32
Full wwPDB NMR Structure Validation Report i Feb 20, 2018 – 10:17 pm GMT PDB ID : 2KKI Title : Solution structure of human Interleukin 1a Authors : Mohan, S.K.; Chang, H.-K.; Yu, C. Deposited on : 2009-06-24 This is a Full wwPDB NMR 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/NMRValidationReportHelp 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: Cyrange : Kirchner and Güntert (2011) NmrClust : Kelley et al. (1996) MolProbity : 4.02b-467 Percentile statistics : 20171227.v01 (using entries in the PDB archive December 27th 2017) RCI : v_1n_11_5_13_A (Berjanski et al., 2005) PANAV : Wang et al. (2010) ShiftChecker : trunk30686 Ideal geometry (proteins) : Engh & Huber (2001) Ideal geometry (DNA, RNA) : Parkinson et al. (1996) Validation Pipeline (wwPDB-VP) : trunk30686

Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

  • Upload
    others

  • View
    2

  • Download
    0

Embed Size (px)

Citation preview

Page 1: Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

Full wwPDB NMR Structure Validation Report i○

Feb 20, 2018 – 10:17 pm GMT

PDB ID : 2KKITitle : Solution structure of human Interleukin 1a

Authors : Mohan, S.K.; Chang, H.-K.; Yu, C.Deposited on : 2009-06-24

This is a Full wwPDB NMR Structure Validation Report for a publicly released PDB entry.

We welcome your comments at [email protected] user guide is available at

https://www.wwpdb.org/validation/2017/NMRValidationReportHelpwith 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:

Cyrange : Kirchner and Güntert (2011)NmrClust : Kelley et al. (1996)

MolProbity : 4.02b-467Percentile statistics : 20171227.v01 (using entries in the PDB archive December 27th 2017)

RCI : v_1n_11_5_13_A (Berjanski et al., 2005)PANAV : Wang et al. (2010)

ShiftChecker : trunk30686Ideal geometry (proteins) : Engh & Huber (2001)

Ideal geometry (DNA, RNA) : Parkinson et al. (1996)Validation Pipeline (wwPDB-VP) : trunk30686

Page 2: Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

Page 2 Full wwPDB NMR Structure Validation Report 2KKI

1 Overall quality at a glance i○

The following experimental techniques were used to determine the structure:SOLUTION NMR

The overall completeness of chemical shifts assignment was not calculated.

Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown inthe following graphic. The table shows the number of entries on which the scores are based.

Metric Whole archive(#Entries)

NMR archive(#Entries)

Clashscore 136279 12091Ramachandran outliers 132675 10835

Sidechain outliers 132484 10811

The table below summarises the geometric issues observed across the polymeric chains and theirfit to the experimental data. The red, orange, yellow and green segments indicate the fractionof residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria. A cyansegment indicates the fraction of residues that are not part of the well-defined cores, and a grey seg-ment represents the fraction of residues that are not modelled. The numeric value for each fractionis indicated below the corresponding segment, with a dot representing fractions <=5%

Mol Chain Length Quality of chain

1 A 151

Page 3: Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

Page 3 Full wwPDB NMR Structure Validation Report 2KKI

2 Ensemble composition and analysis i○

This entry contains 14 models. Model 11 is the overall representative, medoid model (most similarto other models). The authors have identified model 1 as representative, based on the followingcriterion: lowest energy.

The following residues are included in the computation of the global validation metrics.

Well-defined (core) protein residuesWell-defined core Residue range (total) Backbone RMSD (Å) Medoid model

1 A:13-A:144, A:148-A:159(144)

0.36 11

Ill-defined regions of proteins are excluded from the global statistics.

Ligands and non-protein polymers are included in the analysis.

The models can be grouped into 3 clusters and 2 single-model clusters were found.

Cluster number Models1 6, 8, 9, 13, 142 5, 7, 11, 123 1, 2, 4

Single-model clusters 3; 10

Page 4: Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

Page 4 Full wwPDB NMR Structure Validation Report 2KKI

3 Entry composition i○

There is only 1 type of molecule in this entry. The entry contains 2423 atoms, of which 1208 arehydrogens and 0 are deuteriums.

• Molecule 1 is a protein called Interleukin-1 alpha.

Mol Chain Residues Atoms Trace

1 A 151 Total C H N O S2423 782 1208 197 232 4 0

Page 5: Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

Page 5 Full wwPDB NMR Structure Validation Report 2KKI

4 Residue-property plots i○

4.1 Average score per residue in the NMR ensemble

These plots are provided for all protein, RNA and DNA chains in the entry. The first graphic is thesame as shown in the summary in section 1 of this report. The second graphic shows the sequencewhere residues are colour-coded according to the number of geometric quality criteria for whichthey contain at least one outlier: green = 0, yellow = 1, orange = 2 and red = 3 or more. Stretchesof 2 or more consecutive residues without any outliers are shown as green connectors. Residueswhich are classified as ill-defined in the NMR ensemble, are shown in cyan with an underlinecolour-coded according to the previous scheme. Residues which were present in the experimentalsample, but not modelled in the final structure are shown in grey.

• Molecule 1: Interleukin-1 alpha

Chain A:

N9 V10

K11

Y12

N13

F14

M15

R16

I17

I18

K19

Y20

E21

F22

I23

L24

N25

D26

A27

L28

N29

Q30

S31

I32

I33

R34

L40

T41

A42

L45

L48

D49

E50

A51

V52

K53

F54

D55

M56

G57

A58

Y59

K60

D64

K67

I68

T69

V70

I71

L72

R73

I74

L79

Y80

V81

T82

A83

Q84

D85

E86

D87

Q88

P89

V90

L91

L92

K93

E97

T101

I102

T103

G104

S105

E106

T107

N108

L109

L110

F111

F112

K119

N120

Y121

F122

T123

S124

V125

A126

H127

P128

N129

L130

F131

I132

A133

T134

K135

Q136

D137

Y138

W139

V140

C141

L142

A143

G144

G145

P146

P147

S148

I149

T150

D151

F152

Q153

I154

L155

E156

N157

Q158

A159

4.2 Scores per residue for each member of the ensemble

Colouring as in section 4.1 above.

4.2.1 Score per residue for model 1

• Molecule 1: Interleukin-1 alpha

Chain A:

N9 V10

K11

Y12

N13

F14

M15

R16

I17

I18

K19

Y20

E21

F22

I23

L24

N25

D26

A27

L28

N29

Q30

S31

I32

I33

R34

L40

T41

A42

L45

H46

N47

L48

D49

E50

A51

V52

K53

F54

D55

M56

G57

A58

Y59

K60

S61

D64

D65

A66

K67

V70

I71

L72

R73

I74

L79

Y80

V81

T82

A83

Q84

D85

E86

D87

Q88

P89

V90

L91

L92

K93

E94

I98

P99

K100

T101

I102

T103

G104

S105

E106

T107

N108

L109

L110

F111

F112

W113

E114

K119

F122

T123

S124

V125

A126

H127

P128

N129

L130

F131

I132

A133

T134

K135

Q136

W139

V140

C141

L142

A143

G144

G145

P146

P147

S148

I149

T150

D151

F152

Q153

I154

L155

E156

N157

Q158

A159

Page 6: Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

Page 6 Full wwPDB NMR Structure Validation Report 2KKI

4.2.2 Score per residue for model 2

• Molecule 1: Interleukin-1 alpha

Chain A:

N9 V10

K11

Y12

N13

F14

M15

R16

I17

I18

K19

Y20

I23

L24

N25

D26

A27

L28

N29

Q30

S31

I32

I33

R34

D37

L40

T41

A42

L45

L48

D49

E50

A51

V52

K53

F54

D55

M56

Y59

D64

K67

I68

T69

V70

I71

L72

R73

L79

Y80

V81

T82

A83

E86

D87

Q88

P89

V90

L91

L92

K93

E97

K100

T101

I102

T103

G104

S105

E106

T107

N108

L109

L110

F111

F112

K119

N120

Y121

F122

T123

S124

V125

A126

H127

P128

N129

L130

F131

I132

A133

T134

K135

Q136

D137

Y138

W139

V140

C141

L142

A143

G144

G145

P146

P147

S148

I149

T150

D151

F152

L155

E156

N157

Q158

A159

4.2.3 Score per residue for model 3

• Molecule 1: Interleukin-1 alpha

Chain A:

N9 V10

K11

Y12

N13

F14

M15

R16

I17

I18

K19

Y20

I23

L24

N25

D26

A27

L28

N29

Q30

S31

I32

I33

R34

L40

T41

A42

A43

A44

L45

H46

N47

L48

D49

E50

A51

V52

K53

F54

D55

M56

Y59

K60

D64

K67

I68

T69

V70

I71

L72

R73

I74

S75

K76

Y80

V81

T82

E86

D87

Q88

P89

V90

L91

L92

K93

E94

M95

P96

E97

I98

P99

K100

T101

I102

T103

G104

S105

E106

T107

N108

L109

L110

F111

F112

K119

N120

Y121

F122

T123

S124

H127

P128

N129

L130

F131

I132

A133

T134

K135

Q136

W139

V140

C141

L142

A143

G144

G145

P146

P147

S148

I149

F152

Q153

I154

L155

E156

N157

Q158

A159

4.2.4 Score per residue for model 4

• Molecule 1: Interleukin-1 alpha

Chain A:

N9 V10

K11

Y12

I18

K19

Y20

E21

F22

I23

L24

N25

D26

A27

L28

N29

Q30

S31

I32

I33

R34

A35

L40

T41

A42

L45

L48

D49

E50

A51

V52

K53

F54

D55

M56

G57

A58

Y59

D64

K67

I68

T69

V70

I71

L72

R73

I74

S75

K76

L79

Y80

V81

T82

E86

D87

Q88

P89

V90

L91

L92

K93

I102

T103

G104

S105

E106

T107

N108

L109

L110

F111

F112

W113

E114

K119

N120

Y121

F122

T123

S124

V125

A126

H127

P128

N129

L130

F131

I132

A133

T134

K135

Q136

V140

C141

L142

A143

G144

G145

P146

P147

S148

I149

T150

D151

F152

L155

E156

N157

Q158

A159

Page 7: Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

Page 7 Full wwPDB NMR Structure Validation Report 2KKI

4.2.5 Score per residue for model 5

• Molecule 1: Interleukin-1 alpha

Chain A:

N9 V10

K11

Y12

N13

F14

M15

R16

I17

I18

K19

F22

I23

L24

N25

D26

A27

L28

N29

Q30

S31

I32

I33

R34

L40

T41

A42

L45

L48

D49

E50

K53

F54

D55

M56

G57

A58

Y59

K60

D64

T69

V70

I71

L72

R73

I74

S75

K76

T77

Q78

L79

Y80

V81

T82

A83

E86

D87

Q88

P89

V90

L91

L92

K93

E97

K100

T101

I102

T103

G104

S105

E106

T107

N108

L109

L110

F111

T115

K119

N120

Y121

F122

T123

S124

H127

L130

F131

I132

A133

T134

K135

Q136

D137

Y138

W139

V140

C141

L142

G145

P146

P147

S148

I149

T150

D151

F152

Q153

I154

L155

E156

A159

4.2.6 Score per residue for model 6

• Molecule 1: Interleukin-1 alpha

Chain A:

N9 V10

K11

Y12

N13

F14

M15

R16

I17

I18

K19

Y20

E21

F22

I23

L24

N25

D26

A27

L28

N29

Q30

S31

I32

I33

R34

L40

T41

A42

L45

L48

D49

E50

A51

F54

D55

M56

Y59

K60

D64

K67

I68

T69

V70

I71

L72

R73

I74

L79

Y80

V81

T82

A83

Q84

D85

E86

D87

Q88

P89

V90

L91

L92

K93

I98

P99

K100

T101

I102

T103

G104

S105

E106

T107

N108

L109

L110

F111

F112

K119

N120

Y121

F122

T123

S124

V125

A126

H127

P128

N129

L130

F131

I132

A133

T134

K135

Q136

D137

Y138

W139

V140

C141

L142

A143

G144

G145

P146

P147

S148

I149

T150

D151

F152

Q153

I154

L155

E156

N157

Q158

A159

4.2.7 Score per residue for model 7

• Molecule 1: Interleukin-1 alpha

Chain A:

N9 V10

K11

Y12

N13

F14

M15

R16

I17

I18

K19

F22

I23

L24

N25

D26

A27

L28

N29

Q30

S31

I32

I33

R34

A35

L40

T41

A42

A43

A44

L45

L48

D49

E50

A51

V52

K53

F54

D55

M56

G57

A58

Y59

K60

D64

V70

I71

L72

R73

L79

Y80

V81

T82

A83

Q84

D85

E86

D87

Q88

P89

V90

L91

L92

K93

I98

P99

K100

T101

I102

T103

G104

N108

L109

L110

F111

F112

H116

K119

F122

T123

S124

H127

P128

N129

L130

F131

I132

A133

T134

K135

Q136

D137

Y138

C141

L142

A143

G144

G145

P146

P147

S148

I149

T150

D151

F152

Q153

I154

L155

E156

N157

Q158

A159

Page 8: Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

Page 8 Full wwPDB NMR Structure Validation Report 2KKI

4.2.8 Score per residue for model 8

• Molecule 1: Interleukin-1 alpha

Chain A:

N9 V10

K11

Y12

N13

F14

M15

R16

I17

I18

K19

Y20

E21

F22

I23

L24

N25

D26

A27

L28

N29

Q30

S31

I32

I33

R34

L40

T41

A42

L45

H46

N47

L48

D49

E50

A51

V52

K53

F54

D55

M56

G57

A58

Y59

K60

D64

T69

V70

I71

L72

R73

I74

S75

K76

T77

Q78

L79

Y80

V81

T82

A83

Q84

D85

E86

D87

Q88

P89

V90

L91

L92

K93

E94

M95

P96

T101

I102

T103

G104

S105

E106

T107

N108

L109

L110

F111

K119

N120

Y121

F122

T123

S124

H127

L130

F131

I132

A133

T134

K135

Q136

D137

Y138

W139

V140

C141

L142

A143

G144

G145

P146

P147

S148

I149

T150

D151

F152

Q153

I154

L155

A159

4.2.9 Score per residue for model 9

• Molecule 1: Interleukin-1 alpha

Chain A:

N9 V10

K11

Y12

N13

F14

M15

R16

I17

I18

K19

F22

I23

L24

N25

D26

A27

L28

N29

Q30

S31

I32

I33

R34

L40

T41

A42

A43

A44

L45

L48

D49

E50

A51

V52

K53

F54

D55

M56

G57

A58

Y59

K60

D64

T69

V70

I71

L72

R73

I74

T77

Y80

V81

T82

A83

Q84

D85

E86

D87

Q88

P89

V90

L91

L92

K93

E97

T101

I102

T103

G104

S105

E106

T107

N108

L109

L110

F111

K119

N120

Y121

F122

T123

S124

V125

N129

L130

F131

I132

A133

T134

K135

Y138

W139

V140

C141

L142

A143

G144

G145

P146

P147

S148

I149

T150

D151

F152

L155

E156

N157

Q158

A159

4.2.10 Score per residue for model 10

• Molecule 1: Interleukin-1 alpha

Chain A:

N9 V10

K11

Y12

N13

F14

M15

R16

I17

I18

K19

I23

L24

N25

D26

A27

L28

N29

Q30

S31

I32

I33

L40

T41

A42

A43

A44

L45

L48

A51

V52

K53

F54

D55

M56

G57

A58

Y59

K60

D64

K67

I68

T69

V70

I71

L72

R73

Q78

L79

Y80

V81

T82

A83

Q84

D85

E86

D87

Q88

P89

V90

L91

L92

K93

P96

E97

I98

T101

I102

T103

G104

N108

L109

L110

F111

F112

K119

N120

Y121

F122

T123

S124

V125

A126

H127

P128

N129

L130

F131

I132

A133

T134

K135

Q136

D137

Y138

W139

V140

C141

L142

A143

G144

G145

P146

P147

S148

I149

T150

D151

F152

Q153

I154

L155

A159

Page 9: Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

Page 9 Full wwPDB NMR Structure Validation Report 2KKI

4.2.11 Score per residue for model 11 (medoid)

• Molecule 1: Interleukin-1 alpha

Chain A:

N9 V10

K11

Y12

N13

F14

M15

R16

I17

I18

K19

Y20

E21

F22

I23

L24

N25

D26

A27

L28

N29

Q30

S31

I32

I33

R34

L40

T41

A42

A43

A44

L45

L48

D49

E50

K53

F54

D55

M56

G57

A58

Y59

K60

D64

K67

I68

T69

V70

I71

L72

R73

L79

Y80

V81

T82

A83

Q84

D85

E86

D87

Q88

P89

V90

L91

L92

K93

E94

M95

P96

E97

I98

T101

I102

T103

G104

S105

E106

T107

N108

L109

L110

F111

T115

K119

N120

Y121

F122

T123

S124

V125

A126

H127

P128

N129

L130

F131

I132

A133

T134

K135

Q136

V140

C141

L142

A143

G144

G145

P146

P147

S148

I149

T150

D151

F152

Q153

I154

L155

Q158

A159

4.2.12 Score per residue for model 12

• Molecule 1: Interleukin-1 alpha

Chain A:

N9 V10

K11

Y12

N13

F14

M15

R16

I17

I18

K19

Y20

E21

F22

I23

L24

N25

D26

A27

L28

N29

Q30

S31

I32

I33

L40

T41

A42

A43

A44

L45

H46

N47

L48

D49

E50

A51

V52

K53

F54

D55

M56

G57

A58

Y59

K60

D64

K67

V70

I71

L72

R73

Q78

L79

Y80

V81

T82

A83

E86

D87

Q88

P89

V90

L91

L92

K93

E94

M95

P96

E97

T101

I102

T103

G104

S105

E106

T107

N108

L109

L110

F111

K119

N120

Y121

F122

T123

S124

V125

A126

H127

P128

N129

L130

F131

I132

A133

T134

K135

Q136

V140

C141

L142

A143

G144

G145

P146

P147

S148

I149

T150

D151

F152

Q153

I154

L155

E156

N157

Q158

A159

4.2.13 Score per residue for model 13

• Molecule 1: Interleukin-1 alpha

Chain A:

N9 V10

K11

Y12

N13

F14

M15

R16

I17

I18

K19

Y20

E21

F22

I23

L24

N25

D26

A27

L28

N29

Q30

S31

I32

I33

R34

D37

L40

T41

A42

A43

A44

L45

H46

N47

L48

D49

E50

A51

V52

K53

F54

D55

M56

G57

A58

Y59

K60

D64

K67

V70

I71

L72

R73

I74

S75

K76

Y80

V81

T82

A83

E86

D87

Q88

P89

V90

L91

L92

K93

E97

I98

P99

K100

T101

I102

T103

G104

S105

E106

T107

N108

L109

L110

F111

E114

K119

N120

Y121

F122

T123

P128

N129

L130

F131

I132

A133

T134

K135

Q136

D137

Y138

W139

V140

C141

L142

A143

G144

G145

P146

P147

S148

I149

T150

D151

F152

Q153

I154

L155

E156

N157

Q158

A159

Page 10: Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

Page 10 Full wwPDB NMR Structure Validation Report 2KKI

4.2.14 Score per residue for model 14

• Molecule 1: Interleukin-1 alpha

Chain A:

N9 V10

K11

Y12

N13

F14

M15

R16

I17

I18

K19

Y20

E21

F22

I23

L24

N25

D26

A27

L28

N29

Q30

S31

I32

I33

L40

T41

A42

L45

H46

N47

L48

D49

E50

K53

F54

D55

M56

G57

A58

Y59

K60

D64

K67

I68

T69

V70

I71

L72

R73

L79

Y80

V81

T82

A83

E86

D87

Q88

P89

V90

L91

L92

K93

E94

M95

P96

E97

I98

T101

I102

T103

G104

S105

E106

T107

N108

L109

L110

F111

F112

W113

E114

T115

H116

K119

N120

Y121

F122

T123

S124

H127

L130

F131

I132

A133

T134

K135

Q136

V140

C141

L142

A143

G144

G145

P146

P147

S148

I149

T150

D151

F152

Q153

I154

L155

E156

N157

Q158

A159

Page 11: Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

Page 11 Full wwPDB NMR Structure Validation Report 2KKI

5 Refinement protocol and experimental data overview i○

The models were refined using the following method: simulated annealing.

Of the 200 calculated structures, 14 were deposited, based on the following criterion: structureswith the least restraint violations.

The following table shows the software used for structure solution, optimisation and refinement.

Software name Classification VersionCNS refinement

No chemical shift data was provided. No validations of the models with respect to experimentalNMR restraints is performed at this time.

Page 12: Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

Page 12 Full wwPDB NMR Structure Validation Report 2KKI

6 Model quality i○

6.1 Standard geometry i○

The Z score for a bond length (or angle) is the number of standard deviations the observed valueis removed from the expected value. A bond length (or angle) with |Z| > 5 is considered an outlierworth inspection. RMSZ is the (average) root-mean-square of all Z scores of the bond lengths (orangles).

Mol Chain Bond lengths Bond anglesRMSZ #Z>5 RMSZ #Z>5

1 A 0.55±0.03 1±1/1185 (0.0±0.1%) 0.65±0.03 0±0/1607 (0.0±0.0%)All All 0.55 7/16590 (0.0%) 0.65 0/22498 (0.0%)

Chiral center outliers are detected by calculating the chiral volume of a chiral center and verifyingif the center is modelled as a planar moiety or with the opposite hand. A planarity outlier isdetected by checking planarity of atoms in a peptide group, atoms in a mainchain group or atomsof a sidechain that are expected to be planar.

