Full wwpdb X-ray Structure Validation Report i
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- Πελάγιος Καλογιάννης
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1 Full wwpdb X-ray Structure Validation Report i Mar 13, :34 pm GMT PDB ID : 3QAZ Title : IL-2 mutant D10 ternary complex Authors : Levin, A.M.; Bates, D.L.; Ring, A.M.; Lin, J.T.; Su, L.; Krieg, C.; Bowman, G.R.; Novick, P.; Pande, V.S.; Khort, H.E.; Boyman, O.; Gathman, C.G.; Garcia, K.C. Deposited on : Resolution : 3.80 Å(reported) This is a Full wwpdb X-ray Structure Validation Report for a publicly released PDB 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. The following versions of software and data (see references i ) were used in the production of this report: MolProbity : 4.02b-467 Mogul : (157068), CSD as539be (2018) Xtriage (Phenix) : 1.13 EDS : trunk31020 Percentile statistics : v01 (using entries in the PDB archive December 27th 2017) Refmac : CCP4 : 7.0 (Gargrove) Ideal geometry (proteins) : Engh & Huber (2001) Ideal geometry (DNA, RNA) : Parkinson et al. (1996) Validation Pipeline (wwpdb-vp) : trunk31020
2 Page 2 Full wwpdb X-ray Structure Validation Report 3QAZ 1 Overall quality at a glance i The following experimental techniques were used to determine the structure: X-RAY DIFFRACTION The reported resolution of this entry is 3.80 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 Similar resolution (#Entries) (#Entries, resolution range(å)) R free ( ) Clashscore ( ) Ramachandran outliers ( ) Sidechain outliers ( ) RSRZ outliers ( ) The table below summarises the geometric issues observed across the polymeric chains and their fit 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. 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 fit to the electron density. The numeric value is given above the bar. Mol Chain Length Quality of chain 1 A D G J M P 136
3 Page 3 Full wwpdb X-ray Structure Validation Report 3QAZ Mol Chain Length Quality of chain 1 S V Y b e h B E H K N Q T W Z c f i C F I L O R U 202
4 Page 4 Full wwpdb X-ray Structure Validation Report 3QAZ Mol Chain Length Quality of chain 3 X a d g j 202 The following table lists non-polymeric compounds, carbohydrate monomers and non-standard residues in protein, DNA, RNA chains that are outliers for geometric or electron-density-fit criteria: Mol Type Chain Res Chirality Geometry Clashes Electron density 4 NAG K X -
5 Page 5 Full wwpdb X-ray Structure Validation Report 3QAZ 2 Entry composition i There are 4 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 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 Interleukin-2. Mol Chain Residues Atoms ZeroOcc AltConf Trace 1 A 121 Total C N O S D 121 Total C N O S G 121 Total C N O S J 121 Total C N O S M 121 Total C N O S P 121 Total C N O S S 121 Total C N O S V 121 Total C N O S Y 120 Total C N O S b 119 Total C N O S e 121 Total C N O S h 121 Total C N O S There are 108 discrepancies between the modelled and reference sequences: Chain Residue Modelled Actual Comment Reference A -2 - EXPRESSION TAG UNP P60568 A -1 - EXPRESSION TAG UNP P60568 A 0 - EXPRESSION TAG UNP P60568 A 74 HIS GLN ENGINEERED MUTATION UNP P60568 A 80 PHE LEU ENGINEERED MUTATION UNP P60568
6 Page 6 Full wwpdb X-ray Structure Validation Report 3QAZ Chain Residue Modelled Actual Comment Reference A 81 ARG ENGINEERED MUTATION UNP P60568 A 85 VAL LEU ENGINEERED MUTATION UNP P60568 A 86 VAL ILE ENGINEERED MUTATION UNP P60568 A 92 PHE ILE ENGINEERED MUTATION UNP P60568 D -2 - EXPRESSION TAG UNP P60568 D -1 - EXPRESSION TAG UNP P60568 D 0 - EXPRESSION TAG UNP P60568 D 74 HIS GLN ENGINEERED MUTATION UNP P60568 D 80 PHE LEU ENGINEERED MUTATION UNP P60568 D 81 ARG ENGINEERED MUTATION UNP P60568 D 85 VAL LEU ENGINEERED MUTATION UNP P60568 D 86 VAL ILE ENGINEERED MUTATION UNP P60568 D 92 PHE ILE ENGINEERED MUTATION UNP P60568 G -2 - EXPRESSION TAG UNP P60568 G -1 - EXPRESSION TAG UNP P60568 G 0 - EXPRESSION TAG UNP P60568 G 74 HIS GLN ENGINEERED MUTATION UNP P60568 G 80 PHE LEU ENGINEERED MUTATION UNP P60568 G 81 ARG ENGINEERED MUTATION UNP P60568 G 85 VAL LEU ENGINEERED MUTATION UNP P60568 G 86 VAL ILE ENGINEERED MUTATION UNP P60568 G 92 PHE ILE ENGINEERED MUTATION UNP P60568 J -2 - EXPRESSION TAG UNP P60568 J -1 - EXPRESSION TAG UNP P60568 J 0 - EXPRESSION TAG UNP P60568 J 74 HIS GLN ENGINEERED MUTATION UNP P60568 J 80 PHE LEU ENGINEERED MUTATION UNP P60568 J 81 ARG ENGINEERED MUTATION UNP P60568 J 85 VAL LEU ENGINEERED MUTATION UNP P60568 J 86 VAL ILE ENGINEERED MUTATION UNP P60568 J 92 PHE ILE ENGINEERED MUTATION UNP P60568 M -2 - EXPRESSION TAG UNP P60568 M -1 - EXPRESSION TAG UNP P60568 M 0 - EXPRESSION TAG UNP P60568 M 74 HIS GLN ENGINEERED MUTATION UNP P60568 M 80 PHE LEU ENGINEERED MUTATION UNP P60568 M 81 ARG ENGINEERED MUTATION UNP P60568 M 85 VAL LEU ENGINEERED MUTATION UNP P60568 M 86 VAL ILE ENGINEERED MUTATION UNP P60568 M 92 PHE ILE ENGINEERED MUTATION UNP P60568 P -2 - EXPRESSION TAG UNP P60568 P -1 - EXPRESSION TAG UNP P60568
