Table 2 Summary of crystal structure determination and refinement.

From: Entropy-driven binding of gut bacterial β-glucuronidase inhibitors ameliorates irinotecan-induced toxicity

 

BdGUS

 

Apo form

Inhibitor 1

Inhibitor 2

Inhibitor 3

Inhibitor 4

PDB code

6LD6

6LDB

6LDD

6LDO

6LDC

Data collection

Space group

P21

P21

P21

P21

P21

Cell dimensions

     

 a, b, c (Å)

92.583, 104.902, 160.62

92.69, 104.64, 160.504

92.606, 105.928, 161.89

92.645, 104.77, 161.044

93.142, 104.814, 160.819

 α, β, γ (°)

90, 91.16, 90

90, 91.29, 90

90, 91.33, 90

90, 91.22, 90

90, 91.08, 90

Resolution (Å)

29.6–2.204

(2.283–2.204)

24.85–1.651

(1.71–1.651)

29.59–2.449

(2.536–2.449)

26.6–1.881

(1.948–1.881)

27.84–2.175

(2.253–2.175)

Rsym or Rmerge

0.086 (0.385)

0.054 (0.418)

0.088 (0.471)

0.089 (0.513)

0.055 (0.189)

Ι / σΙ

18.9 (4.3)

22.0 (3.8)

14.8 (2.9)

20.1 (2.5)

23.8 (5.7)

Completeness (%)

98.9 (90.3)

93.8 (90.4)

93.14 (46.62)

92.33 (60.9)

97.08 (77.86)

Redundancy

4.3 (4.0)

3.4 (3.4)

3.7 (3.8)

3.4 (4.2)

4.1 (2.9)

Refinement

Resolution (Å)

29.6–2.204

(2.283–2.204)

24.85–1.651

(1.71–1.651)

29.59–2.449

(2.536–2.449)

26.6–1.881

(1.948–1.881)

27.84–2.175

(2.253–2.175)

No. reflections

154377

343510

155860

241740

160237

Rwork / Rfree

0.1519/0.1991

0.1555/0.1825

0.1443/0.2056

0.1419/0.1747

0.1426/0.1912

No. atoms

     

 Protein

19636

19660

19636

19636

19552

 Ligand/ion

0

44

56

68

80

 Water

1935

2689

1949

1608

2030

B-factors

22.80

21.31

23.60

27.70

21.20

 Protein

22.10

19.91

23.50

26.40

20.20

 Ligand/ion

 

20.00

25.70

35.10

24.50

 Water

30.00

31.57

25.90

38.60

29.90

R.m.s. deviations

     

 Bond lengths (Å)

0.008

0.015

0.008

0.007

0.007

 Bond angles (°)

1.11

1.36

1.14

1.10

1.06

Ramachandran favored (%)

97

97

96

97

97

Ramachandran outliers (%)

0

0.041

0.12

0

0.042

 

EcGUS

 

Inhibitor 1

Inhibitor 2

Inhibitor 3

Inhibitor 4

PDB code

6LEG

6LEJ

6LEL

6LEM

Data collection

Space group

C2

C2

C2

C2

Cell dimensions

    

 a, b, c (Å)

207.527, 75.926, 168.281

167.686, 76.551, 125.426

165.781, 76.72, 124.888

68.361, 76.404, 126.4

 α, β, γ (°)

90, 96.79, 90

90, 124.85, 90

90, 124.636, 90

90, 124.966, 90

Resolution (Å)

29.79–2.603

(2.696–2.603)

29.75–2.617

(2.711–2.617)

29.47–2.498

(2.588–2.498)

28.25–3.188

(3.302–3.188)

Rsym or Rmerge

0.179 (0.897)

0.092 (0.642)

0.111 (0.763)

0.172 (0.953)

Ι / σΙ

13.3 (1.5)

17.8 (2.0)

15.7 (1.6)

9.7 (1.1)

Completeness (%)

99.2 (94.7)

97.9 (89.1)

97.9 (90.3)

98.4 (91.2)

Redundancy

3.4 (3.4)

5.3 (4.6)

3.6 (2.8)

6.0 (2.9)

Refinement

Resolution (Å)

29.79–2.603

(2.696–2.603)

29.75–2.617

(2.711–2.617)

29.47–2.498

(2.588–2.498)

28.25–3.188

(3.302–3.188)

No. reflections

79253

61283

43895

21727

Rwork / Rfree

0.2317/0.2877

0.2367/0.2795

0.2378/0.2868

0.2108/0.2695

No. atoms

    

 Protein

19223

9507

9521

9446

 Ligand/ion

44

28

34

40

 Water

231

65

125

0

B-factors

51.32

57.16

58.33

77.73

 Protein

51.54

57.36

58.74

77.75

 Ligand/ion

30.99

36.81

32.28

71.98

 Water

36.23

36.94

33.90

 

R.m.s. deviations

    

 Bond lengths (Å)

0.008

0.012

0.013

0.003

 Bond angles (°)

1.04

1.53

1.64

0.66

Ramachandran favored (%)

93

92

93

90

Ramachandran outliers (%)

0.97

0.77

0.94

1.12

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