Mol Chain Chirality Planarity1 A 0.0±0.0 0.9±0.9All All 0 13

All unique bond outliers are listed below. They are sorted according to the Z-score of the worstoccurrence in the ensemble.

Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å) ModelsWorst Total

1 A 80 TYR CE1-CZ 8.31 1.49 1.38 11 21 A 59 TYR CE1-CZ 7.28 1.48 1.38 2 21 A 59 TYR CE2-CZ -6.55 1.30 1.38 2 11 A 131 PHE CE1-CZ 5.81 1.48 1.37 8 11 A 80 TYR CE2-CZ -5.39 1.31 1.38 11 1

There are no bond-angle outliers.

There are no chirality outliers.

All unique planar outliers are listed below. They are sorted by the frequency of occurrence in theensemble.

Mol Chain Res Type Group Models (Total)1 A 59 TYR Sidechain 51 A 80 TYR Sidechain 31 A 112 PHE Sidechain 2

Continued on next page...

Page 13: Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

Page 13 Full wwPDB NMR Structure Validation Report 2KKI

Continued from previous page...Mol Chain Res Type Group Models (Total)1 A 131 PHE Sidechain 11 A 111 PHE Sidechain 11 A 121 TYR Sidechain 1

6.2 Too-close contacts i○

In the following table, the Non-H and H(model) columns list the number of non-hydrogen atomsand hydrogen atoms in each chain respectively. The H(added) column lists the number of hydrogenatoms added and optimized by MolProbity. The Clashes column lists the number of clashesaveraged over the ensemble.

Mol Chain Non-H H(model) H(added) Clashes1 A 1161 1152 1149 106±9All All 16254 16128 16086 1490

The all-atom clashscore is defined as the number of clashes found per 1000 atoms (includinghydrogen atoms). The all-atom clashscore for this structure is 46.

All unique clashes are listed below, sorted by their clash magnitude.

Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total

1:A:20:TYR:CB 1:A:55:ASP:HA 1.01 1.86 14 11:A:20:TYR:HB3 1:A:55:ASP:HA 0.95 1.34 14 11:A:89:PRO:HA 1:A:141:CYS:HA 0.95 1.37 5 141:A:81:VAL:HB 1:A:111:PHE:HZ 0.93 1.24 3 91:A:31:SER:HB3 1:A:51:ALA:HB2 0.92 1.42 6 11:A:31:SER:HB2 1:A:51:ALA:HB2 0.92 1.42 1 51:A:49:ASP:HB2 1:A:157:ASN:HB2 0.91 1.40 6 61:A:131:PHE:CE1 1:A:150:THR:HG21 0.90 2.02 9 21:A:71:ILE:HG23 1:A:109:LEU:HD21 0.90 1.41 9 81:A:33:ILE:HG22 1:A:51:ALA:HA 0.89 1.44 9 11:A:123:THR:HA 1:A:131:PHE:HB2 0.89 1.43 9 11:A:23:ILE:HB 1:A:155:LEU:HB2 0.88 1.42 2 11

1:A:45:LEU:HD11 1:A:50:GLU:HB3 0.88 1.44 11 81:A:45:LEU:HD12 1:A:48:LEU:HA 0.87 1.46 1 11:A:86:GLU:HG3 1:A:87:ASP:H 0.86 1.30 3 61:A:30:GLN:HG3 1:A:136:GLN:HA 0.85 1.47 14 41:A:135:LYS:HE3 1:A:141:CYS:HB3 0.85 1.48 14 11:A:135:LYS:HD2 1:A:138:TYR:HB2 0.85 1.48 6 31:A:102:ILE:HG23 1:A:106:GLU:HB3 0.84 1.46 13 11:A:81:VAL:HB 1:A:111:PHE:CZ 0.83 2.08 3 9

Continued on next page...

Page 14: Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

Page 14 Full wwPDB NMR Structure Validation Report 2KKI

Continued from previous page...

Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total

1:A:102:ILE:HG23 1:A:106:GLU:HB2 0.83 1.48 1 41:A:33:ILE:HG12 1:A:51:ALA:HA 0.81 1.52 10 81:A:79:LEU:HD23 1:A:92:LEU:HD13 0.81 1.51 4 51:A:102:ILE:HG12 1:A:106:GLU:HB2 0.80 1.49 5 31:A:15:MET:HG3 1:A:16:ARG:HD2 0.80 1.51 8 11:A:112:PHE:CE2 1:A:125:VAL:HA 0.80 2.12 2 21:A:48:LEU:HB2 1:A:157:ASN:HA 0.80 1.53 7 31:A:24:LEU:HD21 1:A:152:PHE:HD1 0.79 1.38 4 11:A:130:LEU:HB3 1:A:142:LEU:HD21 0.79 1.52 9 31:A:119:LYS:HA 1:A:152:PHE:O 0.79 1.76 9 141:A:82:THR:HA 1:A:108:ASN:HB3 0.78 1.56 1 91:A:87:ASP:HA 1:A:142:LEU:O 0.78 1.78 8 141:A:28:LEU:HG 1:A:149:ILE:HG21 0.77 1.55 8 61:A:85:ASP:HA 1:A:130:LEU:HD22 0.77 1.57 6 2

1:A:82:THR:HG23 1:A:93:LYS:HG2 0.77 1.57 1 21:A:84:GLN:HG3 1:A:85:ASP:H 0.77 1.38 11 11:A:133:ALA:HB1 1:A:148:SER:HB3 0.76 1.55 9 121:A:133:ALA:CB 1:A:148:SER:HB3 0.76 2.10 4 91:A:86:GLU:O 1:A:142:LEU:HB3 0.76 1.80 9 141:A:31:SER:HB2 1:A:51:ALA:CB 0.76 2.11 12 61:A:45:LEU:HG 1:A:155:LEU:HD13 0.75 1.59 2 11:A:26:ASP:OD2 1:A:28:LEU:HB2 0.75 1.81 3 61:A:132:ILE:O 1:A:150:THR:HG23 0.75 1.82 4 11:A:56:MET:HA 1:A:71:ILE:O 0.74 1.83 12 141:A:131:PHE:HE1 1:A:150:THR:HG1 0.74 1.26 9 11:A:27:ALA:HB2 1:A:119:LYS:HD2 0.73 1.60 7 41:A:100:LYS:HD3 1:A:100:LYS:H 0.73 1.42 5 11:A:83:ALA:HB1 1:A:130:LEU:HD23 0.73 1.60 1 91:A:79:LEU:HD21 1:A:92:LEU:HD13 0.73 1.60 14 11:A:58:ALA:HA 1:A:70:VAL:HA 0.73 1.59 4 81:A:31:SER:HB2 1:A:45:LEU:HD23 0.72 1.61 4 71:A:131:PHE:HB3 1:A:143:ALA:O 0.72 1.82 8 71:A:26:ASP:OD2 1:A:134:THR:HB 0.72 1.84 8 51:A:59:TYR:HE2 1:A:110:LEU:HD22 0.72 1.42 2 11:A:23:ILE:HB 1:A:155:LEU:HD12 0.72 1.59 7 11:A:67:LYS:HE2 1:A:125:VAL:HA 0.72 1.60 6 31:A:28:LEU:HB3 1:A:136:GLN:HG2 0.72 1.58 10 31:A:19:LYS:HA 1:A:19:LYS:HE2 0.72 1.62 14 11:A:13:ASN:HB2 1:A:102:ILE:HG13 0.72 1.62 12 11:A:13:ASN:OD1 1:A:102:ILE:HB 0.72 1.83 11 31:A:81:VAL:HB 1:A:109:LEU:HD13 0.72 1.62 14 2

Continued on next page...

Page 15: Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

Page 15 Full wwPDB NMR Structure Validation Report 2KKI

Continued from previous page...

Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total

1:A:13:ASN:HB3 1:A:59:TYR:HB3 0.71 1.61 7 11:A:30:GLN:OE1 1:A:136:GLN:HA 0.71 1.84 12 11:A:57:GLY:H 1:A:71:ILE:HG13 0.71 1.46 13 4

1:A:26:ASP:OD1 1:A:28:LEU:HB2 0.71 1.85 4 41:A:24:LEU:O 1:A:31:SER:HA 0.70 1.86 4 131:A:133:ALA:O 1:A:140:VAL:HG23 0.70 1.86 4 31:A:129:ASN:HA 1:A:144:GLY:HA3 0.70 1.62 11 51:A:31:SER:CB 1:A:51:ALA:HB2 0.70 2.16 12 51:A:52:VAL:HB 1:A:74:ILE:HD13 0.70 1.63 13 11:A:80:TYR:CE2 1:A:109:LEU:HB2 0.70 2.22 5 11:A:40:LEU:HD13 1:A:92:LEU:HD11 0.69 1.62 7 51:A:45:LEU:HD11 1:A:50:GLU:CB 0.69 2.17 14 71:A:82:THR:HG23 1:A:93:LYS:HB3 0.69 1.63 4 31:A:82:THR:HG22 1:A:108:ASN:HB3 0.69 1.64 6 31:A:54:PHE:HA 1:A:73:ARG:O 0.69 1.87 3 131:A:35:ALA:HB2 1:A:41:THR:HG22 0.68 1.64 7 21:A:32:ILE:HB 1:A:40:LEU:HD21 0.68 1.65 3 5

1:A:15:MET:HG3 1:A:16:ARG:HG3 0.68 1.65 12 21:A:82:THR:CG2 1:A:93:LYS:HB3 0.68 2.18 4 21:A:134:THR:HA 1:A:140:VAL:HG12 0.68 1.65 9 21:A:18:ILE:HD12 1:A:56:MET:HG2 0.68 1.65 1 11:A:17:ILE:HD13 1:A:17:ILE:H 0.68 1.48 3 11:A:13:ASN:CB 1:A:59:TYR:HB2 0.68 2.19 8 21:A:23:ILE:HD13 1:A:53:LYS:HB3 0.67 1.64 2 51:A:24:LEU:HD21 1:A:152:PHE:CD1 0.67 2.22 4 11:A:28:LEU:HB2 1:A:30:GLN:HE22 0.67 1.50 11 11:A:86:GLU:HG2 1:A:87:ASP:H 0.67 1.49 13 81:A:13:ASN:ND2 1:A:59:TYR:HB2 0.67 2.04 6 21:A:27:ALA:H 1:A:151:ASP:HB2 0.67 1.50 10 7

1:A:21:GLU:HG3 1:A:53:LYS:HD2 0.67 1.66 11 21:A:86:GLU:HG3 1:A:87:ASP:N 0.67 2.05 11 61:A:120:ASN:HB3 1:A:152:PHE:CD1 0.67 2.24 2 41:A:26:ASP:HB3 1:A:134:THR:OG1 0.67 1.88 9 51:A:32:ILE:HA 1:A:42:ALA:HA 0.67 1.65 2 13

1:A:28:LEU:HD21 1:A:149:ILE:HG13 0.66 1.65 12 71:A:80:TYR:CD2 1:A:109:LEU:HD22 0.66 2.24 3 41:A:28:LEU:HD13 1:A:136:GLN:HB2 0.66 1.66 1 51:A:28:LEU:HD13 1:A:136:GLN:HG3 0.66 1.67 2 21:A:28:LEU:HD11 1:A:149:ILE:HD13 0.66 1.66 6 61:A:30:GLN:HG2 1:A:136:GLN:HA 0.66 1.65 8 11:A:136:GLN:NE2 1:A:136:GLN:H 0.66 1.87 8 1

Continued on next page...

