 13 74 220 150 163 156 139 203 194 214 17 181 24 243 139 237 163 146 261 233 69 76 70 201 149 22 202 158 231 201 29 221 104. GLY TYR TYR GLY LEU ASN PHE LYS LEU ASP GLU LEU PHE LEU ASP ASP GLY LEU ASP GLN TYR THR ARG ASP GLU LEU CYS PRO LYS ILE ASN ALA TRP PHE THR THR LYS ILE TRP ILE SER PRO. 3.0 2.9 2.9 2.9 2.9 2.9 2.8 2.8 2.8 2.8 2.8 2.8 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.7 2.6 2.6 2.6 2.6 2.6 2.6 2.6 2.6 2.5 2.5 2.5 2.5 2.5 2.5 2.5 2.5 2.5 2.5 2.5 2.5 2.5 2.5. Continued on next page.... 4ISK.

(46) Page 46. Full wwPDB X-ray Structure Validation Report. Continued from previous page.... Mol Chain Res Type RSRZ 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1. F G G G H H D H C D E H F G H H A A A D E H H G G F E G A H A G A G H H H F E F D C. 19 102 121 163 213 85 107 181 149 86 89 121 70 103 237 87 201 23 164 156 234 201 66 218 108 107 145 201 146 157 86 23 52 233 70 147 226 202 73 203 243 150. ASN PRO ASN LEU MET ASP ARG TYR PHE GLU ASP ASN ALA THR GLU ASN TRP GLY TYR ASP ARG TRP ASP LEU HIS ARG PRO TRP CYS GLY GLU GLY LEU LYS ALA HIS PRO THR HIS GLY ARG PHE. 2.4 2.4 2.4 2.4 2.4 2.4 2.4 2.4 2.4 2.4 2.4 2.3 2.3 2.3 2.3 2.3 2.3 2.3 2.2 2.2 2.2 2.2 2.2 2.2 2.2 2.2 2.2 2.2 2.1 2.1 2.1 2.1 2.1 2.1 2.1 2.1 2.1 2.1 2.1 2.1 2.1 2.1. Continued on next page.... 4ISK.

(47) Page 47. Full wwPDB X-ray Structure Validation Report. 4ISK. Continued from previous page.... Mol Chain Res Type RSRZ 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1. 6.2. G G H G D F F G G E G D F H D G. 192 178 88 176 23 85 88 234 217 237 130 27 149 116 13 224. CYS ILE GLY PHE GLY ASP GLY ARG HIS GLU VAL LEU PHE LEU ASP PRO. 2.1 2.1 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0. Non-standard residues in protein, DNA, RNA chains. O i. In the following table, the Atoms column lists the number of modelled atoms in the group and the number dened in the chemical component dictionary. The B-factors column lists the minimum, median, 95th percentile and maximum values of B factors of atoms in the group. The column labelled `Q< 0.9' lists the number of atoms with occupancy less than 0.9.. Mol Type Chain Res Atoms RSCC RSR B-factors(Å ) Q<0.9 2. 1 1 1 1 1 1 1 1. 6.3. CXM CXM CXM CXM CXM CXM CXM CXM. H G D A B F E C. Carbohydrates. 1 1 1 1 1 1 1 1. 11/12 11/12 11/12 11/12 11/12 11/12 11/12 11/12. O i. There are no carbohydrates in this entry.. 0.87 0.92 0.95 0.96 0.96 0.97 0.97 0.98. 0.17 0.11 0.08 0.09 0.07 0.07 0.06 0.05. 27,46,97,97 26,40,58,58 19,31,41,41 17,26,75,75 12,23,56,56 22,29,49,49 17,27,39,39 17,27,36,36. 0 0 0 0 0 0 0 0.

