Table 1 Data collection and refinement statistics

From: Structural characterization of HypX responsible for CO biosynthesis in the maturation of NiFe-hydrogenase

Table 1 (SEPARATED 1/2)

 

HypX (Form I)

HypX (Form II)

SeMet-peak (Form II)

THF-bound HypX (Form I)

Data collection

Space group

C2221

P41212

P41212

C2221

Cell dimensions

 a, b, c (Å)

79.8, 124.3, 290.9

88.3, 88.3, 162.7

88.9, 88.9, 163.2

80.0 123.7 290.0

 α, β, γ (○)

90, 90, 90

90, 90, 90

90, 90, 90

90, 90, 90

Wavelength (Å)

0.90000

0.90000

0.97910

0.90000

Resolution (Å)

42.47–1.79 (1.86–1.79) a

44.16–2.40 (2.49–2.40)

42.89–2.40 (2.54–2.40)

42.31–2.10 (2.18–2.10)

Observed reflections

1,006,078 (98,817)b

373,199 (36,841)

375,584 (60,954)

577,575 (55,080)

R merge c

0.073 (1.094)

0.096(0.670)

0.105 (0.656)

0.071 (0.861)

I/σI

16.77 (1.60)

19.47 (4.26)

17.83 (4.04)

15.24 (1.80)

Completeness (%)

98.8 (89.1)

99.4 (99.1)

99.9 (99.7)

99.88 (99.53)

Redundancy

7.5 (7.5)

14.5 (14.7)

14.3 (14.5)

6.9 (6.7)

Refinement

 Resolution (Å)

42.47–1.79

44.16–2.40

 

42.31–2.10

 Unique reflections

134,916

25,794

 

84,116

 Rwork/Rfreed

0.173/0.196

0.183/0.241

 

0.178/0.213

No. atoms

  Protein

9306

4459

 

9069

  Ligand/ion

108

48

 

140

  Water

392

16

 

196

B-factors

  Protein

35.69

56.14

 

61.37

  Ligand/ion

31.25

35.16

 

58.93

  Water

36.88

39.34

 

49.39

R.m.s. deviations

  Bond lengths (Å)

0.008

0.009

 

0.008

  Bond angles (○)

1.14

1.16

 

0.81

 PDB ID

6J0P

6J1E

 

6J1F

Table 1 (SEPARATED 2/2)

 

R9A-Q15A-R131A-R542A

Q15A-R131A-S194A-Q195A-N306A-R542A

A392F-I419F

THF-bound A392F-I419F

Data collection

Space group

P41212

C2221

I222

I222

Cell dimensions

 a, b, c (Å)

88.5 88.5 161.8

79.9 124.4 290.6

72.7 139.6 167.7

69.4 141.9 170.9

 α, β, γ (○)

90, 90, 90

90, 90, 90

90, 90, 90

90, 90, 90

Wavelength (Å)

0.90000

0.90000

0.90000

0.90000

Resolution (Å)

42.67–2.50 (2.59–2.50)

47.25–2.10 (2.18–2.10)

44.85–2.29 (2.38–2.29)

39.09–2.00 (2.05–2.00)

Observed reflections

314,881 (32,056)

562,302 (53,424)

256,066 (23,709)

2,953,944 (163,839)

R merge c

0.148 (1.002)

0.059 (0.842)

0.045 (0.548)

0.176 (1.259)

I/σI

12.30 (2.18)

17.09 (2.12)

20.13 (2.20)

14.97 (3.46)

Completeness (%)

99.8 (99.1)

99.76 (98.51)

99.47 (95.73)

99.92 (99.89)

Redundancy

13.7 (14.4)

6.7 (6.5)

6.6 (6.5)

51.5 (39.2)

Refinement

Resolution (Å)

42.67–2.50

47.25–2.10

44.85–2.29

39.09–2.00

Unique reflections

22,960

84,408

38,512

57,352

Rwork/Rfreed

0.180/0.241

0.200/0.237

0.176/0.211

0.180/0.214

No. atoms

  Protein

4416

9152

4590

4606

  Ligand/ion

54

12

46

92

  Water

12

76

30

80

B-factors

  Protein

59.41

60.33

75.2

54.73

  Ligand/ion

63.42

65.41

111.44

78.19

  Water

48.15

47.52

63.4

50.71

R.m.s. deviations

  Bond lengths (Å)

0.009

0.009

0.008

0.008

  Bond angles (○)

1.18

0.89

1.17

1.14

 PDB ID

6J1G

6J1H

6J1I

6J1J

  1. aValues in parentheses are for highest-resolution shell
  2. bOne crystal was used in each structure except THF-bound A392F-I419F. In THF-bound A392F-I419F structure, a full data set from eight crystals are merged
  3. cRmerge(I) = Σǀ I (k) − < I > ǀ / Σ I (k), where I (k) is the value of the kth measurement of the intensity of a reflection, < I > is the mean value of the intensity of that reflection and the summation is the overall measurement
  4. dRwork = Σhkl|Fobs(hkl) − Fcalc(hkl)|/ΣhklFobs(hkl), where Fobs and Fcalc are the observed and calculated structure factors, respectively. Rfree is the R-factor computed for a test set of reflections that were omitted from the refinement process
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