Page 16: Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

Page 16 Full wwPDB NMR Structure Validation Report 2KKI

Continued from previous page...

Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total

1:A:59:TYR:CE1 1:A:71:ILE:HG23 0.65 2.26 8 11:A:13:ASN:CB 1:A:59:TYR:HB3 0.65 2.20 7 11:A:30:GLN:OE1 1:A:43:ALA:HA 0.65 1.92 3 11:A:80:TYR:CE1 1:A:108:ASN:HB2 0.65 2.26 11 21:A:54:PHE:CD2 1:A:72:LEU:HG 0.65 2.26 8 111:A:59:TYR:CD1 1:A:102:ILE:HG13 0.65 2.27 3 11:A:67:LYS:HB3 1:A:112:PHE:CD1 0.65 2.27 2 31:A:71:ILE:HD13 1:A:98:ILE:HG21 0.65 1.69 13 11:A:122:PHE:HB2 1:A:132:ILE:HB 0.65 1.69 5 141:A:133:ALA:HA 1:A:150:THR:HA 0.64 1.69 10 81:A:129:ASN:HA 1:A:144:GLY:CA 0.64 2.23 1 51:A:25:ASN:OD1 1:A:29:ASN:HA 0.64 1.92 2 31:A:133:ALA:O 1:A:140:VAL:HG13 0.64 1.92 6 61:A:80:TYR:CD1 1:A:93:LYS:HB3 0.64 2.27 11 31:A:45:LEU:CD1 1:A:48:LEU:HA 0.64 2.23 1 11:A:82:THR:HG23 1:A:93:LYS:CG 0.64 2.23 7 31:A:25:ASN:ND2 1:A:29:ASN:HA 0.64 2.08 11 31:A:71:ILE:HG21 1:A:98:ILE:HG22 0.64 1.68 1 21:A:129:ASN:HA 1:A:144:GLY:HA2 0.64 1.69 13 51:A:82:THR:CG2 1:A:91:LEU:HB2 0.64 2.23 11 101:A:59:TYR:CE2 1:A:69:THR:HG21 0.64 2.28 2 11:A:15:MET:HG2 1:A:60:LYS:HB2 0.63 1.68 13 21:A:82:THR:HG22 1:A:108:ASN:CB 0.63 2.24 1 31:A:14:PHE:HB3 1:A:100:LYS:HA 0.63 1.69 3 21:A:81:VAL:HG13 1:A:90:VAL:HG21 0.63 1.69 9 11:A:124:SER:HB3 1:A:127:HIS:O 0.63 1.92 14 91:A:135:LYS:HG3 1:A:139:TRP:O 0.63 1.94 1 21:A:15:MET:HB3 1:A:58:ALA:O 0.63 1.92 12 41:A:72:LEU:H 1:A:109:LEU:HD11 0.63 1.53 8 21:A:25:ASN:O 1:A:152:PHE:HA 0.63 1.93 6 81:A:82:THR:HB 1:A:93:LYS:HB2 0.63 1.69 12 101:A:26:ASP:HB3 1:A:134:THR:HB 0.63 1.70 5 21:A:26:ASP:CG 1:A:134:THR:HB 0.63 2.14 8 1

1:A:48:LEU:HD13 1:A:155:LEU:HB3 0.63 1.69 13 11:A:102:ILE:HD12 1:A:106:GLU:HB3 0.62 1.72 6 11:A:149:ILE:HD12 1:A:149:ILE:H 0.62 1.53 10 11:A:82:THR:OG1 1:A:108:ASN:HB3 0.62 1.94 3 101:A:78:GLN:HB3 1:A:96:PRO:HA 0.62 1.71 8 21:A:13:ASN:HB3 1:A:60:LYS:N 0.62 2.10 8 51:A:59:TYR:HE1 1:A:71:ILE:HG23 0.62 1.54 8 11:A:59:TYR:CE2 1:A:110:LEU:HD22 0.62 2.26 2 1

Continued on next page...

Page 17: Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

Page 17 Full wwPDB NMR Structure Validation Report 2KKI

Continued from previous page...

Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total

1:A:59:TYR:CE2 1:A:69:THR:HB 0.62 2.30 9 11:A:32:ILE:HG22 1:A:42:ALA:HB2 0.61 1.72 12 51:A:109:LEU:HG 1:A:109:LEU:O 0.61 1.95 9 71:A:120:ASN:HB2 1:A:152:PHE:CD1 0.61 2.30 5 31:A:93:LYS:HD2 1:A:108:ASN:HB2 0.61 1.71 4 11:A:112:PHE:CE1 1:A:125:VAL:HG23 0.61 2.30 2 21:A:86:GLU:HG3 1:A:144:GLY:H 0.61 1.56 8 51:A:59:TYR:OH 1:A:110:LEU:HD23 0.61 1.96 14 21:A:133:ALA:HB2 1:A:148:SER:HB3 0.61 1.71 10 31:A:45:LEU:HD11 1:A:155:LEU:HD12 0.61 1.72 1 11:A:82:THR:HG22 1:A:108:ASN:CG 0.61 2.15 7 21:A:47:ASN:HB3 1:A:50:GLU:HB2 0.61 1.73 12 11:A:24:LEU:HG 1:A:152:PHE:HD2 0.60 1.54 6 61:A:24:LEU:HG 1:A:152:PHE:CD2 0.60 2.31 5 61:A:13:ASN:HB3 1:A:59:TYR:HB2 0.60 1.73 8 11:A:123:THR:HA 1:A:131:PHE:CB 0.60 2.23 9 11:A:79:LEU:HD21 1:A:92:LEU:HB3 0.60 1.72 8 11:A:80:TYR:OH 1:A:108:ASN:HB2 0.60 1.97 11 11:A:30:GLN:HG2 1:A:42:ALA:CB 0.60 2.26 11 21:A:18:ILE:HB 1:A:56:MET:O 0.60 1.97 4 111:A:28:LEU:CB 1:A:30:GLN:HE22 0.60 2.10 7 21:A:59:TYR:C 1:A:59:TYR:CD1 0.60 2.76 2 2

1:A:84:GLN:HG3 1:A:85:ASP:N 0.60 2.12 11 11:A:109:LEU:O 1:A:109:LEU:HG 0.59 1.95 11 41:A:20:TYR:HB3 1:A:55:ASP:OD1 0.59 1.97 11 51:A:28:LEU:CD1 1:A:149:ILE:HG13 0.59 2.26 8 11:A:80:TYR:CD2 1:A:109:LEU:HD13 0.59 2.32 11 11:A:25:ASN:OD1 1:A:153:GLN:HB2 0.59 1.97 10 11:A:22:PHE:HB2 1:A:154:ILE:HG13 0.59 1.74 7 11:A:30:GLN:HG2 1:A:42:ALA:HB1 0.59 1.72 7 21:A:135:LYS:HD3 1:A:138:TYR:HB2 0.59 1.73 9 11:A:23:ILE:HG21 1:A:48:LEU:O 0.59 1.97 1 61:A:13:ASN:HB2 1:A:59:TYR:HB2 0.59 1.72 6 21:A:24:LEU:HD13 1:A:54:PHE:CE1 0.59 2.32 1 11:A:20:TYR:HB2 1:A:55:ASP:OD1 0.59 1.98 1 21:A:18:ILE:HG22 1:A:19:LYS:HG3 0.59 1.74 7 21:A:133:ALA:CA 1:A:150:THR:HG22 0.59 2.28 9 51:A:31:SER:OG 1:A:45:LEU:HB2 0.58 1.98 9 2

1:A:102:ILE:HG13 1:A:106:GLU:HB2 0.58 1.74 9 11:A:71:ILE:HG21 1:A:98:ILE:HG23 0.58 1.75 11 11:A:32:ILE:HD13 1:A:140:VAL:HG21 0.58 1.73 6 1

Continued on next page...

Page 18: Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

Page 18 Full wwPDB NMR Structure Validation Report 2KKI

Continued from previous page...

Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total

1:A:28:LEU:HB3 1:A:30:GLN:HE22 0.58 1.58 7 21:A:28:LEU:CD2 1:A:149:ILE:HG13 0.58 2.28 12 71:A:45:LEU:HD12 1:A:50:GLU:HB3 0.58 1.76 12 11:A:80:TYR:CD2 1:A:95:MET:HB3 0.58 2.33 14 41:A:67:LYS:HB2 1:A:112:PHE:CD1 0.58 2.34 1 41:A:13:ASN:HB2 1:A:60:LYS:N 0.58 2.14 10 31:A:99:PRO:HG2 1:A:102:ILE:HG12 0.58 1.75 13 11:A:32:ILE:HB 1:A:40:LEU:CD2 0.57 2.28 3 41:A:122:PHE:HZ 1:A:152:PHE:HB3 0.57 1.59 9 11:A:112:PHE:HB2 1:A:123:THR:HB 0.57 1.76 10 21:A:32:ILE:HD11 1:A:40:LEU:HD23 0.57 1.74 5 31:A:121:TYR:HB3 1:A:131:PHE:CE1 0.57 2.34 3 51:A:119:LYS:HE3 1:A:121:TYR:CZ 0.57 2.34 10 11:A:23:ILE:HB 1:A:155:LEU:CB 0.57 2.29 10 21:A:80:TYR:O 1:A:93:LYS:HG3 0.57 2.00 1 11:A:48:LEU:CB 1:A:157:ASN:HA 0.57 2.29 7 31:A:13:ASN:ND2 1:A:102:ILE:HB 0.57 2.13 9 21:A:102:ILE:CG2 1:A:106:GLU:HB2 0.57 2.25 1 21:A:80:TYR:HD2 1:A:109:LEU:HD22 0.57 1.59 9 31:A:136:GLN:HA 1:A:136:GLN:OE1 0.57 1.98 3 11:A:22:PHE:HB2 1:A:154:ILE:HG23 0.57 1.75 13 11:A:89:PRO:HA 1:A:141:CYS:CA 0.57 2.27 12 21:A:80:TYR:HB3 1:A:109:LEU:HD13 0.57 1.74 7 51:A:18:ILE:HD11 1:A:58:ALA:HB2 0.57 1.75 11 51:A:82:THR:HG21 1:A:91:LEU:HB2 0.57 1.77 11 101:A:81:VAL:H 1:A:109:LEU:HD13 0.57 1.59 5 3

1:A:109:LEU:HD12 1:A:111:PHE:CE2 0.57 2.35 5 31:A:133:ALA:HA 1:A:150:THR:HG22 0.57 1.75 9 41:A:86:GLU:HG2 1:A:87:ASP:N 0.57 2.15 1 61:A:130:LEU:HG 1:A:142:LEU:HD21 0.57 1.76 2 71:A:60:LYS:HE2 1:A:68:ILE:HD12 0.57 1.74 10 11:A:79:LEU:HD11 1:A:92:LEU:HB3 0.57 1.76 10 21:A:28:LEU:HB3 1:A:136:GLN:HE21 0.56 1.59 5 51:A:57:GLY:H 1:A:71:ILE:HG22 0.56 1.59 14 1

1:A:26:ASP:OD1 1:A:30:GLN:HG2 0.56 2.00 12 11:A:80:TYR:HD1 1:A:93:LYS:HB3 0.56 1.57 11 11:A:107:THR:O 1:A:110:LEU:HG 0.56 2.01 2 101:A:13:ASN:CG 1:A:59:TYR:HB2 0.56 2.21 6 11:A:48:LEU:HB3 1:A:157:ASN:HA 0.56 1.76 12 11:A:111:PHE:CE2 1:A:132:ILE:HG13 0.56 2.36 13 11:A:28:LEU:HD21 1:A:149:ILE:HG12 0.56 1.78 4 2

Continued on next page...

