Table 1 Crystallization conditions and data collection statistics.

From: Copper mediated amyloid-β binding to Transthyretin

Structure

TTR-Fe

TTR-Mn

TTR-Cu

TTR-Cu-Aβ

PDB code

5N5Q

5N62

5N7C

Not deposited

Metal-Ligand

Fe

Mn

Cu

Cu-Aβ

Crystallization

27% polyethylene glycol 4,000 (PEG4K), 0.2 M imidazole malate, pH 6.0

26% PEG4K, 0.2 M imidazole malate, pH 6.0

21% PEG4K, 0.14 M imidazole malate, pH 6.0, 3.6% MPEG 5 K, 0.03 M sodium acetate, pH 5.5

Co-crystallization with Aβ 1–28 and CuCl2 in 21% PEG4K, 0.14 M imidazole malate, pH 6.0, 3.6% MPEG, 5 K, 0.1 M sodium acetate, pH 5.5

Cryoprotectant

40% SM3*, 25% MPEG 5 K, 0.1 M CHC (90% acid/10% basic), 30 mM FeCl2, 2 h soak.

40% CM7*, 25% MPEG 5 K, 5 mM MnCl2, 10 min soak.

40% SM3*, 25% MPEG 5 K, 0.1 M CHC(90% acid/10% basic), 30 mM CuCl2 30 min soak.

40% CM1*, 25% MPEG 5 K, 0.1 M CHC (90% acid/10% basic), 30 mM CuCl2 30 min soak.

Data Collection

anomalous

anomalous

anomalous

non anomalous

Source

Soleil Proxima-2

Soleil Proxima-2

Soleil Proxima-2

Soleil Proxima-2

Wavelength (Å)

1.739153

1.891993

1.175919

0.980035

Space group

P21212

P21212

P21212

P21212

Unit-cell (Å)

42.82 83.10 65.34

43.27 85.83 63.90

42.99 82.54 67.77

43.10 82.75 67.14

Molec./asym.

2

2

2

2

Resolution (Å)

50–2.53/2.68–2.53

50–1.8/1.85–1.80

50–2.45/2.59–2.45

50–2.14/2.27–2.14

CC1/2 (%)

99.6/30.0

99.8/39.0

99.8/89.0

99.9/52.5

〈I/σ(I)〉

8.28/0.83

11.53/1.52

14.75/3.29

13.0/1.10

R-merge (%)

20.0/198

17.6/217

10.7/67.2

12.9/215

R-factor (%)

18.5/182

16.3/202

9.9/62.1

12.4/222

Completeness (%)

99.2/95.3

100/100

99.5/96.7

99.8/98.9

Multiplicity

13.21/6.87 (anomalous)

7.37 (anomalous)

13.7/7.0 (anomalous)

13.1

Refinement

REFMAC5

Phenix

REFMAC5

REFMAC5

Resolution (Å)

40.91–2.53/2.60–2.53

38.63–1.80/1.89–1.80

41.06–2.45/2.51–2.45

38.23–2.43/2.49–2.43

No. of reflections

8113/548 (non-anomalous)

22723/2658 (anomalous)

8868/467 (non-anomalous)

9042/650 (non-anomalous)

R-work

19.2/41.0

19.5/28.4

16.9/20.3

20.9/31.0

R-free

25.3/40.4

24.4/33.2

25.4/43.1

29.7/44.4

RMSD Bond lengths (Å)

0.013

0.009

0.009

0.015

RMSD Bond angles (°)

1.6

1.025

1.714

1.773

Ramachandran favored

96.0%

98.0%

94.0%

96.9%

Ramachandran outliers

0

0

0

3

  1. Cryoprotection: SM1: 12.5% diethylene glycol + 12.5% glycerol + 12.5% 1,2-propanediol + 25% DMSO + 25% 1,4-dioxane; SM3: 25% diethylene glycol + 25% ethylene glycol + 25% glycerol + 25% 1,4-dioxane; CM1: 12.5% diethylene glycol + 37.5% 1,2-propanediol + 12.5% DMSO; CM7: 12.5% di-ethylene glycol + 12.5% ethylene glycol + 12.5% glycerol + 25% 1,2-propanediol + 12.5% DMSO68. Cryoprotectant solution is formulated with 40% v/v mixed compounds (CM), 50% v/v precipitant and 10% v/v buffer69. CHC: Linear mixed buffer composed of citric acid, HEPES and CHES; acid mix at pH 4.0, basic at pH 10.070. CC1/2: Data quality correlation coefficient71. Data collection statistics are from XDS60. Refinement statistics are from REFMAC563 or phenix.refine (Phenix)65.
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