7 Page 7 Full wwpdb X-ray Structure Validation Report 3QAZ Chain Residue Modelled Actual Comment Reference P 0 - EXPRESSION TAG UNP P60568 P 74 HIS GLN ENGINEERED MUTATION UNP P60568 P 80 PHE LEU ENGINEERED MUTATION UNP P60568 P 81 ARG ENGINEERED MUTATION UNP P60568 P 85 VAL LEU ENGINEERED MUTATION UNP P60568 P 86 VAL ILE ENGINEERED MUTATION UNP P60568 P 92 PHE ILE ENGINEERED MUTATION UNP P60568 S -2 - EXPRESSION TAG UNP P60568 S -1 - EXPRESSION TAG UNP P60568 S 0 - EXPRESSION TAG UNP P60568 S 74 HIS GLN ENGINEERED MUTATION UNP P60568 S 80 PHE LEU ENGINEERED MUTATION UNP P60568 S 81 ARG ENGINEERED MUTATION UNP P60568 S 85 VAL LEU ENGINEERED MUTATION UNP P60568 S 86 VAL ILE ENGINEERED MUTATION UNP P60568 S 92 PHE ILE ENGINEERED MUTATION UNP P60568 V -2 - EXPRESSION TAG UNP P60568 V -1 - EXPRESSION TAG UNP P60568 V 0 - EXPRESSION TAG UNP P60568 V 74 HIS GLN ENGINEERED MUTATION UNP P60568 V 80 PHE LEU ENGINEERED MUTATION UNP P60568 V 81 ARG ENGINEERED MUTATION UNP P60568 V 85 VAL LEU ENGINEERED MUTATION UNP P60568 V 86 VAL ILE ENGINEERED MUTATION UNP P60568 V 92 PHE ILE ENGINEERED MUTATION UNP P60568 Y -2 - EXPRESSION TAG UNP P60568 Y -1 - EXPRESSION TAG UNP P60568 Y 0 - EXPRESSION TAG UNP P60568 Y 74 HIS GLN ENGINEERED MUTATION UNP P60568 Y 80 PHE LEU ENGINEERED MUTATION UNP P60568 Y 81 ARG ENGINEERED MUTATION UNP P60568 Y 85 VAL LEU ENGINEERED MUTATION UNP P60568 Y 86 VAL ILE ENGINEERED MUTATION UNP P60568 Y 92 PHE ILE ENGINEERED MUTATION UNP P60568 b -2 - EXPRESSION TAG UNP P60568 b -1 - EXPRESSION TAG UNP P60568 b 0 - EXPRESSION TAG UNP P60568 b 74 HIS GLN ENGINEERED MUTATION UNP P60568 b 80 PHE LEU ENGINEERED MUTATION UNP P60568 b 81 ARG ENGINEERED MUTATION UNP P60568 b 85 VAL LEU ENGINEERED MUTATION UNP P60568 b 86 VAL ILE ENGINEERED MUTATION UNP P60568
8 Page 8 Full wwpdb X-ray Structure Validation Report 3QAZ Chain Residue Modelled Actual Comment Reference b 92 PHE ILE ENGINEERED MUTATION UNP P60568 e -2 - EXPRESSION TAG UNP P60568 e -1 - EXPRESSION TAG UNP P60568 e 0 - EXPRESSION TAG UNP P60568 e 74 HIS GLN ENGINEERED MUTATION UNP P60568 e 80 PHE LEU ENGINEERED MUTATION UNP P60568 e 81 ARG ENGINEERED MUTATION UNP P60568 e 85 VAL LEU ENGINEERED MUTATION UNP P60568 e 86 VAL ILE ENGINEERED MUTATION UNP P60568 e 92 PHE ILE ENGINEERED MUTATION UNP P60568 h -2 - EXPRESSION TAG UNP P60568 h -1 - EXPRESSION TAG UNP P60568 h 0 - EXPRESSION TAG UNP P60568 h 74 HIS GLN ENGINEERED MUTATION UNP P60568 h 80 PHE LEU ENGINEERED MUTATION UNP P60568 h 81 ARG ENGINEERED MUTATION UNP P60568 h 85 VAL LEU ENGINEERED MUTATION UNP P60568 h 86 VAL ILE ENGINEERED MUTATION UNP P60568 h 92 PHE ILE ENGINEERED MUTATION UNP P60568 Molecule 2 is a protein called Interleukin-2 receptor subunit beta. Mol Chain Residues Atoms ZeroOcc AltConf Trace 2 B 195 Total C N O S E 196 Total C N O S H 196 Total C N O S K 196 Total C N O S N 195 Total C N O S Q 195 Total C N O S T 196 Total C N O S W 196 Total C N O S Z 196 Total C N O S c 196 Total C N O S
9 Page 9 Full wwpdb X-ray Structure Validation Report 3QAZ Mol Chain Residues Atoms ZeroOcc AltConf Trace 2 f 196 Total C N O S i 196 Total C N O S There are 60 discrepancies between the modelled and reference sequences: Chain Residue Modelled Actual Comment Reference B -1 ENGINEERED MUTATION UNP P14784 B 0 ENGINEERED MUTATION UNP P14784 B 3 GLN ASN ENGINEERED MUTATION UNP P14784 B 17 GLN ASN ENGINEERED MUTATION UNP P14784 B 45 GLN ASN ENGINEERED MUTATION UNP P14784 E -1 ENGINEERED MUTATION UNP P14784 E 0 ENGINEERED MUTATION UNP P14784 E 3 GLN ASN ENGINEERED MUTATION UNP P14784 E 17 GLN ASN ENGINEERED MUTATION UNP P14784 E 45 GLN ASN ENGINEERED MUTATION UNP P14784 H -1 ENGINEERED MUTATION UNP P14784 H 0 ENGINEERED MUTATION UNP P14784 H 3 GLN ASN ENGINEERED MUTATION UNP P14784 H 17 GLN ASN ENGINEERED MUTATION UNP P14784 H 45 GLN ASN ENGINEERED MUTATION UNP P14784 K -1 ENGINEERED MUTATION UNP P14784 K 0 ENGINEERED MUTATION UNP P14784 K 3 GLN ASN ENGINEERED MUTATION UNP P14784 K 17 GLN ASN ENGINEERED MUTATION UNP P14784 K 45 GLN ASN ENGINEERED MUTATION UNP P14784 N -1 ENGINEERED MUTATION UNP P14784 N 0 ENGINEERED MUTATION UNP P14784 N 3 GLN ASN ENGINEERED MUTATION UNP P14784 N 17 GLN ASN ENGINEERED MUTATION UNP P14784 N 45 GLN ASN ENGINEERED MUTATION UNP P14784 Q -1 ENGINEERED MUTATION UNP P14784 Q 0 ENGINEERED MUTATION UNP P14784 Q 3 GLN ASN ENGINEERED MUTATION UNP P14784 Q 17 GLN ASN ENGINEERED MUTATION UNP P14784 Q 45 GLN ASN ENGINEERED MUTATION UNP P14784 T -1 ENGINEERED MUTATION UNP P14784 T 0 ENGINEERED MUTATION UNP P14784 T 3 GLN ASN ENGINEERED MUTATION UNP P14784 T 17 GLN ASN ENGINEERED MUTATION UNP P14784
10 Page 10 Full wwpdb X-ray Structure Validation Report 3QAZ Chain Residue Modelled Actual Comment Reference T 45 GLN ASN ENGINEERED MUTATION UNP P14784 W -1 ENGINEERED MUTATION UNP P14784 W 0 ENGINEERED MUTATION UNP P14784 W 3 GLN ASN ENGINEERED MUTATION UNP P14784 W 17 GLN ASN ENGINEERED MUTATION UNP P14784 W 45 GLN ASN ENGINEERED MUTATION UNP P14784 Z -1 ENGINEERED MUTATION UNP P14784 Z 0 ENGINEERED MUTATION UNP P14784 Z 3 GLN ASN ENGINEERED MUTATION UNP P14784 Z 17 GLN ASN ENGINEERED MUTATION UNP P14784 Z 45 GLN ASN ENGINEERED MUTATION UNP P14784 c -1 ENGINEERED MUTATION UNP P14784 c 0 ENGINEERED MUTATION UNP P14784 c 3 GLN ASN ENGINEERED MUTATION UNP P14784 c 17 GLN ASN ENGINEERED MUTATION UNP P14784 c 45 GLN ASN ENGINEERED MUTATION UNP P14784 f -1 ENGINEERED MUTATION UNP P14784 f 0 ENGINEERED MUTATION UNP P14784 f 3 GLN ASN ENGINEERED MUTATION UNP P14784 f 17 GLN ASN ENGINEERED MUTATION UNP P14784 f 45 GLN ASN ENGINEERED MUTATION UNP P14784 i -1 ENGINEERED MUTATION UNP P14784 i 0 ENGINEERED MUTATION UNP P14784 i 3 GLN ASN ENGINEERED MUTATION UNP P14784 i 17 GLN ASN ENGINEERED MUTATION UNP P14784 i 45 GLN ASN ENGINEERED MUTATION UNP P14784 Molecule 3 is a protein called Cytokine receptor common subunit gamma. Mol Chain Residues Atoms ZeroOcc AltConf Trace 3 C 188 Total C N O S F 186 Total C N O S I 188 Total C N O S L 191 Total C N O S O 191 Total C N O S R 188 Total C N O S