Page 19: Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

Page 19 Full wwPDB NMR Structure Validation Report 2KKI

Continued from previous page...

Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total

1:A:59:TYR:HD2 1:A:71:ILE:HD13 0.56 1.60 11 21:A:81:VAL:HG13 1:A:90:VAL:HG11 0.56 1.76 8 31:A:28:LEU:HD13 1:A:136:GLN:CG 0.56 2.30 4 11:A:13:ASN:HD22 1:A:102:ILE:HB 0.56 1.60 13 11:A:131:PHE:CE1 1:A:150:THR:CG2 0.56 2.84 9 11:A:102:ILE:HD12 1:A:110:LEU:HD21 0.56 1.76 10 21:A:25:ASN:O 1:A:153:GLN:HG2 0.56 2.01 11 41:A:31:SER:OG 1:A:45:LEU:HB3 0.55 2.01 6 11:A:119:LYS:HA 1:A:153:GLN:HG2 0.55 1.77 10 21:A:127:HIS:HB3 1:A:130:LEU:HD13 0.55 1.77 11 11:A:132:ILE:HG22 1:A:152:PHE:HE2 0.55 1.61 1 31:A:99:PRO:HB2 1:A:102:ILE:HG12 0.55 1.76 1 11:A:23:ILE:CD1 1:A:49:ASP:HA 0.55 2.31 3 81:A:49:ASP:HB2 1:A:157:ASN:CB 0.55 2.31 14 31:A:80:TYR:CE2 1:A:109:LEU:HD22 0.55 2.37 11 11:A:30:GLN:HB3 1:A:42:ALA:HB1 0.55 1.78 9 31:A:13:ASN:HA 1:A:60:LYS:O 0.55 2.02 9 31:A:67:LYS:HB3 1:A:112:PHE:CE1 0.55 2.36 2 21:A:20:TYR:HD2 1:A:56:MET:N 0.55 1.99 14 1

1:A:115:THR:HG22 1:A:120:ASN:OD1 0.55 2.02 11 11:A:121:TYR:HB3 1:A:131:PHE:CZ 0.55 2.37 3 51:A:31:SER:HB3 1:A:51:ALA:CB 0.55 2.27 6 11:A:45:LEU:HD21 1:A:48:LEU:HA 0.55 1.79 12 11:A:34:ARG:HA 1:A:40:LEU:CD1 0.55 2.32 7 81:A:30:GLN:HA 1:A:44:ALA:HA 0.55 1.78 11 51:A:49:ASP:CB 1:A:157:ASN:HB2 0.55 2.32 9 31:A:122:PHE:CZ 1:A:152:PHE:HB3 0.54 2.37 9 11:A:68:ILE:H 1:A:68:ILE:HD13 0.54 1.61 4 1

1:A:79:LEU:HD13 1:A:92:LEU:HD13 0.54 1.79 5 21:A:13:ASN:HB2 1:A:100:LYS:O 0.54 2.02 1 11:A:23:ILE:HG12 1:A:49:ASP:HA 0.54 1.78 8 11:A:81:VAL:HB 1:A:109:LEU:CD1 0.54 2.31 14 21:A:19:LYS:HB3 1:A:22:PHE:CE2 0.54 2.37 5 31:A:69:THR:HG23 1:A:110:LEU:HA 0.54 1.79 14 21:A:13:ASN:N 1:A:101:THR:HA 0.54 2.18 12 5

1:A:123:THR:HG22 1:A:128:PRO:HA 0.54 1.79 2 51:A:32:ILE:HG13 1:A:32:ILE:O 0.54 2.03 1 51:A:82:THR:CA 1:A:108:ASN:HB3 0.54 2.32 1 41:A:37:ASP:HA 1:A:79:LEU:HD21 0.54 1.78 2 11:A:13:ASN:HB3 1:A:60:LYS:O 0.54 2.03 3 11:A:83:ALA:CB 1:A:130:LEU:HD23 0.54 2.32 2 3

Continued on next page...

Page 20: Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

Page 20 Full wwPDB NMR Structure Validation Report 2KKI

Continued from previous page...

Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total

1:A:28:LEU:HD12 1:A:136:GLN:NE2 0.54 2.17 8 11:A:28:LEU:HB3 1:A:136:GLN:OE1 0.54 2.02 3 11:A:30:GLN:HG3 1:A:136:GLN:CB 0.54 2.33 6 11:A:110:LEU:HB3 1:A:125:VAL:HG12 0.54 1.79 10 21:A:71:ILE:HG21 1:A:98:ILE:HD12 0.54 1.80 11 11:A:28:LEU:HG 1:A:149:ILE:HG13 0.54 1.80 5 11:A:24:LEU:HD23 1:A:32:ILE:HD11 0.53 1.80 12 11:A:127:HIS:O 1:A:130:LEU:HG 0.53 2.04 6 1

1:A:20:TYR:CE2 1:A:56:MET:HG3 0.53 2.38 14 11:A:25:ASN:OD1 1:A:45:LEU:HD22 0.53 2.03 1 11:A:27:ALA:H 1:A:151:ASP:CB 0.53 2.15 10 6

1:A:30:GLN:OE1 1:A:136:GLN:HG2 0.53 2.04 2 11:A:23:ILE:HD13 1:A:53:LYS:HG2 0.53 1.80 3 61:A:25:ASN:HD21 1:A:45:LEU:HD12 0.53 1.64 6 11:A:28:LEU:HD11 1:A:149:ILE:CD1 0.53 2.33 10 11:A:34:ARG:HB3 1:A:52:VAL:HG11 0.52 1.81 3 11:A:45:LEU:HG 1:A:48:LEU:O 0.52 2.05 14 31:A:115:THR:HA 1:A:120:ASN:HD22 0.52 1.64 14 11:A:32:ILE:O 1:A:32:ILE:HG13 0.52 2.05 3 11:A:45:LEU:H 1:A:45:LEU:CD1 0.52 2.17 10 1

1:A:16:ARG:HD2 1:A:58:ALA:HB3 0.52 1.81 5 31:A:59:TYR:HE2 1:A:71:ILE:HG12 0.52 1.64 5 11:A:26:ASP:OD1 1:A:26:ASP:N 0.52 2.42 8 11:A:80:TYR:CE2 1:A:109:LEU:CB 0.52 2.93 5 11:A:69:THR:HG21 1:A:110:LEU:HD22 0.52 1.80 8 11:A:110:LEU:CB 1:A:125:VAL:HG12 0.52 2.35 2 11:A:71:ILE:CD1 1:A:98:ILE:HG23 0.52 2.35 7 11:A:30:GLN:HE21 1:A:136:GLN:N 0.52 2.02 8 11:A:30:GLN:HB2 1:A:43:ALA:CA 0.52 2.35 7 11:A:45:LEU:CD1 1:A:50:GLU:HB3 0.52 2.33 12 51:A:45:LEU:CD2 1:A:48:LEU:HA 0.52 2.35 12 11:A:135:LYS:HG2 1:A:138:TYR:HB2 0.52 1.81 10 21:A:45:LEU:HD21 1:A:48:LEU:O 0.52 2.06 12 11:A:48:LEU:HD13 1:A:156:GLU:O 0.51 2.05 7 61:A:89:PRO:CA 1:A:141:CYS:HA 0.51 2.32 3 11:A:49:ASP:HB3 1:A:157:ASN:OD1 0.51 2.05 13 4

1:A:109:LEU:HD12 1:A:111:PHE:HE2 0.51 1.65 2 21:A:27:ALA:N 1:A:151:ASP:HB2 0.51 2.21 10 1

1:A:80:TYR:CE1 1:A:93:LYS:HB3 0.51 2.40 10 21:A:70:VAL:HB 1:A:111:PHE:CE1 0.51 2.40 4 1

1:A:28:LEU:HD12 1:A:136:GLN:CD 0.51 2.25 8 1Continued on next page...

Page 21: Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

Page 21 Full wwPDB NMR Structure Validation Report 2KKI

Continued from previous page...

Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total

1:A:30:GLN:HE21 1:A:136:GLN:CA 0.51 2.19 8 11:A:18:ILE:HG22 1:A:19:LYS:H 0.51 1.64 14 11:A:71:ILE:HD12 1:A:98:ILE:HG23 0.51 1.83 7 11:A:26:ASP:CB 1:A:134:THR:HB 0.51 2.35 5 2

1:A:81:VAL:HG13 1:A:90:VAL:CG1 0.51 2.35 14 21:A:81:VAL:HG13 1:A:90:VAL:CG2 0.51 2.36 9 11:A:18:ILE:HG13 1:A:57:GLY:HA2 0.51 1.82 14 31:A:68:ILE:HD13 1:A:68:ILE:H 0.51 1.66 11 11:A:80:TYR:HE2 1:A:109:LEU:HD22 0.51 1.64 11 11:A:15:MET:HB3 1:A:58:ALA:C 0.50 2.26 12 31:A:120:ASN:HB2 1:A:152:PHE:HD1 0.50 1.66 5 11:A:23:ILE:HG13 1:A:48:LEU:O 0.50 2.07 12 11:A:26:ASP:HB3 1:A:134:THR:CB 0.50 2.36 5 31:A:79:LEU:HD11 1:A:92:LEU:HD22 0.50 1.83 8 11:A:158:GLN:HA 1:A:158:GLN:HE21 0.50 1.67 11 11:A:82:THR:HG22 1:A:91:LEU:O 0.50 2.06 10 61:A:45:LEU:HG 1:A:155:LEU:CD1 0.50 2.34 2 21:A:74:ILE:HG22 1:A:76:LYS:H 0.50 1.67 4 1