(48) Page 48 6.4. Full wwPDB X-ray Structure Validation Report. Ligands. 4ISK. O i. In the following table, the Atoms column lists the number of modelled atoms in the group and the number dened in the chemical component dictionary. The B-factors column lists the minimum, median, 95th percentile and maximum values of B factors of atoms in the group. The column labelled `Q< 0.9' lists the number of atoms with occupancy less than 0.9.. Mol Type Chain Res Atoms RSCC RSR B-factors(Å ) Q<0.9 2. 4 4 4 4 4 4 4 5 2 4 3 5 5 5 2 3 2 5 3 3 3 3 3. 1JY 1JY 1JY 1JY 1JY 1JY 1JY UMC UMP 1JY MG UMC UMC UMC UMP MG UMP UMC MG MG MG MG MG. E B G H F A C H G D E E F B A G C D D H B A C. 303 303 303 303 302 303 303 301 301 303 302 301 301 301 301 302 301 301 302 302 302 302 302. 47/47 47/47 47/47 47/47 47/47 47/47 47/47 20/20 20/20 47/47 1/1 20/20 20/20 20/20 20/20 1/1 20/20 20/20 1/1 1/1 1/1 1/1 1/1. 0.90 0.90 0.90 0.91 0.91 0.92 0.92 0.92 0.93 0.93 0.95 0.95 0.96 0.96 0.96 0.97 0.97 0.97 0.97 0.98 0.99 0.99 0.99. 0.15 0.13 0.14 0.14 0.16 0.15 0.12 0.12 0.10 0.13 0.06 0.11 0.10 0.12 0.11 0.03 0.11 0.09 0.09 0.06 0.03 0.08 0.05. 18,32,79,84 14,22,56,70 13,29,60,62 18,34,98,104 24,38,103,107 14,23,42,59 10,23,42,54 22,30,37,37 16,28,39,47 16,24,45,61 39,39,39,39 19,26,33,39 22,29,34,37 18,24,30,31 15,23,29,33 33,33,33,33 14,21,29,32 11,22,29,35 28,28,28,28 36,36,36,36 26,26,26,26 24,24,24,24 24,24,24,24. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0. The following is a graphical depiction of the model t to experimental electron density of all instances of the Ligand of Interest. In addition, ligands with molecular weight > 250 and outliers as shown on the geometry validation Tables will also be included. Each t is shown from dierent orientation to approximate a three-dimensional view..

(49) Page 49. Full wwPDB X-ray Structure Validation Report. Electron density around 1JY E 303: 2mFo -DFc (at 0.7 rmsd) in gray mFo -DFc (at 3 rmsd) in purple (negative) and green (positive). Electron density around 1JY B 303: 2mFo -DFc (at 0.7 rmsd) in gray mFo -DFc (at 3 rmsd) in purple (negative) and green (positive). 4ISK.

(50) Page 50. Full wwPDB X-ray Structure Validation Report. Electron density around 1JY G 303: 2mFo -DFc (at 0.7 rmsd) in gray mFo -DFc (at 3 rmsd) in purple (negative) and green (positive). Electron density around 1JY H 303: 2mFo -DFc (at 0.7 rmsd) in gray mFo -DFc (at 3 rmsd) in purple (negative) and green (positive). 4ISK.

(51) Page 51. Full wwPDB X-ray Structure Validation Report. Electron density around 1JY F 302: 2mFo -DFc (at 0.7 rmsd) in gray mFo -DFc (at 3 rmsd) in purple (negative) and green (positive). Electron density around 1JY A 303: 2mFo -DFc (at 0.7 rmsd) in gray mFo -DFc (at 3 rmsd) in purple (negative) and green (positive). 4ISK.

(52) Page 52. Full wwPDB X-ray Structure Validation Report. Electron density around 1JY C 303: 2mFo -DFc (at 0.7 rmsd) in gray mFo -DFc (at 3 rmsd) in purple (negative) and green (positive). 4ISK.

(53) Page 53. Full wwPDB X-ray Structure Validation Report. Electron density around UMC H 301: 2mFo -DFc (at 0.7 rmsd) in gray mFo -DFc (at 3 rmsd) in purple (negative) and green (positive). 4ISK.

(54) Page 54. Full wwPDB X-ray Structure Validation Report. Electron density around UMP G 301: 2mFo -DFc (at 0.7 rmsd) in gray mFo -DFc (at 3 rmsd) in purple (negative) and green (positive). 4ISK.

(55) Page 55. Full wwPDB X-ray Structure Validation Report. Electron density around 1JY D 303: 2mFo -DFc (at 0.7 rmsd) in gray mFo -DFc (at 3 rmsd) in purple (negative) and green (positive). Electron density around UMC E 301: 2mFo -DFc (at 0.7 rmsd) in gray mFo -DFc (at 3 rmsd) in purple (negative) and green (positive). 4ISK.

(56) Page 56. Full wwPDB X-ray Structure Validation Report. Electron density around UMC F 301: 2mFo -DFc (at 0.7 rmsd) in gray mFo -DFc (at 3 rmsd) in purple (negative) and green (positive). Electron density around UMC B 301: 2mFo -DFc (at 0.7 rmsd) in gray mFo -DFc (at 3 rmsd) in purple (negative) and green (positive). 4ISK.

(57) Page 57. Full wwPDB X-ray Structure Validation Report. Electron density around UMP A 301: 2mFo -DFc (at 0.7 rmsd) in gray mFo -DFc (at 3 rmsd) in purple (negative) and green (positive). Electron density around UMP C 301: 2mFo -DFc (at 0.7 rmsd) in gray mFo -DFc (at 3 rmsd) in purple (negative) and green (positive). 4ISK.

(58) Page 58. Full wwPDB X-ray Structure Validation Report. Electron density around UMC D 301: 2mFo -DFc (at 0.7 rmsd) in gray mFo -DFc (at 3 rmsd) in purple (negative) and green (positive). 6.5. Other polymers. O i. There are no such residues in this entry.. 4ISK.

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