11 Page 11 Full wwpdb X-ray Structure Validation Report 3QAZ Mol Chain Residues Atoms ZeroOcc AltConf Trace 3 U 191 Total C N O S X 191 Total C N O S a 191 Total C N O S d 191 Total C N O S g 191 Total C N O S j 191 Total C N O S There are 48 discrepancies between the modelled and reference sequences: Chain Residue Modelled Actual Comment Reference C 31 - EXPRESSION TAG UNP P31785 C 32 - EXPRESSION TAG UNP P31785 C 33 - EXPRESSION TAG UNP P31785 C 53 GLN ASN ENGINEERED MUTATION UNP P31785 F 31 - EXPRESSION TAG UNP P31785 F 32 - EXPRESSION TAG UNP P31785 F 33 - EXPRESSION TAG UNP P31785 F 53 GLN ASN ENGINEERED MUTATION UNP P31785 I 31 - EXPRESSION TAG UNP P31785 I 32 - EXPRESSION TAG UNP P31785 I 33 - EXPRESSION TAG UNP P31785 I 53 GLN ASN ENGINEERED MUTATION UNP P31785 L 31 - EXPRESSION TAG UNP P31785 L 32 - EXPRESSION TAG UNP P31785 L 33 - EXPRESSION TAG UNP P31785 L 53 GLN ASN ENGINEERED MUTATION UNP P31785 O 31 - EXPRESSION TAG UNP P31785 O 32 - EXPRESSION TAG UNP P31785 O 33 - EXPRESSION TAG UNP P31785 O 53 GLN ASN ENGINEERED MUTATION UNP P31785 R 31 - EXPRESSION TAG UNP P31785 R 32 - EXPRESSION TAG UNP P31785 R 33 - EXPRESSION TAG UNP P31785 R 53 GLN ASN ENGINEERED MUTATION UNP P31785 U 31 - EXPRESSION TAG UNP P31785 U 32 - EXPRESSION TAG UNP P31785 U 33 - EXPRESSION TAG UNP P31785
12 Page 12 Full wwpdb X-ray Structure Validation Report 3QAZ Chain Residue Modelled Actual Comment Reference U 53 GLN ASN ENGINEERED MUTATION UNP P31785 X 31 - EXPRESSION TAG UNP P31785 X 32 - EXPRESSION TAG UNP P31785 X 33 - EXPRESSION TAG UNP P31785 X 53 GLN ASN ENGINEERED MUTATION UNP P31785 a 31 - EXPRESSION TAG UNP P31785 a 32 - EXPRESSION TAG UNP P31785 a 33 - EXPRESSION TAG UNP P31785 a 53 GLN ASN ENGINEERED MUTATION UNP P31785 d 31 - EXPRESSION TAG UNP P31785 d 32 - EXPRESSION TAG UNP P31785 d 33 - EXPRESSION TAG UNP P31785 d 53 GLN ASN ENGINEERED MUTATION UNP P31785 g 31 - EXPRESSION TAG UNP P31785 g 32 - EXPRESSION TAG UNP P31785 g 33 - EXPRESSION TAG UNP P31785 g 53 GLN ASN ENGINEERED MUTATION UNP P31785 j 31 - EXPRESSION TAG UNP P31785 j 32 - EXPRESSION TAG UNP P31785 j 33 - EXPRESSION TAG UNP P31785 j 53 GLN ASN ENGINEERED MUTATION UNP P31785 Molecule 4 is N-ACETYL-D-GLUCOSAMINE (three-letter code: NAG) (formula: C 8 H 15 NO 6 ). Mol Chain Residues Atoms ZeroOcc AltConf 4 B 1 Total C N O
13 Page 13 Full wwpdb X-ray Structure Validation Report 3QAZ Mol Chain Residues Atoms ZeroOcc AltConf 4 C 1 Total C N O C 1 Total C N O C 1 Total C N O C 1 Total C N O C 1 Total C N O E 1 Total C N O F 1 Total C N O F 1 Total C N O F 1 Total C N O F 1 Total C N O F 1 Total C N O H 1 Total C N O I 1 Total C N O I 1 Total C N O I 1 Total C N O I 1 Total C N O I 1 Total C N O K 1 Total C N O K 1 Total C N O L 1 Total C N O L 1 Total C N O
14 Page 14 Full wwpdb X-ray Structure Validation Report 3QAZ Mol Chain Residues Atoms ZeroOcc AltConf 4 L 1 Total C N O L 1 Total C N O N 1 Total C N O O 1 Total C N O O 1 Total C N O O 1 Total C N O O 1 Total C N O O 1 Total C N O Q 1 Total C N O R 1 Total C N O R 1 Total C N O R 1 Total C N O R 1 Total C N O R 1 Total C N O T 1 Total C N O U 1 Total C N O U 1 Total C N O W 1 Total C N O X 1 Total C N O X 1 Total C N O Z 1 Total C N O
15 Page 15 Full wwpdb X-ray Structure Validation Report 3QAZ Mol Chain Residues Atoms ZeroOcc AltConf 4 a 1 Total C N O a 1 Total C N O c 1 Total C N O c 1 Total C N O d 1 Total C N O f 1 Total C N O g 1 Total C N O g 1 Total C N O i 1 Total C N O i 1 Total C N O j 1 Total C N O
16 Page 16 Full wwpdb X-ray Structure Validation Report 3QAZ 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 geometryand 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 fit 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: Interleukin-2 Chain A: F80 D81 P82 R83 D84 V85 V86 S87 N88 I89 N90 V91 F92 V93 G98 GLU F103 M104 C105 E106 Y107 A112 T113 I114 V115 E116 F117 L118 N119 R120 W121 I122 T123 F124 C125 Q126 S127 I128 I129 S130 T131 L132 T133 S6 T7 Q11 L12 Q13 L14 E15 H16 L17 L18 L19 D20 M23 I24 I28 Y31 LYS ASN K35 L36 T37 R38 M39 L40 Y45 M46 P47 A50 L56 L59 E60 E61 E62 P65 L66 V69 A73 H74 S75 Molecule 1: Interleukin-2 Chain D: L70 N71 L72 N77 F78 H79 F80 D81 P82 V85 I89 N90 V91 F92 V93 L94 E95 L96 K97 G98 GLU F103 T111 A112 T113 I114 V115 E116 F117 W121 I122 C125 Q126 S127 I128 I129 S130 T131 L132 T133 S6 T7 K8 K9 T10 Q11 L12 Q13 L14 E15 H16 L17 L18 L19 D20 L21 Q22 M23 I24 I28 Y31 LYS ASN K35 F42 K43 F44 Y45 M46 P47 E52 L53 K54 H55 L56 Q57 C58 L59 E60 E61 E62 L63 L66 E67 E68 V69 Molecule 1: Interleukin-2 Chain G: F78 D81 P82 R83 D84 V85 V86 S87 N88 I89 N90 V91 F92 V93 L94 E95 L96 K97 G98 GLU F103 M104 Y107 T111 A112 T113 I114 V115 E116 F117 L118 N119 R120 W121 I122 T123 F124 C125 Q126 S127 I128 T131 L132 T133 S6 L12 Q13 L14 E15 H16 L17 L18 L19 D20 M23 I28 Y31 LYS ASN K35 L36 T37 R38 M39 L40 T41 F44 Y45 M46 P47 T51 E52 L53 K54 H55 L56 L59 E60 E61 E62 L63 K64 P65 L66 E67 E68 V69 L70 Molecule 1: Interleukin-2 Chain J: K64 P65 L66 E67 E68 V69 L70 N71 L72 A73 H74 S75 F78 H79 F80 D81 P82 R83 D84 V85 V86 S87 N88 I89 F92 V93 L94 E95 L96 K97 G98 GLU F103 T111 A112 T113 I114 V115 E116 F117 L118 N119 I122 T123 F124 C125 Q126 S127 I128 I129 S130 T131 L132 S6 T7 K8 K9 T10 Q11 L12 Q13 L14 E15 H16 L17 L18 L19 D20 L21 Q22 M23 I24 L25 Y31 LYS ASN K35 L36 T37 R38 M39 L40 T41 F42 Y45 M46 P47 A50 T51 E52 L53 K54 H55 L56 Q57 C58 L59 E60 E61 E62 L63