1:A:107:THR:HG23 1:A:110:LEU:HD11 0.50 1.82 8 11:A:80:TYR:CB 1:A:93:LYS:HE2 0.50 2.36 1 11:A:48:LEU:HD12 1:A:156:GLU:O 0.50 2.06 13 11:A:24:LEU:HD22 1:A:32:ILE:CG2 0.50 2.36 13 41:A:82:THR:OG1 1:A:91:LEU:HB2 0.50 2.07 6 41:A:131:PHE:O 1:A:142:LEU:HD12 0.50 2.06 6 13

1:A:45:LEU:HD11 1:A:48:LEU:O 0.50 2.07 12 11:A:28:LEU:CG 1:A:149:ILE:HG13 0.50 2.36 5 71:A:13:ASN:N 1:A:102:ILE:H 0.50 2.05 12 21:A:70:VAL:HB 1:A:111:PHE:CZ 0.50 2.42 4 11:A:86:GLU:CG 1:A:87:ASP:H 0.50 2.17 5 41:A:30:GLN:HB2 1:A:43:ALA:N 0.50 2.22 13 11:A:22:PHE:HZ 1:A:56:MET:HG3 0.49 1.66 7 11:A:42:ALA:HB3 1:A:135:LYS:O 0.49 2.07 8 61:A:70:VAL:HG22 1:A:111:PHE:CE2 0.49 2.41 9 11:A:28:LEU:HB2 1:A:30:GLN:OE1 0.49 2.07 8 21:A:59:TYR:C 1:A:59:TYR:HD1 0.49 2.10 2 1

1:A:49:ASP:HB2 1:A:157:ASN:HB3 0.49 1.84 7 11:A:131:PHE:HE1 1:A:150:THR:HG21 0.49 1.63 9 11:A:78:GLN:NE2 1:A:78:GLN:H 0.49 2.05 12 11:A:131:PHE:CB 1:A:144:GLY:HA2 0.49 2.37 3 11:A:112:PHE:CD2 1:A:123:THR:HB 0.49 2.43 2 21:A:15:MET:HB2 1:A:59:TYR:C 0.49 2.27 7 1

Continued on next page...

Page 22: Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

Page 22 Full wwPDB NMR Structure Validation Report 2KKI

Continued from previous page...

Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total

1:A:111:PHE:CE1 1:A:132:ILE:HG13 0.49 2.43 10 11:A:132:ILE:HG22 1:A:152:PHE:HZ 0.49 1.68 4 11:A:25:ASN:HD21 1:A:45:LEU:HD13 0.49 1.66 1 11:A:48:LEU:HD22 1:A:155:LEU:HD13 0.49 1.84 11 11:A:135:LYS:HE2 1:A:141:CYS:HB3 0.49 1.85 3 11:A:28:LEU:CD2 1:A:149:ILE:HG12 0.49 2.38 4 41:A:74:ILE:HD13 1:A:74:ILE:H 0.49 1.66 6 21:A:131:PHE:O 1:A:142:LEU:HA 0.49 2.07 2 41:A:33:ILE:HG22 1:A:51:ALA:CA 0.49 2.30 9 11:A:81:VAL:HG11 1:A:111:PHE:HZ 0.49 1.68 8 11:A:34:ARG:HG3 1:A:52:VAL:HG11 0.49 1.84 8 11:A:129:ASN:CA 1:A:144:GLY:HA2 0.49 2.38 13 31:A:29:ASN:HD22 1:A:29:ASN:N 0.49 2.06 7 11:A:89:PRO:HB3 1:A:139:TRP:CD1 0.49 2.42 1 11:A:14:PHE:HB3 1:A:100:LYS:CA 0.49 2.36 3 11:A:13:ASN:H 1:A:101:THR:CA 0.49 2.20 6 21:A:13:ASN:O 1:A:59:TYR:HB3 0.49 2.07 5 2

1:A:102:ILE:HG23 1:A:106:GLU:CB 0.49 2.32 1 11:A:109:LEU:HD12 1:A:111:PHE:HE1 0.49 1.66 13 1

1:A:37:ASP:O 1:A:92:LEU:HD11 0.49 2.07 13 11:A:33:ILE:HG23 1:A:51:ALA:HA 0.49 1.85 13 11:A:15:MET:HG2 1:A:60:LYS:CG 0.48 2.38 7 11:A:45:LEU:HD21 1:A:50:GLU:HB3 0.48 1.85 3 21:A:74:ILE:HG12 1:A:76:LYS:H 0.48 1.68 3 11:A:69:THR:OG1 1:A:110:LEU:HA 0.48 2.09 6 41:A:80:TYR:C 1:A:80:TYR:CD1 0.48 2.86 12 2

1:A:149:ILE:HD12 1:A:149:ILE:N 0.48 2.24 10 21:A:74:ILE:HG13 1:A:76:LYS:H 0.48 1.68 13 11:A:120:ASN:HB2 1:A:152:PHE:CE1 0.48 2.44 12 21:A:82:THR:HG23 1:A:93:LYS:CB 0.48 2.39 7 41:A:71:ILE:HG13 1:A:109:LEU:CD2 0.48 2.38 10 31:A:71:ILE:CG2 1:A:109:LEU:HD21 0.48 2.28 6 41:A:13:ASN:O 1:A:13:ASN:ND2 0.48 2.47 6 3

1:A:25:ASN:ND2 1:A:45:LEU:HD12 0.48 2.24 6 11:A:69:THR:HG23 1:A:111:PHE:H 0.48 1.69 2 11:A:71:ILE:HD11 1:A:99:PRO:HD2 0.48 1.86 7 11:A:69:THR:OG1 1:A:125:VAL:HG11 0.48 2.09 2 11:A:133:ALA:HB1 1:A:148:SER:CB 0.47 2.37 5 21:A:80:TYR:HE1 1:A:108:ASN:HB2 0.47 1.64 11 11:A:85:ASP:HA 1:A:130:LEU:CD2 0.47 2.34 6 21:A:26:ASP:OD1 1:A:30:GLN:N 0.47 2.44 6 3

Continued on next page...

Page 23: Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

Page 23 Full wwPDB NMR Structure Validation Report 2KKI

Continued from previous page...

Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total

1:A:69:THR:HA 1:A:111:PHE:O 0.47 2.09 10 11:A:48:LEU:HB3 1:A:156:GLU:O 0.47 2.09 12 21:A:103:THR:O 1:A:105:SER:N 0.47 2.46 3 41:A:24:LEU:HB3 1:A:32:ILE:HG22 0.47 1.85 4 31:A:59:TYR:CD1 1:A:102:ILE:HD12 0.47 2.43 1 11:A:93:LYS:NZ 1:A:109:LEU:HB2 0.47 2.24 1 11:A:23:ILE:HG13 1:A:49:ASP:HA 0.47 1.86 2 11:A:72:LEU:HD23 1:A:81:VAL:HG21 0.47 1.86 1 41:A:13:ASN:CG 1:A:102:ILE:HB 0.47 2.30 11 31:A:102:ILE:CD1 1:A:110:LEU:HD21 0.47 2.39 7 11:A:93:LYS:HG3 1:A:93:LYS:O 0.47 2.09 7 11:A:30:GLN:CD 1:A:136:GLN:HA 0.47 2.30 13 21:A:13:ASN:HB2 1:A:60:LYS:H 0.47 1.69 6 11:A:30:GLN:HG3 1:A:136:GLN:HB3 0.47 1.86 6 11:A:18:ILE:HG22 1:A:19:LYS:N 0.47 2.24 14 31:A:25:ASN:ND2 1:A:45:LEU:HD13 0.47 2.24 1 11:A:82:THR:HG22 1:A:108:ASN:ND2 0.47 2.25 1 11:A:92:LEU:HD12 1:A:92:LEU:O 0.47 2.08 13 11:A:131:PHE:HE1 1:A:150:THR:CB 0.47 2.23 9 11:A:131:PHE:HE1 1:A:150:THR:CG2 0.47 2.21 9 11:A:13:ASN:HB3 1:A:102:ILE:HG22 0.47 1.87 9 11:A:149:ILE:N 1:A:149:ILE:HD12 0.47 2.25 9 21:A:45:LEU:H 1:A:45:LEU:HD13 0.47 1.70 10 1

1:A:107:THR:HA 1:A:110:LEU:HD21 0.47 1.87 2 11:A:112:PHE:CD1 1:A:125:VAL:HG23 0.47 2.44 2 11:A:30:GLN:HG3 1:A:43:ALA:HA 0.47 1.87 9 11:A:13:ASN:HB2 1:A:59:TYR:CB 0.47 2.40 6 11:A:124:SER:HB2 1:A:127:HIS:O 0.47 2.10 2 21:A:45:LEU:HD12 1:A:48:LEU:N 0.46 2.25 3 21:A:149:ILE:HG22 1:A:151:ASP:OD2 0.46 2.10 10 11:A:53:LYS:HG3 1:A:75:SER:OG 0.46 2.10 8 11:A:122:PHE:O 1:A:131:PHE:HB2 0.46 2.10 9 1

1:A:110:LEU:HD21 1:A:126:ALA:HB2 0.46 1.87 1 31:A:30:GLN:HB2 1:A:42:ALA:HB1 0.46 1.87 12 21:A:111:PHE:CD2 1:A:132:ILE:HG13 0.46 2.45 13 11:A:64:ASP:HB3 1:A:67:LYS:O 0.46 2.11 2 21:A:45:LEU:HD12 1:A:48:LEU:CA 0.46 2.30 1 11:A:82:THR:HA 1:A:108:ASN:CB 0.46 2.40 14 31:A:136:GLN:N 1:A:136:GLN:NE2 0.46 2.61 8 11:A:95:MET:HG2 1:A:106:GLU:HG3 0.46 1.86 8 11:A:80:TYR:HB2 1:A:93:LYS:O 0.46 2.10 14 2

Continued on next page...

Page 24: Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

Page 24 Full wwPDB NMR Structure Validation Report 2KKI

Continued from previous page...

Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total

1:A:109:LEU:O 1:A:109:LEU:CG 0.46 2.62 11 11:A:73:ARG:HD3 1:A:98:ILE:HD11 0.46 1.86 11 11:A:26:ASP:HB3 1:A:151:ASP:O 0.46 2.11 7 41:A:94:GLU:O 1:A:94:GLU:HG2 0.46 2.11 3 1

1:A:24:LEU:HD22 1:A:32:ILE:HG12 0.46 1.87 10 11:A:115:THR:HA 1:A:120:ASN:ND2 0.46 2.26 14 11:A:19:LYS:HE3 1:A:22:PHE:CE2 0.46 2.46 1 21:A:100:LYS:HD3 1:A:100:LYS:N 0.46 2.21 5 11:A:28:LEU:HD23 1:A:28:LEU:N 0.46 2.26 8 11:A:19:LYS:HE2 1:A:154:ILE:HD12 0.46 1.87 1 11:A:80:TYR:C 1:A:80:TYR:HD1 0.46 2.15 12 1

1:A:59:TYR:CE2 1:A:69:THR:CB 0.46 2.99 9 11:A:112:PHE:O 1:A:122:PHE:HA 0.46 2.10 1 11:A:24:LEU:HG 1:A:152:PHE:CD1 0.46 2.46 1 11:A:93:LYS:HD2 1:A:108:ASN:CB 0.45 2.41 4 11:A:33:ILE:HG12 1:A:51:ALA:CA 0.45 2.40 8 11:A:58:ALA:HB2 1:A:70:VAL:HG12 0.45 1.87 8 11:A:120:ASN:HB3 1:A:152:PHE:HD1 0.45 1.70 2 11:A:45:LEU:HD23 1:A:155:LEU:HD12 0.45 1.87 12 11:A:25:ASN:HD21 1:A:29:ASN:HA 0.45 1.69 11 11:A:131:PHE:HD1 1:A:132:ILE:N 0.45 2.09 10 11:A:59:TYR:CZ 1:A:69:THR:HG21 0.45 2.46 4 1

1:A:111:PHE:CD1 1:A:132:ILE:HG13 0.45 2.46 3 11:A:52:VAL:HG23 1:A:54:PHE:CE1 0.45 2.46 8 11:A:45:LEU:CD1 1:A:155:LEU:HD12 0.45 2.41 1 11:A:93:LYS:HZ1 1:A:109:LEU:HB2 0.45 1.70 7 11:A:72:LEU:HD22 1:A:81:VAL:HG23 0.45 1.87 4 11:A:99:PRO:HB2 1:A:102:ILE:CG1 0.45 2.42 1 11:A:49:ASP:OD1 1:A:157:ASN:HB2 0.45 2.12 12 11:A:86:GLU:HA 1:A:143:ALA:HA 0.45 1.88 7 31:A:127:HIS:HB2 1:A:130:LEU:HD22 0.45 1.88 3 31:A:20:TYR:HB3 1:A:55:ASP:HB3 0.45 1.87 3 11:A:121:TYR:HA 1:A:150:THR:O 0.45 2.11 9 21:A:19:LYS:HB3 1:A:22:PHE:HE2 0.45 1.69 5 31:A:57:GLY:N 1:A:71:ILE:HG13 0.45 2.23 13 1

1:A:32:ILE:HD11 1:A:40:LEU:HB3 0.45 1.87 9 11:A:80:TYR:HD2 1:A:109:LEU:CD2 0.45 2.25 2 21:A:111:PHE:HB2 1:A:122:PHE:HB3 0.45 1.88 4 11:A:25:ASN:O 1:A:153:GLN:N 0.45 2.49 7 5

1:A:15:MET:HB3 1:A:58:ALA:HB3 0.45 1.89 7 11:A:120:ASN:HB3 1:A:152:PHE:CE1 0.45 2.47 9 4

Continued on next page...

Page 25: Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

Page 25 Full wwPDB NMR Structure Validation Report 2KKI

Continued from previous page...

Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total

1:A:15:MET:HB2 1:A:60:LYS:HB2 0.45 1.88 1 11:A:79:LEU:HD11 1:A:92:LEU:CB 0.45 2.41 10 11:A:72:LEU:O 1:A:109:LEU:HD11 0.45 2.13 5 21:A:13:ASN:CB 1:A:60:LYS:O 0.44 2.65 3 11:A:13:ASN:H 1:A:101:THR:HA 0.44 1.72 8 2

1:A:59:TYR:CE2 1:A:71:ILE:HG12 0.44 2.47 5 11:A:78:GLN:CB 1:A:96:PRO:HA 0.44 2.39 8 11:A:32:ILE:HG23 1:A:54:PHE:HE1 0.44 1.70 13 11:A:33:ILE:O 1:A:40:LEU:HG 0.44 2.13 14 4

1:A:115:THR:HA 1:A:120:ASN:OD1 0.44 2.12 5 11:A:86:GLU:O 1:A:88:GLN:N 0.44 2.50 3 91:A:93:LYS:O 1:A:93:LYS:HG3 0.44 2.13 6 2

1:A:30:GLN:OE1 1:A:134:THR:HG22 0.44 2.12 11 11:A:71:ILE:CD1 1:A:99:PRO:HD2 0.44 2.41 7 21:A:16:ARG:HD3 1:A:16:ARG:O 0.44 2.13 5 11:A:136:GLN:H 1:A:136:GLN:CD 0.44 2.14 8 11:A:32:ILE:HD13 1:A:152:PHE:CE1 0.44 2.47 8 11:A:109:LEU:HD12 1:A:111:PHE:CD2 0.44 2.47 14 11:A:33:ILE:HG12 1:A:51:ALA:CB 0.44 2.42 7 21:A:132:ILE:HG22 1:A:152:PHE:CE2 0.44 2.45 1 21:A:32:ILE:HD13 1:A:140:VAL:CG2 0.44 2.40 6 11:A:32:ILE:CD1 1:A:40:LEU:HD23 0.44 2.42 5 11:A:94:GLU:O 1:A:94:GLU:HG3 0.44 2.13 1 1

1:A:112:PHE:HB3 1:A:123:THR:HB 0.44 1.90 7 21:A:26:ASP:N 1:A:26:ASP:OD1 0.44 2.45 11 2

1:A:111:PHE:CE1 1:A:132:ILE:HG12 0.44 2.48 14 11:A:23:ILE:HB 1:A:155:LEU:O 0.44 2.13 7 1

1:A:45:LEU:HD23 1:A:48:LEU:HA 0.44 1.88 6 31:A:74:ILE:HD11 1:A:79:LEU:HB2 0.44 1.90 1 11:A:20:TYR:CG 1:A:55:ASP:HA 0.44 2.43 14 11:A:80:TYR:CB 1:A:93:LYS:HE3 0.44 2.43 7 11:A:26:ASP:HA 1:A:151:ASP:O 0.44 2.12 9 21:A:98:ILE:O 1:A:98:ILE:HD12 0.44 2.12 10 1

1:A:28:LEU:HG 1:A:149:ILE:CG1 0.44 2.42 5 11:A:109:LEU:HD12 1:A:111:PHE:CE1 0.44 2.47 13 11:A:102:ILE:CD1 1:A:106:GLU:HB3 0.44 2.43 6 11:A:23:ILE:CG1 1:A:49:ASP:HA 0.44 2.43 8 11:A:57:GLY:N 1:A:71:ILE:HG22 0.44 2.27 14 11:A:59:TYR:OH 1:A:71:ILE:HD11 0.43 2.13 7 11:A:30:GLN:NE2 1:A:136:GLN:HE21 0.43 2.11 11 21:A:111:PHE:CE1 1:A:132:ILE:HD11 0.43 2.47 6 1

Continued on next page...

Page 26: Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

Page 26 Full wwPDB NMR Structure Validation Report 2KKI

Continued from previous page...

Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total

1:A:33:ILE:HA 1:A:52:VAL:HG22 0.43 1.89 12 11:A:26:ASP:CB 1:A:134:THR:OG1 0.43 2.66 13 21:A:15:MET:HB3 1:A:58:ALA:CB 0.43 2.43 7 11:A:80:TYR:CD1 1:A:80:TYR:C 0.43 2.91 10 11:A:30:GLN:NE2 1:A:136:GLN:NE2 0.43 2.67 7 11:A:15:MET:HG2 1:A:60:LYS:CB 0.43 2.43 7 11:A:139:TRP:CD1 1:A:140:VAL:N 0.43 2.86 3 11:A:25:ASN:HB2 1:A:155:LEU:CD1 0.43 2.44 2 11:A:30:GLN:HB2 1:A:44:ALA:N 0.43 2.28 11 11:A:13:ASN:CG 1:A:60:LYS:HB3 0.43 2.34 3 1

1:A:131:PHE:HD1 1:A:132:ILE:H 0.43 1.54 10 11:A:119:LYS:CA 1:A:152:PHE:O 0.43 2.65 5 11:A:13:ASN:HA 1:A:100:LYS:O 0.43 2.13 2 21:A:80:TYR:OH 1:A:97:GLU:O 0.43 2.37 14 11:A:45:LEU:HD22 1:A:45:LEU:C 0.43 2.33 2 11:A:32:ILE:HD13 1:A:140:VAL:HG23 0.43 1.90 11 11:A:80:TYR:HB2 1:A:109:LEU:HD13 0.43 1.91 10 11:A:124:SER:HB3 1:A:130:LEU:HB2 0.43 1.91 7 21:A:95:MET:SD 1:A:96:PRO:HD2 0.43 2.54 12 21:A:110:LEU:HB3 1:A:125:VAL:CG1 0.43 2.43 10 21:A:56:MET:HG2 1:A:71:ILE:O 0.43 2.14 14 11:A:54:PHE:CA 1:A:73:ARG:O 0.43 2.66 14 11:A:15:MET:HB2 1:A:59:TYR:CA 0.43 2.43 11 11:A:15:MET:SD 1:A:16:ARG:HD2 0.42 2.54 7 11:A:135:LYS:HE2 1:A:141:CYS:CB 0.42 2.43 3 11:A:28:LEU:HB3 1:A:136:GLN:CD 0.42 2.35 3 11:A:28:LEU:HG 1:A:149:ILE:CG2 0.42 2.38 8 11:A:74:ILE:HD11 1:A:77:THR:OG1 0.42 2.14 8 11:A:86:GLU:CD 1:A:144:GLY:H 0.42 2.18 4 11:A:141:CYS:SG 1:A:142:LEU:N 0.42 2.91 10 41:A:82:THR:O 1:A:90:VAL:HG23 0.42 2.15 9 11:A:134:THR:O 1:A:149:ILE:HB 0.42 2.14 8 11:A:73:ARG:HG3 1:A:73:ARG:O 0.42 2.14 8 11:A:90:VAL:HG12 1:A:142:LEU:HD13 0.42 1.90 2 11:A:69:THR:HG22 1:A:110:LEU:HB2 0.42 1.89 9 11:A:34:ARG:HA 1:A:40:LEU:HD12 0.42 1.92 4 11:A:13:ASN:O 1:A:59:TYR:HB2 0.42 2.14 14 11:A:102:ILE:O 1:A:102:ILE:HG23 0.42 2.14 11 3

1:A:73:ARG:HB2 1:A:80:TYR:CE1 0.42 2.50 4 11:A:13:ASN:HB3 1:A:60:LYS:H 0.42 1.75 8 11:A:34:ARG:HG2 1:A:40:LEU:HD12 0.42 1.92 8 1

Continued on next page...

Page 27: Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

Page 27 Full wwPDB NMR Structure Validation Report 2KKI

Continued from previous page...

Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total

1:A:131:PHE:HB3 1:A:144:GLY:HA2 0.42 1.90 3 11:A:30:GLN:NE2 1:A:44:ALA:HB2 0.42 2.30 10 11:A:30:GLN:HE21 1:A:136:GLN:HA 0.42 1.74 8 11:A:123:THR:HA 1:A:131:PHE:HD1 0.42 1.74 4 11:A:120:ASN:N 1:A:152:PHE:O 0.42 2.53 10 1

1:A:77:THR:HG23 1:A:79:LEU:HG 0.42 1.91 5 11:A:23:ILE:HD13 1:A:155:LEU:O 0.42 2.15 8 11:A:56:MET:HE3 1:A:70:VAL:HG21 0.42 1.91 8 11:A:112:PHE:CE1 1:A:125:VAL:CG2 0.42 3.01 2 11:A:13:ASN:H 1:A:102:ILE:N 0.42 2.13 12 11:A:119:LYS:C 1:A:120:ASN:HD22 0.42 2.18 11 1

1:A:23:ILE:HD11 1:A:49:ASP:OD2 0.41 2.15 7 11:A:18:ILE:HB 1:A:56:MET:HG3 0.41 1.91 10 11:A:28:LEU:HG 1:A:149:ILE:HG12 0.41 1.92 3 11:A:86:GLU:CG 1:A:87:ASP:N 0.41 2.79 3 11:A:116:HIS:O 1:A:119:LYS:HG2 0.41 2.15 14 1

1:A:20:TYR:CD2 1:A:56:MET:N 0.41 2.86 14 11:A:74:ILE:HG13 1:A:77:THR:O 0.41 2.14 9 11:A:26:ASP:O 1:A:29:ASN:HA 0.41 2.15 10 1

1:A:55:ASP:OD2 1:A:73:ARG:HD3 0.41 2.16 4 11:A:34:ARG:HB2 1:A:52:VAL:HG11 0.41 1.91 7 11:A:80:TYR:HB3 1:A:93:LYS:HE2 0.41 1.90 1 11:A:102:ILE:HD11 1:A:106:GLU:HB2 0.41 1.92 3 11:A:110:LEU:C 1:A:111:PHE:HD1 0.41 2.18 8 11:A:20:TYR:CE1 1:A:22:PHE:HB2 0.41 2.51 14 11:A:26:ASP:CG 1:A:28:LEU:HB2 0.41 2.36 2 11:A:22:PHE:CB 1:A:154:ILE:HG23 0.41 2.43 13 11:A:23:ILE:N 1:A:23:ILE:HD12 0.41 2.31 8 1

1:A:13:ASN:HB2 1:A:102:ILE:CG1 0.41 2.40 12 11:A:80:TYR:CE2 1:A:109:LEU:HB3 0.41 2.51 11 11:A:64:ASP:HB3 1:A:125:VAL:HG11 0.41 1.91 9 11:A:28:LEU:HG 1:A:149:ILE:CB 0.41 2.46 5 11:A:135:LYS:HG2 1:A:138:TYR:HB3 0.41 1.92 8 11:A:70:VAL:HG22 1:A:111:PHE:O 0.41 2.16 7 11:A:30:GLN:HG3 1:A:136:GLN:OE1 0.41 2.16 3 1

1:A:150:THR:HG22 1:A:150:THR:O 0.41 2.15 4 11:A:78:GLN:O 1:A:78:GLN:HG2 0.41 2.16 5 1

1:A:24:LEU:HD13 1:A:54:PHE:CD1 0.41 2.51 1 11:A:59:TYR:CE2 1:A:69:THR:CG2 0.41 3.03 2 11:A:67:LYS:HD2 1:A:125:VAL:HA 0.41 1.92 11 11:A:131:PHE:CB 1:A:143:ALA:O 0.41 2.69 11 1

Continued on next page...

Page 28: Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

Page 28 Full wwPDB NMR Structure Validation Report 2KKI

Continued from previous page...

Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total

1:A:30:GLN:HE21 1:A:136:GLN:NE2 0.41 2.13 7 11:A:119:LYS:HD2 1:A:151:ASP:OD1 0.41 2.15 6 11:A:15:MET:HG3 1:A:16:ARG:CD 0.41 2.37 8 11:A:47:ASN:HB3 1:A:50:GLU:HG3 0.41 1.91 1 1

1:A:110:LEU:HD12 1:A:126:ALA:HB2 0.41 1.93 2 11:A:82:THR:HG22 1:A:91:LEU:H 0.41 1.76 2 11:A:30:GLN:HA 1:A:44:ALA:CA 0.41 2.45 11 11:A:133:ALA:HB3 1:A:141:CYS:O 0.41 2.16 7 11:A:53:LYS:O 1:A:74:ILE:HA 0.41 2.15 3 1

1:A:74:ILE:CD1 1:A:79:LEU:HB2 0.41 2.46 6 11:A:32:ILE:HG22 1:A:42:ALA:CB 0.41 2.45 10 21:A:32:ILE:HD11 1:A:54:PHE:CE1 0.41 2.50 8 11:A:15:MET:HG2 1:A:60:LYS:HG2 0.40 1.92 7 11:A:13:ASN:HB3 1:A:102:ILE:CG2 0.40 2.46 6 11:A:119:LYS:HB2 1:A:151:ASP:HB3 0.40 1.93 10 11:A:26:ASP:OD1 1:A:29:ASN:N 0.40 2.54 4 11:A:25:ASN:HB3 1:A:153:GLN:HG3 0.40 1.93 5 11:A:15:MET:SD 1:A:60:LYS:HD2 0.40 2.56 14 11:A:67:LYS:HE2 1:A:128:PRO:HG3 0.40 1.92 13 11:A:80:TYR:HB3 1:A:93:LYS:HE3 0.40 1.92 7 11:A:57:GLY:O 1:A:71:ILE:HG12 0.40 2.16 8 1

1:A:23:ILE:HD11 1:A:49:ASP:HA 0.40 1.92 3 11:A:16:ARG:NH1 1:A:18:ILE:HA 0.40 2.31 10 11:A:18:ILE:HG12 1:A:57:GLY:HA2 0.40 1.93 4 11:A:28:LEU:HB3 1:A:30:GLN:OE1 0.40 2.16 12 11:A:84:GLN:OE1 1:A:88:GLN:HB3 0.40 2.16 7 11:A:98:ILE:HD12 1:A:99:PRO:HD2 0.40 1.93 6 11:A:69:THR:CG2 1:A:110:LEU:HA 0.40 2.46 8 11:A:69:THR:HG21 1:A:110:LEU:CD2 0.40 2.47 8 1

6.3 Torsion angles i○

6.3.1 Protein backbone i○

In the following table, the Percentiles column shows the percent Ramachandran outliers of the chainas a percentile score with respect to all PDB entries followed by that with respect to all NMRentries. The Analysed column shows the number of residues for which the backbone conformationwas analysed and the total number of residues.

Mol Chain Analysed Favoured Allowed Outliers Percentiles

1 A 143/151 (95%) 124±1 (86±1%) 16±1 (11±1%) 4±0 (3±0%) 10 46Continued on next page...

Page 29: Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

Page 29 Full wwPDB NMR Structure Validation Report 2KKI

Continued from previous page...Mol Chain Analysed Favoured Allowed Outliers Percentiles

All All 2002/2114 (95%) 1730 (86%) 221 (11%) 51 (3%) 10 46

All 5 unique Ramachandran outliers are listed below. They are sorted by the frequency of occur-rence in the ensemble.

Mol Chain Res Type Models (Total)1 A 104 GLY 141 A 64 ASP 141 A 18 ILE 141 A 97 GLU 71 A 84 GLN 2

6.3.2 Protein sidechains i○

In the following table, the Percentiles column shows the percent sidechain outliers of the chainas a percentile score with respect to all PDB entries followed by that with respect to all NMRentries. The Analysed column shows the number of residues for which the sidechain conformationwas analysed and the total number of residues.

Mol Chain Analysed Rotameric Outliers Percentiles

1 A 127/133 (95%) 113±3 (89±3%) 14±3 (11±3%) 11 55

All All 1778/1862 (95%) 1582 (89%) 196 (11%) 11 55

All 71 unique residues with a non-rotameric sidechain are listed below. They are sorted by thefrequency of occurrence in the ensemble.

Mol Chain Res Type Models (Total)1 A 16 ARG 131 A 131 PHE 121 A 45 LEU 101 A 152 PHE 91 A 82 THR 81 A 110 LEU 81 A 26 ASP 71 A 64 ASP 61 A 30 GLN 61 A 84 GLN 51 A 93 LYS 51 A 120 ASN 51 A 15 MET 51 A 102 ILE 4

Continued on next page...

Page 30: Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

Page 30 Full wwPDB NMR Structure Validation Report 2KKI

Continued from previous page...Mol Chain Res Type Models (Total)1 A 134 THR 41 A 114 GLU 41 A 13 ASN 41 A 29 ASN 31 A 59 TYR 31 A 139 TRP 31 A 80 TYR 31 A 136 GLN 31 A 47 ASN 31 A 74 ILE 31 A 108 ASN 21 A 155 LEU 21 A 55 ASP 21 A 75 SER 21 A 24 LEU 21 A 68 ILE 21 A 34 ARG 21 A 100 LYS 21 A 130 LEU 21 A 73 ARG 21 A 158 GLN 21 A 125 VAL 21 A 157 ASN 21 A 40 LEU 11 A 70 VAL 11 A 103 THR 11 A 128 PRO 11 A 31 SER 11 A 65 ASP 11 A 95 MET 11 A 98 ILE 11 A 156 GLU 11 A 78 GLN 11 A 88 GLN 11 A 28 LEU 11 A 69 THR 11 A 109 LEU 11 A 54 PHE 11 A 119 LYS 11 A 129 ASN 11 A 53 LYS 11 A 17 ILE 1

Continued on next page...

Page 31: Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

Page 31 Full wwPDB NMR Structure Validation Report 2KKI

Continued from previous page...Mol Chain Res Type Models (Total)1 A 122 PHE 11 A 116 HIS 11 A 111 PHE 11 A 138 TYR 11 A 151 ASP 11 A 60 LYS 11 A 94 GLU 11 A 20 TYR 11 A 19 LYS 11 A 149 ILE 11 A 46 HIS 11 A 22 PHE 11 A 101 THR 11 A 25 ASN 11 A 67 LYS 1

6.3.3 RNA i○

There are no RNA molecules in this entry.

6.4 Non-standard residues in protein, DNA, RNA chains i○

There are no non-standard protein/DNA/RNA residues in this entry.

6.5 Carbohydrates i○

There are no carbohydrates in this entry.

6.6 Ligand geometry i○

There are no ligands in this entry.

6.7 Other polymers i○

There are no such molecules in this entry.

6.8 Polymer linkage issues i○

There are no chain breaks in this entry.

Page 32: Full wwPDB NMR Structure Validation Report i · I149 F152 Q153 I154 L155 E156 N157 Q158 A159 4.2.4 Scoreperresidueformodel4 Molecule1: Interleukin-1alpha ChainA: N9 V10 K11 Y12 I18

Page 32 Full wwPDB NMR Structure Validation Report 2KKI

7 Chemical shift validation i○

No chemical shift data were provided