Table 1 X-ray data collection and refinement statistics for D2HDH structures

From: Potassium binding by carbonyl clusters, halophilic adaptation and catalysis of Haloferax mediterranei D-2-hydroxyacid dehydrogenase

 

NADP+

2KHA

KCl

NAD+

2KHA

NaCl

NADP+

2KHA

NaCl

NADP+

2KHA

2HHA

NaCl

Apo-enzyme

NaCl

NAD+

2KHA

SO42-

NaCl

PDB code

9ibe

8qzb

5mh5

5mha

8qza

5mh6

Data Collection

Space group

P1

P1

P21

P21

P21

P1

Cell dimensions:

a(Å)

66.63

66.18

62.53

62.54

62.35

66.46

b(Å)

75.34

74.78

87.40

76.30

75.99

75.01

c(Å)

78.23

78.17

66.10

66.99

74.59

77.55

α(°)

108.8

109.1

90.0

90.0

90.0

109.1

β(°)

108.0

107.9

96.34

97.04

93.99

107.6

γ(°)

95.5

95.6

90.0

90.0

90.0

95.9

Subunits per asymmetric unit

4

4

2

2

2

4

Resolution (Å)a

52.28–1.26

(1.28–1.26)

46.6–1.16 (1.18–1.16)

52.51–1.4

(1.42–1.4)

38.15–1.57

(1.61–1.57)

29.4–2.25 (2.33–2.25)

46.54–1.35

(1.37–1.35)

Total reflectionsa

1,253,021 (60,722)

1,542,061 (62,913)

1,021,332 (50,216)

174,757

(12,974)

223,285 (6387)

577,246 (28,535)

Unique reflectionsa

332,819 (16,111)

427,918 (18,892)

132,820

(6288)

81,835

(5989)

32,656

(2669)

268,611 (13,112)

Rpima

0.059 (0.99)

0.042 (0.50)

0.036 (0.38)

0.039 (0.40)

0.041 (0.42)

0.061 (0.46)

Mean I/σ(I)a

12.0 (0.8)

17.1 (1.3)

15.4 (2.4)

13.6 (2.2)

11.9 (1.7)

23.6 (2.1)

Completeness (%)a

92.2 (89.4)

93.9 (83.7)

95.5 (91.5)

94.8 (93.7)

98.8 (88.0)

93.0 (91.7)

Multiplicitya

3.8 (3.8)

3.6 (3.3)

7.7 (8.0)

2.1 (2.2)

6.8 (5.1)

2.1 (2.2)

CC1/2a

0.99 (0.33)

0.94 (0.56)

#

#

0.99 (0.79)

#

Refinement

Number of non-H atoms

Protein

9546

9590

4784

4726

4702

9534

Ligands/counter ions

269

267

145

159

7

342

Water

1575

1622

676

451

70

1768

Rwork/Rfree

0.15/0.19

0.135/0.165

0.14/0.17

0.17/0.22

0.19/0.25

0.12/0.16

Average B factor (Å2)

Main chain/side chain

15.6/18.8

14.2/18.2

16.3/23.4

25.7/36.9

65.1/70.7

13.5/21.2

Ligands/counter ions

14.7

14.7

17.8

31.5

52.6

19.6

Water

28.0

30.5

27.7

32.7

44.1

33.1

Rmsd bond length (Å) / angle (°)

0.010/1.8

0.011/1.7

0.01/1.59

0.013/1.67

0.012/1.94

0.012/1.42

  1. 2KHA, 2-ketohexanoic acid; 2HHA, 2-hydroxyhexanoic acid
  2. adata in brackets refers to highest resolution shell
  3. # value not calculated