17 Page 17 Full wwpdb X-ray Structure Validation Report 3QAZ T133 Molecule 1: Interleukin-2 Chain M: H74 S75 F78 D81 P82 R83 D84 V85 V86 S87 N88 I89 N90 V91 F92 V93 G98 GLU F103 A108 T111 A112 T113 I114 V115 E116 F117 L118 N119 R120 W121 I122 T123 F124 C125 Q126 S127 I128 L132 T133 S6 T7 K8 Q11 L12 Q13 L14 E15 H16 L17 L18 L19 D20 L21 Q22 M23 I24 Y31 LYS ASN K35 L36 T37 R38 M39 L40 T41 F42 K43 F44 Y45 M46 P47 K48 K49 A50 L53 K54 H55 L56 Q57 E61 E62 P65 V69 Molecule 1: Interleukin-2 Chain P: V69 L70 N71 L72 F80 D81 P82 R83 D84 V85 V86 S87 N88 I89 N90 V91 F92 V93 G98 GLU F103 M104 Y107 T113 I114 V115 E116 N119 R120 W121 I122 T123 F124 C125 Q126 S127 I128 L132 T133 S6 T7 L12 Q13 L14 E15 H16 L17 L18 L19 D20 L21 Q22 M23 I24 L25 I28 Y31 LYS ASN K35 L36 M39 L40 T41 F42 K43 F44 Y45 K48 E52 L53 K54 H55 L56 L59 E62 L63 K64 P65 L66 E67 E68 Molecule 1: Interleukin-2 Chain S: E68 V69 L70 N77 F78 H79 F80 D81 D84 V85 V86 S87 N88 I89 N90 V91 F92 V93 L94 E95 L96 K97 G98 GLU F103 E106 Y107 A112 T113 I114 V115 E116 F117 L118 W121 I122 C125 Q126 S127 I128 I129 S130 T131 L132 T133 S6 T7 K8 K9 T10 Q11 L12 Q13 H16 L17 L18 L19 D20 I24 G27 I28 Y31 LYS ASN K35 L36 M39 L40 F44 K48 K49 A50 T51 E52 L53 K54 H55 L56 Q57 C58 L59 E60 E61 E62 L63 K64 P65 L66 E67 Molecule 1: Interleukin-2 Chain V: N71 L72 F78 H79 F80 D81 P82 R83 D84 V85 V86 S87 N88 I89 N90 V91 F92 V93 L94 E95 L96 K97 G98 GLU F103 M104 C105 E106 Y107 A108 A112 T113 I114 V115 E116 F117 L118 N119 R120 W121 I122 T123 F124 C125 Q126 S127 I128 I129 S130 T131 L132 T133 S6 T10 Q13 L14 E15 H16 L17 L18 L19 D20 I24 I28 Y31 LYS ASN K35 L36 T37 R38 M39 L40 T41 F42 K43 F44 Y45 M46 E52 L53 L56 Q57 C58 L59 E60 E61 E62 L63 K64 P65 L66 E67 E68 V69 L70 Molecule 1: Interleukin-2 Chain Y: S6 T7 K8 Q11 L12 Q13 L14 E15 H16 L17 L18 L19 D20 L21 Q22 M23 I24 L25 N26 G27 I28 Y31 LYS ASN K35 L36 T37 R38 M39 L40 T41 K49 A50 T51 E52 L53 K54 H55 L56 Q57 C58 L59 E62 L63 K64 P65 L66
18 Page 18 Full wwpdb X-ray Structure Validation Report 3QAZ E67 E68 V69 L70 N71 L72 K76 N77 F78 D81 P82 R83 D84 V85 V86 S87 N88 I89 N90 V91 F92 V93 L94 E95 L96 K97 G98 GLU F103 M104 C105 E106 A112 T113 I114 V115 E116 F117 R120 W121 I122 T123 F124 C125 Q126 S127 I128 I129 S130 T131 L132 Molecule 1: Interleukin-2 Chain b: S6 T7 Y31 LYS ASN K35 F44 Y45 Q57 N77 G98 GLU F103 T131 LEU Molecule 1: Interleukin-2 Chain e: S6 Y31 LYS ASN K35 N77 P82 F92 G98 GLU F103 T133 Molecule 1: Interleukin-2 Chain h: S6 Y31 LYS ASN K35 M39 G98 GLU F103 T133 Molecule 2: Interleukin-2 receptor subunit beta Chain B: Q177 Y178 E179 V182 K185 P186 L187 T192 T193 W194 S195 S198 R204 T205 K206 P207 LEU GLY LYS L72 T73 T74 V75 L80 R81 V82 L83 V92 I95 F98 K99 P100 L104 R105 L106 M107 A108 P109 I110 S111 V114 V117 E118 T119 N123 W126 E127 Q130 H133 Y134 F135 H138 L146 W152 A155 P156 E165 L172 T173 P174 D175 T176 VAL GLN GLY Q7 Y12 N13 S14 R15 A16 Q17 C20 Q24 GLY LEU GLN T31 V35 H36 A37 W38 P39 D40 R41 R42 R43 W44 Q45 Q46 T47 L50 S54 S57 W58 A59 C60 N61 L62 I63 L64 G65 D68 K71 Molecule 2: Interleukin-2 receptor subunit beta Chain E: K161 Q162 K163 Q164 I167 C168 L169 E170 T171 L172 T173 P174 D175 T176 Q177 Y178 E179 F180 Q181 V182 R183 V184 K185 P186 L187 Q188 F191 T192 S198 Q199 A202 F203 R204 T205 K206 P207 LEU GLY LYS V78 R81 V82 L83 I95 Q96 D97 F98 K99 P100 N103 L104 R105 L106 P109 L112 E118 T119 H120 R121 C122 N123 I124 S125 W126 E127 I128 S132 H133 Y134 F135 E136 R137 H138 L139 E140 F141 E142 A143 R144 T145 L146 S147 P148 W152 A155 P156 L157 L158 T159 L160 VAL GLN GLY S6 Y12 N13 S14 R15 A16 Q17 C20 Q24 GLY LEU GLN T31 A37 W38 P39 D40 R41 R42 R43 W44 Q45 Q46 T47 C48 E49 L50 L51 P52 A59 C60 N61 L62 I63 L64 G65 K71 L72 T73 T74 V75 D76 I77
19 Page 19 Full wwpdb X-ray Structure Validation Report 3QAZ Molecule 2: Interleukin-2 receptor subunit beta Chain H: VAL GLN GLY S6 Q7 F8 Y12 N13 S14 R15 A16 Q17 I18 S19 C20 S23 Q24 GLY LEU GLN T31 S32 H36 A37 W38 P39 D40 R41 R42 R43 W44 Q45 Q46 T47 L50 V53 S57 C60 N61 L62 I63 L64 P67 D68 S69 Q70 K71 L72 T73 T74 V75 D76 I77 V78 R81 V82 L83 C84 R85 W90 M93 F98 K99 P100 N103 L104 R105 L106 M107 A108 L112 V115 E118 T119 H120 R121 C122 N123 W126 Q130 A131 S132 H133 Y134 F135 E136 R137 H138 L139 E140 F141 E142 A143 R144 T145 L146 W152 A155 P156 L157 L158 T159 L160 E170 T171 L172 T173 P174 Y178 E179 F180 R183 V184 K185 P186 L187 T192 T193 W194 L201 A202 F203 K206 P207 LEU GLY LYS Molecule 2: Interleukin-2 receptor subunit beta Chain K: VAL GLN GLY S6 Q7 F8 T9 C10 F11 Y12 N13 S14 R15 A16 Q17 I18 S19 C20 V21 W22 S23 Q24 GLY LEU GLN T31 V35 W38 P39 R42 R43 W44 Q45 Q46 L50 L51 S54 Q55 A56 S57 W58 A59 L64 G65 A66 P67 D68 S69 Q70 K71 L72 T73 T74 V75 D76 I77 V78 R81 V82 L83 V92 M93 A94 I95 F98 K99 P100 F101 L104 R105 L106 I110 S111 L112 Q113 V114 V115 H116 V117 E118 T119 H120 R121 C122 N123 I124 E127 I128 S129 Q130 A131 S132 H133 Y134 F135 E136 R137 H138 L139 E140 F141 E142 A143 R144 T145 L146 W152 E153 E154 L158 T159 L160 K161 Q162 K163 Q164 E165 W166 I167 E170 T171 P174 D175 T176 Q177 Y178 E179 F180 Q181 V182 R183 V184 K185 P186 L187 Q188 G189 T192 T193 W194 S195 P196 L201 A202 F203 R204 T205 K206 P207 LEU GLY LYS Molecule 2: Interleukin-2 receptor subunit beta Chain N: VAL GLN GLY Q7 C10 F11 Y12 N13 S14 R15 A16 Q17 I18 S19 C20 Q24 GLY LEU GLN T31 V35 H36 A37 W38 P39 D40 R41 R42 L50 L51 P52 W58 A59 C60 N61 L62 I63 L64 S69 Q70 K71 L72 V75 D76 I77 V78 T79 L80 R81 V82 L83 E86 W90 R91 V92 M93 A94 I95 F98 K99 P100 F101 L104 R105 L106 V114 V115 H116 V117 E118 T119 H120 R121 C122 N123 W126 S129 S132 H133 Y134 H138 L139 E140 F141 E142 A143 R144 T145 L146 T151 W152 A155 P156 L157 L158 T159 L160 K161 Q162 K163 Q164 E165 W166 I167 C168 L169 E170 T171 L172 T173 P174 D175 Y178 E179 F180 Q181 V182 R183 P186 L187 Q188 T192 T193 W194 P200 L201 A202 T205 K206 P207 LEU GLY LYS Molecule 2: Interleukin-2 receptor subunit beta Chain Q: VAL GLN GLY Q7 F11 Y12 N13 A16 Q17 C20 V21 W22 S23 Q24 GLY LEU GLN T31 S32 C33 H36 A37 W38 P39 D40 R41 R42 R43 W44 T47 C48 E49 L50 L51 S54 Q55 A56 S57 W58 A59 C60 N61 L62 I63 L64 G65 A66 P67 D68 S69 Q70 K71 L72 T73 T74 V75 D76 I77 V78 T79 L80 R81 V82 L83 G87 V88 R89 W90 R91 V92 M93 A94 I95 Q96 D97 F98 K99 P100 F101 E102 N103 L104 R105 L106 M107 A108 L112 Q113 V114 V115 H116 V117 E118 T119 H120 R121 C122 N123 S129 S132 H133
