Table 1 Data collection, phasing, and refinement statistics

From: Structural insights into Xanthomonas campestris pv. campestris NAD+ biosynthesis via the NAM salvage pathway

 

Xcc NAMPT + NAM

Xcc NAMPT + NMN

Apo Xcc NAMPT (Tablet-shape)

Apo Xcc NAMPT (Diamond-shape)

Apo Quadruple mutant

PDB ID

7YQR

7YQQ

7YQO

7YQP

8IGZ

Data collection

 Beam line

SSRF beamline BL17U1

SSRF beamline BL17U1

SSRF beamline BL17U1

SSRF beamline BL17U1

SSRF beamline BL19U1

 Wavelength (Å)

0.97918

0.979183

0.979183

0.97918

0.97853

 Resolution range (Å)

26.85–2.00

106.04–2.22

91.61–1.79

100.49–2.08

35.72–3.11

 

(2.07–2.00)c

(2.28–2.22)c

(1.84–1.79)c

(2.13–2.08) c

(3.22–3.11) c

 Space group

P 61 2 2

P 61 2 2

P 21 21 2

P 62 2 2

P 61 2 2

Cell dimensions

 a, b, c (Å)

115.95, 115.95, 317.75

115.74, 115.74, 318.11

91.61, 151.48, 70.81

116.18, 116.18, 160.60

115.76, 115.76, 317.75

 α, β, γ (°)

90, 90, 120

90, 90, 120

90, 90, 90

90, 90, 120

90, 90, 120

 Number of unique/observed reflections

86,028/3,318,004

63,152/2,350,948

93,464/1,223,003

39,123/549,798

23,619/887,823

 Completeness (%)

96.2 (100.0)

99.9 (99.0)

98.77 (95.99)

100.0 (100.0)

99.9 (100.0)

 Rmergea

0.151 (2.247)

0.232 (3.303)

0.109 (1.308)

0.051 (0.378)

0.065 (0.293)

 Rpim

0.025 (0.395)

0.038 (0.620)

0.031 (0.370)

0.013 (0.220)

0.068 (0.415)

 CC1/2

0.999 (0.796)

0.999 (0.775)

0.999 (0.657)

1.000 (0.900)

0.995 (0.915)

 Average I/σ (I)

18.8 (2.1)

21.8 (1.7)

16.8 (2.4)

21.8 (1.9)

10.0 (3.1)

Refinement

 Number of reflections used

85,886 (8432)

58,992 (4602)

92,357 (8881)

25,813 (469)

23,528 (2319)

Average B-value (Ã…2)

 Average B-value for protein atoms

46.94

43.08

32.29

57.08

22.69

 Average B-value for solvent atoms

48.36

45.66

38.47

50.84

 

 Rwork b/Rfree b (%)

0.1872/0.2092

0.1829/0.2179

0.1783/0.1985

0.2185/0.2526

0.2135/0.2552

 Number of atoms

7608

7509

7651

3323

6837

 Macromolecule

7187

7004

7101

3252

6837

 Ligand

NAM (18)

NMN (22) PO4 (5)

GOL (6)

  

 Water

403

478

544

71

 

RMSD from ideal geometry

 RMSD bond length (Å)

0.007

0.009

0.007

0.003

0.003

 RMSD bond angles (°)

0.80

0.98

0.84

0.66

0.66

Ramachandran

 Favored (%)

97.81%

96.86%

98.00%

93.66%

96.40%

 Allowed (%)

2.19%

2.69%

1.89%

1.22%

3.48%

 Disallowed (%)

0.00%

0.45%

0.11%

0.00%

0.12%

  1. aRmerge = Σh Σi | Ih,i − Ih | /ΣhΣiIh,i, where Ih is the mean intensity of the i observations of symmetry related reflections of h.
  2. bRwork = Σ( | |Fp(obs)| − |Fp(calc)||)/Σ|Fp(obs)|; Rfree is an R factor for a pre-selected subset (5%) of reflections that was not included in refinement. Fp, structure factor of protein.
  3. cNumbers in parentheses are corresponding values for the highest resolution shell.
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