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Table 2 X-ray data collection and refinement statistics (molecular replacement)

From: Structural basis for potency differences between GDF8 and GDF11

 

GDF11:FS288 (native)a

apo-GDF8 (native)a

apo-GDF11 (native)a

Data collection

Space group

P 21 21 21

P 21 21 21

P 32 2 1

Unit cell dimension

  a, b, c (Å)

56.0, 59.1, 288.5

29.6, 77.7, 119.5

65.2, 65.2, 101.9

  α, β, γ (°)

90, 90, 90

90, 90, 90

90, 90, 120

 Wavelength (Å)

1.03321

0.97856

1.10537

 Resolution (Å)

2.35 (2.43-2.35)

2.25 (2.32-2.25)

1.9 (1.94-1.9)

  R merge

0.076 (0.519)

0.079 (1.102)

0.069 (0.706)

  R pim

0.046 (0.311)

0.032 (0.436)

0.032 (0.316)

 Mn (I/σI)b

10.0 (2.6)

18.2 (2.0)

10.4 (2.0)

 CC1/2 c

0.74

0.72

0.996

 Completeness (%)

100.0 (100.0)

100.0 (100.0)

100.0 (100.0)

 Redundancy

3.7 (3.8)

7.1 (7.3)

5.8 (5.9)

Refinement

 Resolution (Å)

41.28-2.35

36.96-2.25

49.37-1.9

 No. reflections

40,978 (4,031)

13,776 (1,912)

20,166 (2,642)

  R work (%), R free d (%)

20.3/24.7

23.4/27.7

21.7/25.8

No. of atoms (molecules)

 Protein

6047 (784)

1443 (187)

1395 (181)

 Water

170 (170)

30 (30)

43 (43)

 Citrate

91 (7)

  

 Phosphate

15 (3)

  

 2-Methyl-2,4-pentanediol

 

56 (7)

 

 B-factors (average, Å2)

60.0

65.1

60.3

RMS deviations

 Bond lengths (Å)

0.005

0.003

0.007

 Bond angles (°)

0.960

0.951

0.853

Ramachandran plot

 Favored (%)

97.15

94.44

97.63

 Allowed (%)

2.59

5.56

2.37

 Outliers (%)

0.26

0.0

0.0

 Clashscoree

4.18

6.83

3.33

  1. aValues in parentheses are for highest resolution shell
  2. bMn(I/σI) is defined as < merged < Ih >/sd (< Ih >) > ≈ signal/noise
  3. cCC1/2 for highest resolution shell
  4. d R free calculated from 5% of initial total number of reflections
  5. eDetermined by MolProbity