20 Page 20 Full wwpdb X-ray Structure Validation Report 3QAZ Y134 F135 E136 R137 H138 L139 E140 F141 E142 A143 R144 T145 L146 S147 P148 G149 H150 T151 W152 E153 E154 A155 P156 L157 L158 T159 L160 K161 Q164 I167 C168 L169 E170 T171 P174 D175 T176 Q177 F180 Q181 V182 R183 P186 L187 Q188 G189 T192 T193 W194 W197 S198 T205 K206 P207 LEU GLY LYS Molecule 2: Interleukin-2 receptor subunit beta Chain T: VAL GLN GLY S6 C10 F11 Y12 N13 S14 R15 A16 Q17 I18 S19 C20 V21 W22 S23 Q24 GLY LEU GLN T31 S32 C33 H36 A37 W38 P39 R42 R43 W44 T47 L50 L51 P52 V53 S54 Q55 A56 S57 W58 A59 C60 N61 L62 I63 L64 G65 A66 P67 D68 K71 L72 T73 T74 V75 D76 L80 R81 V82 L83 C84 V88 R89 W90 R91 V92 M93 A94 F98 K99 P100 F101 L104 R105 L106 M107 A108 P109 I110 S111 L112 Q113 E118 T119 H120 R121 C122 N123 I124 S125 W126 E127 I128 S129 Q130 Y134 F135 E136 R137 H138 F141 E142 A143 R144 T145 L146 S147 W152 L157 L158 T159 L160 K161 Q162 K163 Q164 E165 W166 I167 E170 T171 L172 T173 P174 D175 T176 Q177 Y178 E179 F180 Q181 V182 R183 V184 K185 P186 L187 Q188 T192 T193 W194 S198 Q199 P200 L201 A202 K206 P207 LEU GLY LYS Molecule 2: Interleukin-2 receptor subunit beta Chain W: VAL GLN GLY S6 Q7 F8 T9 C10 F11 Y12 N13 S14 R15 A16 Q17 C20 V21 W22 S23 Q24 GLY LEU GLN T31 S32 C33 Q34 V35 H36 A37 W38 R41 R42 R43 W44 Q45 L50 V53 S54 Q55 W58 A59 C60 N61 L62 I63 L64 D68 S69 Q70 T73 T74 V75 D76 I77 V78 T79 L80 R81 V82 L83 C84 R85 R89 W90 R91 V92 M93 A94 I95 Q96 D97 F98 K99 P100 F101 E102 N103 L104 R105 L106 P109 I110 S111 L112 Q113 V114 V115 H116 V117 E118 T119 H120 R121 C122 N123 I124 S125 W126 E127 I128 S129 Q130 A131 S132 H133 Y134 F135 E136 R137 H138 L139 E140 F141 E142 A143 R144 T145 L146 H150 T151 W152 E153 E154 A155 P156 T159 L160 K161 Q164 E165 W166 I167 E170 P174 E179 F180 Q181 V182 R183 V184 K185 P186 L187 Q188 G189 T192 T193 W194 L201 A202 F203 R204 T205 K206 P207 LEU GLY LYS Molecule 2: Interleukin-2 receptor subunit beta Chain Z: VAL GLN GLY S6 Q7 F8 T9 C10 F11 Y12 N13 S14 R15 A16 Q17 I18 S19 C20 V21 Q24 GLY LEU GLN T31 H36 A37 W38 P39 D40 R41 R42 R43 W44 L50 V53 S54 S57 W58 A59 C60 L64 D68 S69 Q70 K71 L72 T73 T74 V75 D76 I77 V78 T79 L80 R81 V82 L83 C84 M93 A94 I95 F98 K99 P100 F101 E102 N103 L104 R105 L106 M107 A108 P109 Q113 V114 V115 H116 V117 E118 T119 H120 R121 C122 N123 I124 S125 W126 S129 Q130 A131 S132 H133 Y134 F135 H138 F141 E142 A143 L146 H150 T151 W152 E153 E154 L158 T159 L160 K161 Q162 K163 Q164 E165 W166 I167 C168 L169 E170 T171 L172 T173 P174 Q177 Y178 E179 F180 Q181 V182 R183 V184 K185 P186 L187 T193 W194 W197 F203 R204 T205 K206 P207 LEU GLY LYS
21 Page 21 Full wwpdb X-ray Structure Validation Report 3QAZ Molecule 2: Interleukin-2 receptor subunit beta Chain c: VAL GLN GLY S6 Q24 GLY LEU GLN T31 R81 L112 P207 LEU GLY LYS Molecule 2: Interleukin-2 receptor subunit beta Chain f: VAL GLN GLY S6 Q24 GLY LEU GLN T31 D76 V92 Q113 H138 E154 D175 P207 LEU GLY LYS Molecule 2: Interleukin-2 receptor subunit beta Chain i: VAL GLN GLY S6 Q24 GLY LEU GLN T31 H138 A143 R144 T145 Q164 L169 E190 P207 LEU GLY LYS Molecule 3: Cytokine receptor common subunit gamma Chain C: T139 L140 H141 K142 L143 L148 N154 R155 F156 L157 E162 H163 T169 D170 W171 D172 H173 V180 D181 Y182 R183 H184 K185 V191 D192 K195 F199 R200 R204 F205 N206 P207 L208 C209 W215 W218 I222 H223 W224 GLY ASN LYS GLU ASN P34 E46 Y47 M48 W52 S55 S56 GLU GLN P60 T61 N62 L63 T64 L65 Y69 L84 G92 C93 Q94 L95 I100 H101 L102 Y103 Q104 T105 F106 Q109 L110 Q111 R114 E115 P116 Q119 A120 T121 L124 K125 L126 W133 N137 L138 Molecule 3: Cytokine receptor common subunit gamma Chain F: S179 V180 D181 Y182 R183 H184 K185 F186 S187 L188 P189 S190 V191 D192 G193 T198 F199 R200 R204 F205 N206 P207 L208 C209 G210 S211 A212 Q213 H214 W215 W218 S219 I222 H223 W224 GLY ASN LYS GLU ASN T105 F106 Q109 L110 Q111 D112 P113 R114 E115 P116 R117 R118 Q119 A120 T121 K125 L126 Q127 N128 L129 V130 I131 P132 W133 A134 P135 E136 N137 L138 T139 L140 H141 K142 L143 S144 E145 S146 Q147 L148 E149 L150 R155 F156 L157 N158 H159 C160 L161 E162 Y167 R168 T169 T176 E177 Q178 P34 L35 F41 V42 F43 N44 V45 E46 Y47 M48 N49 W52 Q53 S54 S55 GLU GLN T61 N62 L63 T64 L65 H66 Y67 W68 V77 Q78 K79 C80 S81 H82 Y83 L84 F85 S86 E87 E88 I89 T90 S91 G92 C93 Q94 L95 Q96 I100 H101 L102 Y103 Q104 Molecule 3: Cytokine receptor common subunit gamma Chain I:
22 Page 22 Full wwpdb X-ray Structure Validation Report 3QAZ V191 D192 K195 R196 Y197 T198 V201 R204 F205 N206 P207 L208 C209 G210 S211 A212 I222 H223 W224 GLY ASN LYS GLU ASN L126 Q127 N128 L129 V130 I131 P132 W133 A134 P135 E136 N137 L138 T139 L140 H141 K142 L143 S144 Q147 L148 E149 L150 N151 W152 F156 L157 N158 H159 C160 L161 E162 H163 L164 V165 R168 T169 D170 H173 S174 W175 Q178 S179 V180 D181 Y182 R183 H184 K185 F186 S187 L188 P189 S190 P34 L35 C40 F41 V42 F43 N44 V45 E46 Y47 M48 N49 W52 S56 GLU GLN P60 T61 N62 L63 T64 L65 H66 Y67 W68 L84 F85 S86 E87 E88 I89 T90 S91 G92 C93 I100 H101 L102 F106 V107 V108 Q109 L110 Q111 R114 R118 M123 Molecule 3: Cytokine receptor common subunit gamma Chain L: Y197 T198 F199 R200 V201 R202 S203 R204 F205 N206 P207 L208 C209 G210 S211 A212 W215 W218 S219 I222 H223 W224 GLY ASN LYS GLU ASN T121 Q122 M123 