NMR Structure: 2,405 (until September 20, 2011)


Overall Statistics (until September 20, 2011)


Table 1. Overview summary of average quality indicators of original and refinement NMR structure

 

Original

Refined (STAP)

 

Steric Clash Score

33.16±39.52

1.57±5.90

RMS Violation of all distance restraints

0.20±0.35

0.13±0.24

 

Optimal Protein Energy

DOPE Score

-8050.74±4572.84

-8587.34±4817.02

Normalized DOPE score

-0.62±1.02

-1.02±0.97

dDFIRE Score

-163.12±89.44

-179.07±96.77

 

 

Ramachandran
Indictors ratio

 

MolProbity

Favorable

83.50±10.09

95.51±4.83

Allowed

12.95±7.36

3.80±3.92

Disallowed

3.54±4.04

0.69±1.48

 

PROCHECK

Favorable

75.66±12.08

89.83±7.45

Allowed

21.04±9.65

8.01±5.80

Generously

2.35±3.31

0.84±1.55

Disallowed

0.96±1.72

1.32±2.01

 

 

Structure Z-Scores
Distribution*

1st Generation Packing Quality

-3.14±1.68

-2.63±1.80

2nd Generation Packing Quality

-2.59±1.27

-1.52±1.55

Ramachandran Plot Appearance

-4.50±1.86

0.65±1.95

1-2Rotamer Normality

-5.25±2.36

-2.07±1.68

Backbone Conformation

-0.93±1.28

-0.80±1.33

 

 

 

 

RMS Z-Scores Distribution**

Bond Lengths

0.48±0.34

0.84±0.12

Bond Angles

0.70±0.39

1.04±0.16

Ω Angle Restraints

0.36±0.51

1.30±0.43

Side Chain Planarity

0.59±0.92

0.68±0.45

Improper dihedral distribution

0.64±0.39

0.79±0.25

Inside/Outside Distribution

1.05±0.10

1.03±0.10

*  Structure Z-score, positive is better than average.
** RMS – Z score should be close to 1.0.
Bold font is indicating best scores

 



# List of common 70 NMR structures

Table 2. Comparison on common 70 NMR structure between STAP and other known databases  (DRESS and RECOORD)

 

Original

STAP

DRESS

RECOORD-CNW

RECOORD-CYW

 

Steric Clash Score

68.26±57.86

1.03±2.44

16.79±9.56

16.31±8.62

16.56±8.46

 

Optimal Protein Energy

DOPE Score

-6098.15±4586.33

-6941.80±5130.94

-6996.31±5244.70

-7274.30±5902.43

-7330.00±6150.59

Normalized DOPE score

-0.21±1.17

-1.00±1.06

-1.01±1.13

-0.95±1.11

-0.96±1.10

dDFIRE Score

-125.95±88.72

-147.52±102.79

-143.07±101.01

-146.95±114.19

-148.66±120.39

 

Ramachandran
Indictors ratio

 

MolProbity

Favorable

75.02±12.37

94.80±4.51

86.38±8.18

84.69±9.00

83.59±9.35

Allowed

18.76±8.87

4.27±3.64

10.71±6.71

11.89±7.03

12.75±7.58

Disallowed

6.22±5.25

0.92±1.55

2.90±2.92

3.43±3.34

3.66±3.29

 

PROCHECK

Favorable

67.02±15.14

88.45±7.60

77.92±11.70

75.33±13.02

73.73±13.88

Allowed

27.18±11.95

8.73±6.08

18.52±9.79

20.20±10.73

21.48±11.54

Generously

4.38±4.10

1.00±1.59

2.06±2.49

2.70±3.00

2.83±2.99

Disallowed

1.42±1.93

1.82±2.19

1.50±2.12

1.77±2.26

1.97±2.29

 

Structure Z-Scores
Distribution*

1st Generation Packing Quality

-3.48±1.71

-2.41±1.73

-2.14±1.72

-2.37±1.97

-2.44±2.03

2nd Generation Packing Quality

-2.96±1.19

-1.28±1.50

-1.89±1.12

-2.09±1.27

-2.08±1.26

Ramachandran Plot Appearance

-5.85±1.92

0.98±2.03

-4.13±1.44

-4.31±1.60

-4.43±1.59

1-2 Rotamer Normality

-6.35±2.35

-1.68±1.68

-2.58±1.59

-2.50±1.42

-2.77±1.40

Backbone Conformation

-1.67±1.50

-1.07±1.42

-1.50±1.40

-1.64±1.37

-1.63±1.33

 

RMS Z-Scores Distribution**

Bond Lengths

0.83±0.34

0.85±0.06

0.84±0.14

0.84±0.13

0.86±0.13

Bond Angles

1.06±0.42

1.03±0.12

0.78±0.12

0.78±0.11

0.80±0.11

Ω Angle Restraints

0.16±0.27

1.31±0.37

0.75±0.15

0.74±0.15

0.75±0.14

Side Chain Planarity

1.71±1.42

0.70±0.37

0.81±0.18

1.27±0.54

1.31±0.58

Improper dihedral distribution

0.92±0.39

0.79±0.17

1.01±0.16

1.19±0.36

1.23±0.38

Inside/Outside Distribution

1.07±0.13

1.06±0.12

1.07±0.12

1.08±0.13

1.08±0.13

*  Structure Z-score, positive is better than average.
** RMS – Z score should be close to 1.
Bold font is indicating best scores.