Skip to main content

Table 1 Data collection and refinement statistics

From: Structure of the stationary phase survival protein YuiC from B.subtilis

Crystal

+NAG (truncated K32-E218)

Apo (P73-E218)

+anhydro (R52-K217)

PDB CODE

4WJT

4WLI

4WLK

Data collection

   

Wavelength (Ã…)

0.9795

0.9200

0.9795

Space group

R3:H (146) (Hexagonal Cell)

C2221 (20)

R3:H (146) (Hexagonal Cell)

Cell dimensions

   

  a, b, c (Å)

145.5, 145.5, 37.8

50.0, 117.3, 61.0

147.2, 147.2, 37.9

 α, β, γ (°)

90, 90, 120

90, 90, 90

90, 90, 120

Resolution (Ã…)a

36.37–1.21 (1.23–1.21)

30.8–1.76 (1.79–1.76)

42.50–2.03 (2.08–2.03)

Total number of reflections a

290513 (14071)

132867 (7892)

74023 (5113)

Number of unique reflections a

89967 (4420)

18150 (1026)

19631 (1439)

Rmerge a

0.043 (0.569)

0.098 (0.745)

0.122 (0.576)

Rmeas a

0.060 (0.792)

0.114 (0.860)

0.162 (0.764)

Rpim a

0.041 (0.549)

0.057 (0.425)

0.106 (0.497)

CC (1/2) a

0.998 (0.607)

0.998 (0.771)

0.983 (0.620)

Solvent content (%)

45.7

53.3

44.0

Molecule/asymmetric unit

2

1

2

Wilson B-factor (Ã…2)

14.4

17.3

21.4

I/σI a

10.3 (2.4)

13 (2.5)

7.5 (2.2)

Completeness (%)a

98.8 (97.2)

99.8 (99.6)

99.4 (98.7)

Redundancy a

3.2 (3.2)

7.3 (7.7)

3.8 (3.6)

Refinement

   

Resolution (Ã…)a

36.39–1.21 (1.23–1.21)

30.798–1.76 (1.85–1.76)

42.51–2.03 (2.14–2.03)

Reflection, working

85213

18131

19628

Reflection, free

4468

927

968

Rwork/Rfree (%)

11.1/14.4

16.2/20.2

16.76/20.80

No of non-H atoms

2815

1264

2506

 Protein

A: 1185 B: 1185

1120

A: 1139 B: 1133

 Others

45 (NAG)

16 (EDO)

56 (1,6-anhydro-disaccharide)

 

13 (Polypropylene glycol)

  
 

16 (DMSO)

  

 Water

371

128

178

B factors (Ã…2)b

24.0

26.6

32.4

 Protein

A: 21.7 B: 21.6

25.5

A: 33.1 B: 31.2

 Others

20.3 (NAG)

35.1 (EDO)

28.0 (1,6-anhydro-disaccharide)

 

44.5 (Polypropylene glycol)

  
 

64.6 (DMSO)

  

 Water

37.0

35.05

36.839

Rmsds

   

 Bond lengths (Å)

0.023

0.016

0.005

 Bond angles (°)

2.2

1.495

0.990

Ramachandran plot

   

 Favoured (%)

98.1

97.8

95.4

 Allowed (%)

1.8

2.4

4.6

 Outliers (%)

0

0

0

  1. a Values in parentheses are for the highest-resolution shell
  2. b Average over all atoms
  3. \( {R}_{merge}=\frac{{\displaystyle {\sum}_{hkl}}{\displaystyle {\sum}_j}\left|{I}_{hkl,j}-\left\langle {I}_{hkl}\right\rangle \right|}{{\displaystyle {\sum}_{hkl}}{\displaystyle {\sum}_j}{I}_{hkl,j}} \)
  4. \( {R}_{meas}=\frac{{\displaystyle {\sum}_{hkl}}\sqrt{\frac{n}{n-1}}{\displaystyle {\sum}_{j=1}^n}\left|{I}_{hkl,j}-\left\langle {I}_{hkl}\right\rangle \right|}{{\displaystyle {\sum}_{hkl}}{\displaystyle {\sum}_j}{I}_{hkl,j}} \)
  5. \( {R}_{\mathrm{p}.\mathrm{i}.\mathrm{m}}=\frac{{\displaystyle {\sum}_{hkl}}\sqrt{\frac{1}{\mathrm{n}-1}}{\displaystyle {\sum}_{j=1}^n}\left|{I}_{hkl,j}-\left\langle {I}_{hkl}\right\rangle \right|}{{\displaystyle {\sum}_{hkl}}{\displaystyle {\sum}_j}{I}_{hkl,j}} \)
  6. where I hkl is the reflection intensity and < I hkl > is the average intensity for multiple measurements of that reflection.