L126 Q127 N128 L129 V130 I131 P132 W133 A134 P135 L138 S144 E145 S146 Q147 L148 E149 L150 N151 N154 H159 E162 H163 L164 V165 Q166 Y167 R168 T169 D172 W175 T176 E177 Q178 S179 V180 D181 Y182 R183 H184 K185 F186 S187 L188 P189 S190 V191 D192 P34 V38 Q39 C40 F41 V42 F43 N44 V45 E46 Y47 M48 N49 W52 S55 S56 E57 P58 Q59 P60 T61 N62 L65 H66 Y67 W68 N71 V77 F85 I89 T90 S91 G92 I100 V107 V108 Q109 L110 Q111 D112 P113 R114 R117 R118 Q119 A120 Molecule 3: Cytokine receptor common subunit gamma Chain O: S190 V191 D192 G193 Q194 K195 R196 Y197 T198 F199 R200 V201 R202 S203 R204 F205 N206 P207 L208 C209 G210 S219 W224 GLY ASN LYS GLU ASN R117 T121 Q122 M123 Q127 W133 A134 P135 L138 T139 L140 L143 S144 Q147 L148 E149 L150 N151 W152 N153 N154 R155 F156 L157 N158 H159 C160 L161 E162 H163 L164 V165 Q166 Y167 R168 T169 D172 H173 S174 W175 T176 E177 Q178 S179 V180 D181 Y182 K185 F186 S187 L188 P189 P34 E37 V38 Q39 C40 F41 V42 F43 N44 V45 E46 Y47 M48 N49 W52 E57 P58 Q59 P60 T61 N62 L63 T64 L65 W68 V77 Y83 L84 I89 G92 C93 Q94 L95 I100 H101 L102 Y103 Q104 V107 V108 Q109 L110 Q111 R114 E115 P116 Molecule 3: Cytokine receptor common subunit gamma Chain R: T198 F199 R200 V201 R202 S203 R204 F205 N206 P207 G210 S211 A212 W224 GLY ASN LYS GLU ASN Q119 A120 Q127 N128 L129 V130 I131 P132 W133 A134 P135 E136 L140 S144 E145 S146 Q147 W152 N153 N154 R155 F156 L157 N158 H159 H163 L164 V165 Q166 Y167 R168 T169 D172 H173 S174 W175 T176 E177 V180 D181 K185 P189 S190 V191 D192 G193 Q194 K195 R196 Y197 P34 C40 F41 V42 F43 N44 V45 E46 Y47 M48 N49 W52 Q53 E57 P58 Q59 P60 T61 N62 L63 T64 L65 H66 Y67 W68 Y69 D75 K76 V77 H82 G92 C93 Q94 L95 I100 H101 L102 Y103 F106 V107 V108 Q109 L110 Q111 D112 P113 R114 Molecule 3: Cytokine receptor common subunit gamma
23 Page 23 Full wwpdb X-ray Structure Validation Report 3QAZ Chain U: L188 P189 S190 V191 D192 K195 R196 Y197 T198 F199 R200 V201 R204 F205 N206 P207 L208 C209 G210 S211 A212 Q213 H214 W215 S216 E217 I222 H223 W224 GLY ASN LYS GLU ASN P116 R117 R118 Q119 A120 T121 Q122 M123 L124 K125 N128 L129 V130 I131 P132 W133 A134 P135 E136 N137 L138 T139 L140 H141 K142 E145 S146 Q147 L148 E149 L150 N151 W152 R155 F156 L157 L161 E162 H163 L164 V165 Q166 Y167 R168 T169 E177 Q178 S179 Y182 R183 H184 K185 F186 S187 P34 L35 V38 Q39 C40 F41 V42 F43 N44 V45 E46 Y47 M48 N49 C50 T51 W52 Q53 S54 S55 P58 N62 L63 T64 L65 H66 Y67 W68 Y69 K70 N71 V77 E88 G92 L95 H101 L102 Y103 F106 V107 V108 Q109 L110 Q111 D112 P113 R114 E115 Molecule 3: Cytokine receptor common subunit gamma Chain X: E177 Q178 S179 V180 D181 Y182 R183 L188 P189 D192 K195 R196 Y197 T198 F199 R200 V201 R202 S203 R204 F205 N206 P207 L208 C209 G210 S211 A212 Q213 H214 W215 S216 E217 W218 S219 H220 P221 I222 H223 W224 GLY ASN LYS GLU ASN F106 V107 V108 Q109 L110 P113 R114 E115 P116 A120 T121 Q122 M123 N128 L129 V130 I131 P132 W133 A134 L138 T139 L140 S144 Q147 L148 E149 L150 N151 W152 N153 N154 R155 F156 L157 N158 H159 C160 L161 E162 H163 L164 V165 Q166 Y167 R168 T169 D170 W171 D172 H173 S174 W175 T176 P34 L35 P36 E37 V38 V42 V45 M48 T51 W52 Q53 S54 S55 S56 E57 P58 T61 N62 L63 T64 L65 H66 Y67 W68 Y69 K70 N71 S72 D73 V77 Q78 K79 C80 Y83 L84 F85 S86 E87 E88 I89 G92 C93 K98 H101 L102 Y103 Molecule 3: Cytokine receptor common subunit gamma Chain a: P34 L35 P36 Q39 C40 F41 V42 V45 C50 T51 W52 P60 T61 N62 L63 T64 L65 S86 Q94 F106 V107 V108 Q111 D112 P113 F156 W171 E177 L188 P189 W224 GLY ASN LYS GLU ASN Molecule 3: Cytokine receptor common subunit gamma Chain d: P34 Q39 N44 V45 T51 S55 S56 E57 P58 Q59 K70 N71 F85 S86 F106 V107 V108 S146 Q147 L148 F156 L157 V191 D192 G193 Q194 W224 GLY ASN LYS GLU ASN Molecule 3: Cytokine receptor common subunit gamma Chain g: P34 V42 F43 T51 S55 Q59 P60 T64 L65 N71 T90 K98 F106 V107 V108 Q109 R118 L126 Q127 W133 H159 R200 W224 GLY ASN LYS GLU ASN Molecule 3: Cytokine receptor common subunit gamma
24 Page 24 Full wwpdb X-ray Structure Validation Report 3QAZ Chain j: P34 E37 V38 Q39 F43 N44 V45 S55 S56 E57 P60 T61 N62 L65 H66 N71 F85 S86 E87 Q96 F106 V107 V108 Q109 L110 Q122 N154 R155 W224 GLY ASN LYS GLU ASN
25 Page 25 Full wwpdb X-ray Structure Validation Report 3QAZ 4 Data and refinement statistics i Property Value Source Space group P 1 Depositor Cell constants Å Å Å a, b, c, α, β, γ Depositor Resolution (Å) Depositor EDS % Data completeness (in resolution range) 93.2 ( ) 94.5 ( ) Depositor EDS R merge (Not available) Depositor R sym (Not available) Depositor < I/σ(I) > (at 3.77Å) Xtriage Refinement program PHENIX (phenix.refine: dev_621) Depositor 0.291, Depositor R, R free 0.286, DCC R free test set 1880 reflections (1.67%) wwpdb-vp Wilson B-factor (Å 2 ) 82.1 Xtriage Anisotropy Xtriage Bulk solvent k sol (e/å 3 ), B sol (Å 2 ) 0.30, 45.8 EDS L-test for twinning 2 < L > = 0.44, < L 2 > = 0.27 Xtriage Estimated twinning fraction for -k,-h,-l Xtriage F o,f c correlation 0.88 EDS Total number of atoms wwpdb-vp Average B, all atoms (Å 2 ) 99.0 wwpdb-vp Xtriage s analysis on translational NCS is as follows: The analyses of the Patterson function reveals a significant off-origin peak that is % of the origin peak, indicating pseudo-translational symmetry. The chance of finding a peak of this or larger height randomly in a structure without pseudo-translational symmetry is equal to e-06. The detected translational NCS is most likely also responsible for the elevated intensity ratio. 1 Intensities estimated from amplitudes. 2 Theoretical values of < L >, < L 2 > for acentric reflections are 0.5, respectively for untwinned datasets, and 0.375, 0.2 for perfectly twinned datasets.
26 Page 26 Full wwpdb X-ray Structure Validation Report 3QAZ 5 Model quality i 5.1 Standard geometry i Bond lengths and bond angles in the following residue types are not validated in this section: NAG 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 >5 RMSZ # Z >5 1 A / / D / / G / / J / / M / / P / / S / / V / /1367 (0.1%) 1 Y / / b / / e / / h / / B / / E / / H / / K / / N / / Q / / T / / W / / Z / / c / / f / / i / / C / / F / / I / / L / /2294 (0.0%) 3 O / / R / / U / / X / /2294
27 Page 27 Full wwpdb X-ray Structure Validation Report 3QAZ Mol Chain Bond lengths Bond angles RMSZ # Z >5 RMSZ # Z >5 3 a / / d / / g / / j / /2294 All All / /70975 (0.0%) There are no bond length outliers. All (2) bond angle outliers are listed below: Mol Chain Res Type Atoms Z Observed( o ) Ideal( o ) 3 L 208 LEU CB-CG-CD V 96 LEU CA-CB-CG There are no chirality outliers. There are no planarity outliers. 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 D G J M P S V Y b e h B E H K
28 Page 28 Full wwpdb X-ray Structure Validation Report 3QAZ Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes 2 N Q T W Z c f i C F I L O R U X a d g j B C E F H I K L N O Q R T U W X Z a c d f g
29 Page 29 Full wwpdb X-ray Structure Validation Report 3QAZ Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes 4 i j 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 33. All (2335) close contacts within the same asymmetric unit are listed below, sorted by their clash magnitude. 1:J:15:GLU:HG2 1:J:129:ILE:HD :W:15:ARG:NE 2:W:131::O :F:206:ASN:OD1 3:F:210:GLY:O :W:110:ILE:HG12 2:W:129::HB :T:123:ASN:HD21 4:T:215:NAG:C :V:81::HB3 1:V:84::HB :K:54::HB3 2:K:57::HB :Q:115:VAL:HG11 4:Q:215:NAG:H :I:204:ARG:N 3:O:114:ARG:O :D:42:PHE:HE1 1:D:72:LEU:HD :J:53:LEU:HD11 1:J:96:LEU:HB :Z:138:HIS:HB3 2:Z:187:LEU:HD :E:162:GLN:NE2 3:F:187::H :M:31:TYR:HH 1:M:35:LYS:N :R:52:TRP:CZ3 3:R:92:GLY:HA :Z:15:ARG:HD2 2:Z:130:GLN:HB :O:57:GLU:HG2 3:O:58::HD :Y:89:ILE:O 1:Y:93:VAL:HG :B:114:VAL:HG11 2:B:117:VAL:HG :Z:98:PHE:HE2 2:Z:100::HA :Z:13:ASN:ND2 2:Z:17:GLN:HB :L:52:TRP:CZ3 3:L:92:GLY:HA :J:16:HIS:CE1 2:K:134:TYR:HB :T:109::HG3 2:T:184:VAL:HG :K:123:ASN:HD21 4:K:215:NAG:C :X:164:LEU:HD11 3:X:177:GLU:HB :Y:81::HB3 1:Y:84::HB :D:42:PHE:CE1 1:D:72:LEU:HD :E:81:ARG:HG2 2:E:95:ILE:HG :K:138:HIS:C 2:K:187:LEU:HG :O:169::H 3:O:172::HB
30 Page 30 Full wwpdb X-ray Structure Validation Report 3QAZ 2:W:119::HB 2:W:174::HG :L:188:LEU:HD22 3:L:199:PHE:HE :F:52:TRP:CZ3 3:F:92:GLY:HA :F:62:ASN:HD21 4:F:300:NAG:C :N:123:ASN:HD21 4:N:215:NAG:C :Z:106:LEU:HD11 2:Z:186::HG :S:89:ILE:O 1:S:93:VAL:HG :W:110:ILE:CG1 2:W:129::HB :W:123:ASN:HD21 4:W:215:NAG:C :I:107:VAL:HG22 3:I:123:MET:HG :E:83:LEU:HD11 2:T:38:TRP:HH :F:206:ASN:OD1 3:F:211::HA :K:146:LEU:HB2 2:K:152:TRP:CH :L:169::H 3:L:172::HB :F:137:ASN:ND2 4:F:400:NAG:C :E:65:GLY:HA3 2:E:71:LYS:HE :T:66::HB1 2:T:67::HD :L:144::HB3 3:L:147:GLN:HB :J:125:CYS:O 1:J:129:ILE:HG :L:62:ASN:HD21 4:L:300:NAG:C :D:60:GLU:HA 1:D:63:LEU:HD :J:15:GLU:HG2 1:J:129:ILE:CD :F:137:ASN:ND2 4:F:400:NAG:O :H:123:ASN:HD21 4:H:215:NAG:C :Z:167:ILE:HG21 2:Z:180:PHE:CZ :F:137:ASN:HD21 4:F:400:NAG:C :Z:98:PHE:CE2 2:Z:100::HA :I:62:ASN:HD21 4:I:300:NAG:C :W:36:HIS:HD1 2:W:38:TRP:HE :X:52:TRP:HZ3 3:X:65:LEU:HD :K:146:LEU:HD13 2:K:152:TRP:CD :W:98:PHE:CE2 2:W:100::HA :O:84:LEU:HD21 4:O:234:NAG:H :D:11:GLN:HA 1:D:14:LEU:HD :F:206:ASN:OD1 3:F:207::HA :U:204:ARG:HD3 3:U:212::O :F:109:GLN:HG3 3:F:121::HG :R:62:ASN:HD21 4:R:300:NAG:C :M:56:LEU:HB3 1:M:93:VAL:HG :J:14:LEU:HD23 1:J:129:ILE:HB :X:38:VAL:HG22 3:X:52:TRP:HB
31 Page 31 Full wwpdb X-ray Structure Validation Report 3QAZ 3:C:62:ASN:HD21 4:C:300:NAG:C :E:162:GLN:HE22 3:F:187::N :Q:17:GLN:HG3 2:Q:63:ILE:HD :E:162:GLN:HE22 3:F:187::CA :Q:12:TYR:OH 2:Q:72:LEU:HB :H:18:ILE:HB 2:H:62:LEU:HB :L:204:ARG:HD3 3:L:212::O :P:31:TYR:HH 1:P:35:LYS:N :J:31:TYR:OH 1:J:35:LYS:HB :C:137:ASN:HD21 4:C:400:NAG:C :K:170:GLU:HB2 3:L:190::HB :K:81:ARG:CD 2:K:95:ILE:HG :N:175::H 2:N:205::HB :C:109:GLN:HG3 3:C:121::HG :S:81::HB3 1:S:84::HB :I:181::OD2 3:I:183:ARG:HD :B:35:VAL:HG22 2:B:82:VAL:HG :T:158:LEU:HD22 3:U:189::HB :E:162:GLN:NE2 3:F:187::N :Q:95:ILE:HG12 2:Q:96:GLN:N :K:146:LEU:HD22 2:K:152:TRP:CE :V:92:PHE:CZ 2:W:73::HB :X:158:ASN:O 3:X:159:HIS:HB :C:84:LEU:HD22 4:C:234:NAG:H :K:15:ARG:HD2 2:K:68::O :V:120:ARG:O 1:V:123::HB :V:66:LEU:CD1 1:V:114:ILE:HD :L:188:LEU:HD22 3:L:199:PHE:CE :V:63:LEU:HD11 1:V:86:VAL:HB :Z:119::HB 2:Z:174::HG :R:156:PHE:HD2 3:R:157:LEU:HG :Z:12:TYR:CE2 2:Z:14::HA :N:50:LEU:HD22 2:N:58:TRP:HB :D:69:VAL:HG11 1:D:114:ILE:HD :E:162:GLN:CD 3:F:187::H :U:107:VAL:HG22 3:U:123:MET:HG :B:15:ARG:HG3 2:B:68::HA :Y:125:CYS:O 1:Y:129:ILE:HG :V:68:GLU:O 1:V:72:LEU:HD :X:132::HB3 3:X:161:LEU:HD :W:110:ILE:CD1 2:W:129::HB
32 Page 32 Full wwpdb X-ray Structure Validation Report 3QAZ 2:N:101:PHE:HA 2:N:104:LEU:HD :E:83:LEU:HD11 2:T:38:TRP:CH :R:156:PHE:CD2 3:R:157:LEU:HG :E:13:ASN:O 2:E:14::HB :U:148:LEU:HD21 3:U:191:VAL:HG :X:165:VAL:HG22 3:X:201:VAL:HG :K:167:ILE:HG21 2:K:180:PHE:CZ :D:31:TYR:OH 1:D:35:LYS:HB :O:165:VAL:HG22 3:O:178:GLN:O :V:97:LYS:HG3 1:V:98:GLY:H :K:14::HG 2:K:135:PHE:HE :T:138:HIS:CE1 3:U:182:TYR:CE :Z:185:LYS:HB2 2:Z:194:TRP:CE :B:50:LEU:HD23 2:B:60:CYS:HB :Q:44:TRP:HH2 2:Q:64:LEU:HD :L:109:GLN:HG3 3:L:121::HG :O:52:TRP:CZ3 3:O:92:GLY:HA :U:52:TRP:CZ3 3:U:92:GLY:HA :H:50:LEU:HD23 2:H:60:CYS:HB :R:163:HIS:ND1 3:R:203::HB :V:124:PHE:O 1:V:128:ILE:HG :D:31:TYR:OH 1:D:35:LYS:HE :T:119::HB 2:T:174::HG :T:50:LEU:HD22 2:T:58:TRP:HB :Z:73::HG22 2:Z:76::OD :F:183:ARG:HD3 3:F:185:LYS:HE :B:13:ASN:ND2 2:B:17:GLN:HB :J:66:LEU:O 1:J:70:LEU:HD :M:16:HIS:HD1 2:N:134:TYR:HB :Z:82:VAL:O 2:Z:83:LEU:HD :F:204:ARG:HH21 3:F:213:GLN:HA :E:164:GLN:HE21 3:F:178:GLN:HG :W:115:VAL:HB 2:W:123:ASN:HD :W:161:LYS:O 3:X:183:ARG:NH :Z:143::HB3 2:Z:158:LEU:HB :J:9:LYS:O 1:J:13:GLN:HG :K:139:LEU:O 2:K:187:LEU:HD :K:137:ARG:O 3:L:181::HB :K:138:HIS:O 2:K:187:LEU:HG :N:118:GLU:O 2:N:205::HG :C:207::CG 3:F:117:ARG:HH
33 Page 33 Full wwpdb X-ray Structure Validation Report 3QAZ 1:V:69:VAL:O 1:V:72:LEU:HB :X:197:TYR:O 3:X:223:HIS:HA :D:16:HIS:HB3 2:E:134:TYR:CD :D:24:ILE:HA 1:D:80:PHE:HE :K:146:LEU:HD22 2:K:152:TRP:CZ :R:154:ASN:HD21 3:R:163:HIS:HE :U:52:TRP:HZ3 3:U:65:LEU:HD :D:11:GLN:HG3 1:D:129:ILE:HG :J:63:LEU:CD2 1:J:66:LEU:HD :A:74:HIS:CG 1:A:75::H :F:68:TRP:HH2 3:F:109:GLN:NE :K:143::HB1 2:K:180:PHE:CE :J:88:ASN:ND2 2:K:42:ARG:HH :P:44:PHE:CZ 1:P:69:VAL:HG :V:28:ILE:O 1:V:36:LEU:HD :E:137:ARG:HB3 3:F:181::HB :D:18:LEU:HD11 1:D:122:ILE:HG :E:119::HB 2:E:174::HG :W:82:VAL:HB 2:W:93:MET:HB :K:121:ARG:HG2 2:K:170:GLU:OE :N:123:ASN:ND2 4:N:215:NAG:C :N:69::HB2 2:N:71:LYS:HE :T:172:LEU:HD22 2:T:178:TYR:CZ :I:181::OD1 3:I:183:ARG:HD :Q:144:ARG:HH11 2:Q:152:TRP:HB :W:13:ASN:HD21 2:W:16::H :K:138:HIS:CA 2:K:187:LEU:HD :O:135::HG2 3:O:201:VAL:HG :T:109::HG3 2:T:184:VAL:CG :U:192::OD2 3:U:195:LYS:HE :C:84:LEU:CD2 4:C:234:NAG:H :Q:115:VAL:CG1 4:Q:215:NAG:H :X:181::OD1 3:X:183:ARG:NH :D:125:CYS:O 1:D:129:ILE:HG :F:204:ARG:HG3 3:F:214:HIS:O :M:16:HIS:ND1 2:N:134:TYR:HB :Y:16:HIS:CE1 2:Z:134:TYR:HB :C:207::HG2 3:F:117:ARG:HH :F:52:TRP:NE1 3:F:63:LEU:HD :B:114:VAL:CG1 2:B:117:VAL:HG :K:104:LEU:O 2:K:192::HG
34 Page 34 Full wwpdb X-ray Structure Validation Report 3QAZ 1:V:95:GLU:HG3 2:W:41:ARG:HH :E:128:ILE:O 2:E:128:ILE:HD :G:45:TYR:CE1 1:G:111::HG :W:109::HG3 2:W:184:VAL:HG :I:138:LEU:HD12 3:I:138:LEU:H :Q:174::HA 2:Q:205::HG :F:52:TRP:HE1 3:F:63:LEU:HD :G:31:TYR:HH 1:G:35:LYS:N :M:35:LYS:HD2 1:M:38:ARG:HH :O:62:ASN:ND2 4:O:300:NAG:H :U:147:GLN:HG2 3:U:189::O :B:123:ASN:HD21 4:B:215:NAG:C :D:11:GLN:HB2 1:D:132:LEU:HD :K:161:LYS:HZ3 3:L:185:LYS:HD :R:154:ASN:HD21 3:R:163:HIS:CE :R:48:MET:HB2 3:R:100:ILE:HD :T:183:ARG:HD2 2:T:194:TRP:HB :X:140:LEU:HG 3:X:222:ILE:HD :M:62:GLU:O 1:M:65::HG :I:47:TYR:HE1 3:I:49:ASN:HD :P:56:LEU:HB3 1:P:93:VAL:HG :T:138:HIS:CE1 3:U:182:TYR:CD :W:189:GLY:HA3 2:W:192::OG :G:37::O 1:G:41::HG :U:164:LEU:HD11 3:U:177:GLU:HB :F:62:ASN:CG 4:F:300:NAG:H :G:44:PHE:HE2 1:G:114:ILE:HB :O:42:VAL:HG22 3:O:100:ILE:HD :W:110:ILE:HG12 2:W:129::CB :D:7::HG22 1:D:132:LEU:HD :E:112:LEU:HG 2:E:126:TRP:HB :I:168:ARG:HG2 3:I:175:TRP:CZ :U:188:LEU:HD11 3:U:199:PHE:HE :D:66:LEU:O 1:D:70:LEU:HD :O:154:ASN:HD21 3:O:163:HIS:CE :W:78:VAL:HG23 2:W:100::HG :J:126:GLN:OE1 3:L:210:GLY:HA :Q:160:LEU:HD13 2:Q:164:GLN:HB :Q:33:CYS:HB3 2:Q:50:LEU:HD :Y:128:ILE:O 1:Y:132:LEU:HG :T:98:PHE:CE2 2:T:100::HA
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CHAPTER 101 FOURIER SERIES FOR PERIODIC FUNCTIONS OF PERIOD
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(1) Describe the process by which mercury atoms become excited in a fluorescent tube (3)
Q1. (a) A fluorescent tube is filled with mercury vapour at low pressure. In order to emit electromagnetic radiation the mercury atoms must first be excited. (i) What is meant by an excited atom? (1) (ii)
Figure 1 T / K Explain, in terms of molecules, why the first part of the graph in Figure 1 is a line that slopes up from the origin.
Q1.(a) Figure 1 shows how the entropy of a molecular substance X varies with temperature. Figure 1 T / K (i) Explain, in terms of molecules, why the entropy is zero when the temperature is zero Kelvin.
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ΠΑΝΕΠΙΣΤΗΜΙΟ ΠΑΤΡΩΝ ΤΜΗΜΑ ΗΛΕΚΤΡΟΛΟΓΩΝ ΜΗΧΑΝΙΚΩΝ ΚΑΙ ΤΕΧΝΟΛΟΓΙΑΣ ΥΠΟΛΟΓΙΣΤΩΝ ΤΟΜΕΑΣ ΣΥΣΤΗΜΑΤΩΝ ΗΛΕΚΤΡΙΚΗΣ ΕΝΕΡΓΕΙΑΣ ιπλωµατική Εργασία του φοιτητή του τµήµατος Ηλεκτρολόγων Μηχανικών και Τεχνολογίας Ηλεκτρονικών